[English] 日本語
Yorodumi
- PDB-4v8q: Complex of SmpB, a tmRNA fragment and EF-Tu-GDP-Kirromycin with t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4v8q
TitleComplex of SmpB, a tmRNA fragment and EF-Tu-GDP-Kirromycin with the 70S ribosome
Components
  • (30S RIBOSOMAL PROTEIN ...) x 20
  • (50S RIBOSOMAL PROTEIN ...) x 31
  • 16S ribosomal RNA
  • 23S ribosomal RNA
  • 5S ribosomal RNA
  • E-SITE or P-SITE TRNA FMET
  • ELONGATION FACTOR TUEF-Tu
  • MRNAMessenger RNA
  • SMALL PROTEIN B SMPB
  • TMRNA DELA
KeywordsRIBOSOME / TMRNA / SMPB / EF-TU
Function / homology
Function and homology information


trans-translation / translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome ...trans-translation / translation elongation factor activity / large ribosomal subunit / regulation of translation / small ribosomal subunit / 5S rRNA binding / transferase activity / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / mRNA binding / GTPase activity / GTP binding / RNA binding / zinc ion binding / metal ion binding / cytoplasm
Similarity search - Function
SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain ...SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Ribosomal protein L1, bacterial-type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / 30S ribosomal protein Thx / 30S ribosomal protein Thx / 30S ribosomal protein / Ribosomal protein L25, long-form / Ribosomal protein L25, beta domain / Ribosomal protein L25, C-terminal / Ribosomal protein TL5, C-terminal domain / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Ribosomal protein S14, type Z / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Translation elongation factor EFTu-like, domain 2 / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Elongation factor Tu domain 2 / Ribosomal protein L1p/L10e family / Ribosomal protein L31 type A / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L31 signature. / Ribosomal protein L31 / Ribosomal protein L31 superfamily / Ribosomal protein L31 / Ribosomal L25p family / Ribosomal protein L25 / Ribosomal protein S14/S29 / Ribosomal protein L36 signature. / Ribosomal protein L25/Gln-tRNA synthetase, N-terminal / Ribosomal protein L32p, bacterial type / Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily / Ribosomal protein L28 / Ribosomal protein L35, conserved site / Ribosomal protein L35 signature. / Ribosomal protein L33, conserved site / Ribosomal protein L33 signature. / Ribosomal protein L35, non-mitochondrial / Ribosomal protein L5, bacterial-type / Ribosomal protein L6, bacterial-type / Ribosomal protein L18, bacterial-type / Ribosomal protein L19, conserved site / Ribosomal protein L19 signature. / Ribosomal protein L36 / Ribosomal protein L36 superfamily / Ribosomal protein L36 / Ribosomal protein L20 signature. / Ribosomal protein S3, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein L27, conserved site / Ribosomal protein L27 signature. / Ribosomal protein S19, bacterial-type / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S11, bacterial-type / Ribosomal protein S13, bacterial-type / Ribosomal protein S20 / Ribosomal protein S20 superfamily / Ribosomal protein S20 / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / Ribosomal protein S4, bacterial-type / Ribosomal protein L34, conserved site / Ribosomal protein L34 signature. / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein L22, bacterial/chloroplast-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L35 / Ribosomal protein L35 superfamily / Ribosomal protein L2, bacterial/organellar-type / Ribosomal protein L35 / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal L28 family / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L28/L24 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / L28p-like
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / KIRROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 ...GUANOSINE-5'-DIPHOSPHATE / KIRROMYCIN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS7 / Large ribosomal subunit protein bL33 / Large ribosomal subunit protein uL2 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL16 / Large ribosomal subunit protein bL19 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein bL27 / Large ribosomal subunit protein bL28 / Large ribosomal subunit protein bL32 / Large ribosomal subunit protein bL34 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein bS20 / Small ribosomal subunit protein uS12 / Elongation factor Tu-A / Small ribosomal subunit protein uS10 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Large ribosomal subunit protein uL29 / 30S ribosomal protein S17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL5 / 30S ribosomal protein S14 type Z / 30S ribosomal protein S8 / 50S ribosomal protein L6 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL36 / Large ribosomal subunit protein bL25 / Small ribosomal subunit protein bTHX / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein bL31 / Small ribosomal subunit protein bS16 / Large ribosomal subunit protein bL35 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein bS18 / SsrA-binding protein / Large ribosomal subunit protein bL17
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Escherichia coli K-12 (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsNeubauer, C. / Gillet, R. / Kelley, A.C. / Ramakrishnan, V.
CitationJournal: Science / Year: 2012
Title: Decoding in the absence of a codon by tmRNA and SmpB in the ribosome.
Authors: Neubauer, C. / Gillet, R. / Kelley, A.C. / Ramakrishnan, V.
History
DepositionDec 10, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4ABR, 4ABS
Revision 1.1Dec 10, 2014Group: Other
Revision 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / entity / entity_src_gen / entity_src_nat / pdbx_entity_src_syn / pdbx_validate_polymer_linkage / struct
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _struct.title
Revision 2.1Oct 9, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: entity_src_nat / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 2.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "OA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A0: 50S RIBOSOMAL PROTEIN L27
A1: 50S RIBOSOMAL PROTEIN L28
A2: 50S RIBOSOMAL PROTEIN L29
A3: 50S RIBOSOMAL PROTEIN L30
A4: 50S RIBOSOMAL PROTEIN L31
A5: 50S RIBOSOMAL PROTEIN L32
A6: 50S RIBOSOMAL PROTEIN L33
A7: 50S RIBOSOMAL PROTEIN L34
A8: 50S RIBOSOMAL PROTEIN L35
A9: 50S RIBOSOMAL PROTEIN L36
AA: 23S ribosomal RNA
AB: 5S ribosomal RNA
AC: 50S RIBOSOMAL PROTEIN L1
AD: 50S RIBOSOMAL PROTEIN L2
AE: 50S RIBOSOMAL PROTEIN L3
AF: 50S RIBOSOMAL PROTEIN L4
AG: 50S RIBOSOMAL PROTEIN L5
AH: 50S RIBOSOMAL PROTEIN L6
AJ: 50S RIBOSOMAL PROTEIN L10
AK: 50S RIBOSOMAL PROTEIN L11
AN: 50S RIBOSOMAL PROTEIN L13
AO: 50S RIBOSOMAL PROTEIN L14
AP: 50S RIBOSOMAL PROTEIN L15
AQ: 50S RIBOSOMAL PROTEIN L16
AR: 50S RIBOSOMAL PROTEIN L17
AS: 50S RIBOSOMAL PROTEIN L18
AT: 50S RIBOSOMAL PROTEIN L19
AU: 50S RIBOSOMAL PROTEIN L20
AV: 50S RIBOSOMAL PROTEIN L21
AW: 50S RIBOSOMAL PROTEIN L22
AX: 50S RIBOSOMAL PROTEIN L23
AY: 50S RIBOSOMAL PROTEIN L24
AZ: 50S RIBOSOMAL PROTEIN L25
B2: SMALL PROTEIN B SMPB
BA: 16S ribosomal RNA
BB: 30S RIBOSOMAL PROTEIN S2
BC: 30S RIBOSOMAL PROTEIN S3
BD: 30S RIBOSOMAL PROTEIN S4
BE: 30S RIBOSOMAL PROTEIN S5
BF: 30S RIBOSOMAL PROTEIN S6
BG: 30S RIBOSOMAL PROTEIN S7
BH: 30S RIBOSOMAL PROTEIN S8
BI: 30S RIBOSOMAL PROTEIN S9
BJ: 30S RIBOSOMAL PROTEIN S10
BK: 30S RIBOSOMAL PROTEIN S11
BL: 30S RIBOSOMAL PROTEIN S12
BM: 30S RIBOSOMAL PROTEIN S13
BN: 30S RIBOSOMAL PROTEIN S14
BO: 30S RIBOSOMAL PROTEIN S15
BP: 30S RIBOSOMAL PROTEIN S16
BQ: 30S RIBOSOMAL PROTEIN S17
BR: 30S RIBOSOMAL PROTEIN S18
BS: 30S RIBOSOMAL PROTEIN S19
BT: 30S RIBOSOMAL PROTEIN S20
BU: 30S RIBOSOMAL PROTEIN THX
BV: E-SITE or P-SITE TRNA FMET
BW: E-SITE or P-SITE TRNA FMET
BX: MRNA
BY: TMRNA DELA
BZ: ELONGATION FACTOR TU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,348,30067
Polymers2,346,81560
Non-polymers1,4857
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.170, 290.760, 250.650
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

+
50S RIBOSOMAL PROTEIN ... , 31 types, 31 molecules A0A1A2A3A4A5A6A7A8A9ACADAEAFAGAHAJAKANAOAPAQARASATAUAVAWAXAYAZ

#1: Protein 50S RIBOSOMAL PROTEIN L27 /


Mass: 9529.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60493
#2: Protein 50S RIBOSOMAL PROTEIN L28 /


Mass: 11004.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60494
#3: Protein 50S RIBOSOMAL PROTEIN L29 /


Mass: 8670.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP6
#4: Protein 50S RIBOSOMAL PROTEIN L30 /


Mass: 6799.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ6
#5: Protein 50S RIBOSOMAL PROTEIN L31 /


Mass: 8300.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJE1
#6: Protein 50S RIBOSOMAL PROTEIN L32 /


Mass: 6722.050 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80339
#7: Protein 50S RIBOSOMAL PROTEIN L33 /


Mass: 6632.896 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P35871
#8: Protein/peptide 50S RIBOSOMAL PROTEIN L34 /


Mass: 6132.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80340
#9: Protein 50S RIBOSOMAL PROTEIN L35 /


Mass: 7506.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SKU1
#10: Protein/peptide 50S RIBOSOMAL PROTEIN L36 /


Mass: 4435.411 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHR2
#13: Protein 50S RIBOSOMAL PROTEIN L1 /


Mass: 24885.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLP7
#14: Protein 50S RIBOSOMAL PROTEIN L2 /


Mass: 30532.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60405
#15: Protein 50S RIBOSOMAL PROTEIN L3 /


Mass: 22450.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN8
#16: Protein 50S RIBOSOMAL PROTEIN L4 /


Mass: 23271.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN9
#17: Protein 50S RIBOSOMAL PROTEIN L5 /


Mass: 21061.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ0
#18: Protein 50S RIBOSOMAL PROTEIN L6 /


Mass: 19568.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ3, UniProt: P0DOY8*PLUS
#19: Protein 50S RIBOSOMAL PROTEIN L10 /


Mass: 11081.651 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RESIDUES 4-133 ARE BUILT AS POLY-ALA / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1
#20: Protein 50S RIBOSOMAL PROTEIN L11 /


Mass: 11932.701 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: BUILT AS POLY-ALA / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1
#21: Protein 50S RIBOSOMAL PROTEIN L13 /


Mass: 15927.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60488
#22: Protein 50S RIBOSOMAL PROTEIN L14 /


Mass: 13323.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP8
#23: Protein 50S RIBOSOMAL PROTEIN L15 /


Mass: 16319.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ7
#24: Protein 50S RIBOSOMAL PROTEIN L16 /


Mass: 15993.909 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60489
#25: Protein 50S RIBOSOMAL PROTEIN L17 /


Mass: 13750.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q9Z9H5
#26: Protein 50S RIBOSOMAL PROTEIN L18 /


Mass: 12639.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ4
#27: Protein 50S RIBOSOMAL PROTEIN L19 /


Mass: 17188.830 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60490
#28: Protein 50S RIBOSOMAL PROTEIN L20 /


Mass: 13779.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60491
#29: Protein 50S RIBOSOMAL PROTEIN L21 /


Mass: 11069.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P60492
#30: Protein 50S RIBOSOMAL PROTEIN L22 /


Mass: 12808.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP3
#31: Protein 50S RIBOSOMAL PROTEIN L23 /


Mass: 10759.808 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP0
#32: Protein 50S RIBOSOMAL PROTEIN L24 /


Mass: 12085.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP9
#33: Protein 50S RIBOSOMAL PROTEIN L25 /


Mass: 23238.572 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHZ1

-
RNA chain , 6 types, 7 molecules AAABBABVBWBXBY

#11: RNA chain 23S ribosomal RNA /


Mass: 947999.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (23S RNA) HAS E.COLI RESIDUE NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E. COLI STRUCTURE IN 2AW4
Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969
#12: RNA chain 5S ribosomal RNA /


Mass: 39540.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969
#35: RNA chain 16S ribosomal RNA /


Mass: 493966.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CHAIN A (16S RNA) HAS E.COLI NUMBERING, BASED ON A STRUCTURAL ALIGNMENT WITH THE CORRESPONDING E.COLI STRUCTURE IN 2AVY.
Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: GenBank: 55979969
#56: RNA chain E-SITE or P-SITE TRNA FMET


Mass: 24802.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Production host: Escherichia coli (E. coli)
#57: RNA chain MRNA / Messenger RNA


Mass: 6228.810 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: SEQUENCE GGCAAGGAGGUAA AAUGU A ONLY THE AAUGU SEQUENCE NEAR THE 3-END WAS ORDERED.
Source: (synth.) Escherichia coli (E. coli)
#58: RNA chain TMRNA DELA


Mass: 28819.168 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The construct was based on the T. thermophilus SSRA gene sequence, containing residues 1-37 and 302-349 linked via a UUCG loop, and included four point mutations (G21A, C317U, G323U, C337A) ...Details: The construct was based on the T. thermophilus SSRA gene sequence, containing residues 1-37 and 302-349 linked via a UUCG loop, and included four point mutations (G21A, C317U, G323U, C337A) to ensure homogenous folding. Transcribed in vitro using T7 RNA polymerase
Source: (synth.) Thermus thermophilus HB8 (bacteria)

-
Protein , 2 types, 2 molecules B2BZ

#34: Protein SMALL PROTEIN B SMPB


Mass: 16785.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PURIFIED USING RECOMBINANT TECHNIQUES / Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8RR57
#59: Protein ELONGATION FACTOR TU / EF-Tu


Mass: 44728.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PURIFIED USING RECOMBINANT TECHNIQUES / Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHN6

-
30S RIBOSOMAL PROTEIN ... , 20 types, 20 molecules BBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBU

#36: Protein 30S RIBOSOMAL PROTEIN S2 /


Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80371
#37: Protein 30S RIBOSOMAL PROTEIN S3 /


Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80372
#38: Protein 30S RIBOSOMAL PROTEIN S4 /


Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80373
#39: Protein 30S RIBOSOMAL PROTEIN S5 /


Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ5
#40: Protein 30S RIBOSOMAL PROTEIN S6 /


Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLP8
#41: Protein 30S RIBOSOMAL PROTEIN S7 /


Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P17291
#42: Protein 30S RIBOSOMAL PROTEIN S8 /


Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS
#43: Protein 30S RIBOSOMAL PROTEIN S9 /


Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80374
#44: Protein 30S RIBOSOMAL PROTEIN S10 /


Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN7
#45: Protein 30S RIBOSOMAL PROTEIN S11 /


Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80376
#46: Protein 30S RIBOSOMAL PROTEIN S12 /


Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHN3
#47: Protein 30S RIBOSOMAL PROTEIN S13 /


Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80377
#48: Protein 30S RIBOSOMAL PROTEIN S14 /


Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS
#49: Protein 30S RIBOSOMAL PROTEIN S15 /


Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJ76
#50: Protein 30S RIBOSOMAL PROTEIN S16 /


Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SJH3
#51: Protein 30S RIBOSOMAL PROTEIN S17 /


Mass: 12325.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS
#52: Protein 30S RIBOSOMAL PROTEIN S18 /


Mass: 10258.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SLQ0
#53: Protein 30S RIBOSOMAL PROTEIN S19 /


Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SHP2
#54: Protein 30S RIBOSOMAL PROTEIN S20 /


Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: P80380
#55: Protein/peptide 30S RIBOSOMAL PROTEIN THX / Ribosome


Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus HB8 (bacteria) / Strain: HB8 - MRC - MSAW1 / References: UniProt: Q5SIH3

-
Non-polymers , 4 types, 7 molecules

#60: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#61: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#62: Chemical ChemComp-KIR / KIRROMYCIN / MOCIMYCIN / DELVOMYCIN / MYC-8003


Mass: 796.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H60N2O12
#63: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 % / Description: NONE
Crystal growpH: 6.5 / Details: 100 MM MES PH 6.5, 20 MM KCL, 8% (W/V) PEG20K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99998
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99998 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 503945 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.24 / Net I/σ(I): 8.8
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.48 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHASERmodel building
CNS1.2refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y11

2y11
PDB Unreleased entry


Resolution: 3.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODELING METHOD USED FLAT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.27 24443 4.7 %INHERITED FROM 2XQD
Rwork0.23 ---
obs0.23 503945 97.9 %-
Displacement parametersBiso mean: 58.9 Å2
Baniso -1Baniso -2Baniso -3
1--7.393 Å20 Å2-8.607 Å2
2---4.704 Å20 Å2
3---12.098 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.464 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6403 Å0.6307 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28796 65030 0 0 93826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.1→3.21 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 1810 4.1 %
Rwork0.331 43406 -
obs--87.7 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more