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- PDB-8hl1: Cryo-EM Structures and Translocation Mechanism of Crenarchaeota R... -

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Entry
Database: PDB / ID: 8hl1
TitleCryo-EM Structures and Translocation Mechanism of Crenarchaeota Ribosome
Components
  • (30S ribosomal protein ...) x 24
  • (50S ribosomal protein ...) x 34
  • 16s rRNA (1493-MER)
  • 23s rRNA (3000-MER)
  • 5s rRNA (122-MER)
  • Conserved proteinConservation
  • DUF2280 domain-containing protein
  • Elongation factor 2EEF2
  • PHE-PHE-PHE-PHE-PHE-PHE
  • Small ribosomal subunit protein uS8
  • mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
  • tRNA (76-MER)
KeywordsRIBOSOME / Sulfolobus acidocaldarius ribosome small subunit
Function / homology
Function and homology information


ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding ...ribonuclease P activity / tRNA 5'-leader removal / translation elongation factor activity / cytosolic ribosome / large ribosomal subunit rRNA binding / large ribosomal subunit / ribosome biogenesis / regulation of translation / small ribosomal subunit / 5S rRNA binding / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / GTP binding / RNA binding / zinc ion binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2, archaeal / Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L14e / Ribosomal protein L1, archaea / : / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / : / Ribosomal protein S9, archaeal ...Translation elongation factor EFG/EF2, archaeal / Domain of unknown function DUF5622 / Domain of unknown function (DUF5622) / Ribosomal protein L14e / Ribosomal protein L1, archaea / : / Ribosomal protein S27ae / Ribosomal protein L40e, archaeal / : / Ribosomal protein S9, archaeal / Ribosomal protein S13, archaeal / Ribosomal protein S17, archaeal / Ribosomal protein S6e, archaeal / Ribosomal protein S4, archaeal / Ribosomal protein S12, archaea / Ribosomal protein S3, archaeal / 30S ribosomal protein S3Ae / Ribosomal protein S7, archaeal / Ribosomal protein S19e, archaeal / Ribosomal protein S11, archaeal / Ribosomal protein S2, archaeal / Ribosomal protein S14, type Z, archaeal / Ribosomal protein S8e, archaeal / Ribosomal protein L19e, archaeal / Ribosomal protein L15e, archaeal / Ribosomal protein L30, archaeal / Ribosomal protein L6P, archaea / Ribosomal protein L14P, archaeal / Ribosomal protein L21e, archaeal / Ribosomal protein L18e, archaea / Ribosomal protein L10e, archaea / Ribosomal protein L32e, archaeal / Ribosomal protein L3, archaeal / Ribosomal protein L4, archaea / Ribosomal protein L5, archaeal / Ribosomal protein L7Ae, archaea / Ribosomal protein L24e / Ribosomal protein L30e / Ribosomal protein L2, archaeal-type / Ribosomal L15/L27a, N-terminal / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal protein L23 / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / metallochaperone-like domain / TRASH domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein L10e, conserved site / Ribosomal protein L10e / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S8e, conserved site / Ribosomal protein L24e, conserved site / Ribosomal protein L34e, conserved site / Ribosomal protein L44e / Ribosomal protein L1, conserved site / Ribosomal S17 / Ribosomal protein S19e / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein L1 / Ribosomal protein S27 / Ribosomal protein S28e conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein S28e / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein L44 / Ribosomal protein L34Ae / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S8e / Ribosomal protein S4, KOW domain / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal protein L30/YlxQ / Ribosomal protein S6e / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / UNKNOWN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS4 ...PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / UNKNOWN / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Uncharacterized protein / Large ribosomal subunit protein uL24 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS8 / Large ribosomal subunit protein uL6 / Large ribosomal subunit protein eL32 / Large ribosomal subunit protein eL19 / Large ribosomal subunit protein uL18 / Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL30 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein eL34 / Large ribosomal subunit protein eL30 / Small ribosomal subunit protein uS12 / Large ribosomal subunit protein eL39 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS10 / Elongation factor 2 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein eL20 / Large ribosomal subunit protein eL31 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS13 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein eL18 / Small ribosomal subunit protein uS2 / Large ribosomal subunit protein uL5 / Large ribosomal subunit protein eL8 / Small ribosomal subunit protein eS19 / Conserved protein / Small ribosomal subunit protein eS27 / Large ribosomal subunit protein eL42 / Uncharacterized protein / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS31 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein eL14 / 50S ribosomal protein L40e / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS28 / Large ribosomal subunit protein eL24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein eL37 / Large ribosomal subunit protein eL21 / Small ribosomal subunit protein eS1 / Large ribosomal subunit protein eL15 / Large ribosomal subunit protein eL43 / Large ribosomal subunit protein uL3 / Large ribosomal subunit protein uL4 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL2 / Small ribosomal subunit protein uS19 / Large ribosomal subunit protein uL22 / Small ribosomal subunit protein uS3 / Large ribosomal subunit protein uL29 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL16
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.93 Å
AuthorsWang, Y.H. / Zhou, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971226 China
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.
Authors: Ying-Hui Wang / Hong Dai / Ling Zhang / Yun Wu / Jingfen Wang / Chen Wang / Cai-Huang Xu / Hai Hou / Bing Yang / Yongqun Zhu / Xing Zhang / Jie Zhou /
Abstract: Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome ...Archaeal ribosomes have many domain-specific features; however, our understanding of these structures is limited. We present 10 cryo-electron microscopy (cryo-EM) structures of the archaeal ribosome from crenarchaeota Sulfolobus acidocaldarius (Sac) at 2.7-5.7 Å resolution. We observed unstable conformations of H68 and h44 of ribosomal RNA (rRNA) in the subunit structures, which may interfere with subunit association. These subunit structures provided models for 12 rRNA expansion segments and 3 novel r-proteins. Furthermore, the 50S-aRF1 complex structure showed the unique domain orientation of aRF1, possibly explaining P-site transfer RNA (tRNA) release after translation termination. Sac 70S complexes were captured in seven distinct steps of the tRNA translocation reaction, confirming conserved structural features during archaeal ribosome translocation. In aEF2-engaged 70S ribosome complexes, 3D classification of cryo-EM data based on 30S head domain identified two new translocation intermediates with 30S head domain tilted 5-6° enabling its disengagement from the translocated tRNA and its release post-translocation. Additionally, we observed conformational changes to aEF2 during ribosome binding and switching from three different states. Our structural and biochemical data provide new insights into archaeal translation and ribosome translocation.
History
DepositionNov 28, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A16S: 16s rRNA (1493-MER)
A23S: 23s rRNA (3000-MER)
AEFG: Elongation factor 2
A5S: 5s rRNA (122-MER)
AL2P: 50S ribosomal protein L2
AL3P: 50S ribosomal protein L3
AL4P: 50S ribosomal protein L4
AL5P: 50S ribosomal protein L5
AL6P: 50S ribosomal protein L6
ALX0: 50S ribosomal protein L18Ae
L10E: 50S ribosomal protein L10e
L13P: 50S ribosomal protein L13
L141: 50S ribosomal protein L14e
L142: 50S ribosomal protein L14e
L14P: 50S ribosomal protein L14
L15E: 50S ribosomal protein L15e
L18E: 50S ribosomal protein L18e
L18P: 50S ribosomal protein L18
L19E: 50S ribosomal protein L19e
L22P: 50S ribosomal protein L22
L23P: 50S ribosomal protein L23
L24E: 50S ribosomal protein L24e
L24P: 50S ribosomal protein L24
L29P: 50S ribosomal protein L29
L30E: 50S ribosomal protein L30e
L30P: 50S ribosomal protein L30
L31E: 50S ribosomal protein L31e
L32E: 50S ribosomal protein L32e
L34E: 50S ribosomal protein L34e
L37A: 50S ribosomal protein L37Ae
L37E: 50S ribosomal protein L37e
L39E: 50S ribosomal protein L39e
L40E: 50S ribosomal protein L40E
L44E: 50S ribosomal protein L44e
L7A1: 50S ribosomal protein L7Ae
L7A2: 50S ribosomal protein L7Ae
L15P: 50S ribosomal protein L15
L21E: 50S ribosomal protein L21e
L45A: DUF2280 domain-containing protein
L46A: Conserved protein
L47A: 50S ribosomal protein L47A
AL1P: 50S ribosomal protein L1
AS3P: 30S ribosomal protein S3
AS7P: 30S ribosomal protein S7
S10P: 30S ribosomal protein S10
S13P: 30S ribosomal protein S13
S14P: 30S ribosomal protein S14 type Z
S17E: 30S ribosomal protein S17e
S19E: 30S ribosomal protein S19e
S19P: 30S ribosomal protein S19
AS9P: 30S ribosomal protein S9
S28E: 30S ribosomal protein S28e
S27A: 30S ribosomal protein S27ae
SL7A: 50S ribosomal protein L7Ae
AS2P: 30S ribosomal protein S2
AS4E: 30S ribosomal protein S4e
AS4P: 30S ribosomal protein S4
AS5P: 30S ribosomal protein S5
AS6E: 30S ribosomal protein S6e
AS8E: 30S ribosomal protein S8e
AS8P: Small ribosomal subunit protein uS8
S11P: 30S ribosomal protein S11
S12P: 30S ribosomal protein S12
S15P: 30S ribosomal protein S15
S17P: 30S ribosomal protein S17
S24E: 30S ribosomal protein S24e
S27E: 30S ribosomal protein S27e
S3AE: 30S ribosomal protein S3Ae
APTN: tRNA (76-MER)
AETN: tRNA (76-MER)
AMRN: mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
APTP: PHE-PHE-PHE-PHE-PHE-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,575,889130
Polymers2,569,48972
Non-polymers6,40058
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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RNA chain , 5 types, 6 molecules A16SA23SA5SAPTNAETNAMRN

#1: RNA chain 16s rRNA (1493-MER)


Mass: 484680.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 68566501
#2: RNA chain 23s rRNA (3000-MER)


Mass: 980552.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 68566501
#4: RNA chain 5s rRNA (122-MER)


Mass: 39440.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: GenBank: 68566501
#66: RNA chain tRNA (76-MER)


Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
#67: RNA chain mRNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3935.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)

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Protein , 4 types, 4 molecules AEFGL45AL46AAS8P

#3: Protein Elongation factor 2 / EEF2 / EF-2


Mass: 81106.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P23112
#37: Protein DUF2280 domain-containing protein


Mass: 11662.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9G6
#38: Protein Conserved protein / Conservation


Mass: 8320.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J953
#58: Protein Small ribosomal subunit protein uS8 / 30S ribosomal protein S8


Mass: 14624.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05636

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50S ribosomal protein ... , 34 types, 37 molecules AL2PAL3PAL4PAL5PAL6PALX0L10EL13PL141L142L14PL15EL18EL18PL19EL22PL23PL24EL24PL29PL30EL30PL31EL32EL34EL37AL37EL39EL40EL44E...

#5: Protein 50S ribosomal protein L2 /


Mass: 24881.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB43
#6: Protein 50S ribosomal protein L3 /


Mass: 38186.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB40
#7: Protein 50S ribosomal protein L4 /


Mass: 27357.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB41
#8: Protein 50S ribosomal protein L5 /


Mass: 19095.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P41202
#9: Protein 50S ribosomal protein L6 /


Mass: 20305.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05637
#10: Protein 50S ribosomal protein L18Ae / Ribosome / 50S ribosomal protein L20e / 50S ribosomal protein LX


Mass: 8926.346 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38613
#11: Protein 50S ribosomal protein L10e / Ribosome


Mass: 18670.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JC84
#12: Protein 50S ribosomal protein L13 /


Mass: 15808.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39473
#13: Protein 50S ribosomal protein L14e / Ribosome


Mass: 9559.101 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAJ9
#14: Protein 50S ribosomal protein L14 /


Mass: 14707.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB50
#15: Protein 50S ribosomal protein L15e / Ribosome


Mass: 20179.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB20
#16: Protein 50S ribosomal protein L18e / Ribosome / HL29e


Mass: 12747.252 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39474
#17: Protein 50S ribosomal protein L18 /


Mass: 21766.139 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05640
#18: Protein 50S ribosomal protein L19e / Ribosome


Mass: 17108.916 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05639
#19: Protein 50S ribosomal protein L22 /


Mass: 17360.293 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB45
#20: Protein 50S ribosomal protein L23 /


Mass: 9261.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB42
#21: Protein 50S ribosomal protein L24e / Ribosome


Mass: 6338.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV2
#22: Protein 50S ribosomal protein L24 /


Mass: 14130.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05633
#23: Protein 50S ribosomal protein L29 /


Mass: 7378.790 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB47
#24: Protein 50S ribosomal protein L30e / Ribosome


Mass: 10391.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11522
#25: Protein 50S ribosomal protein L30 /


Mass: 17819.736 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05642
#26: Protein 50S ribosomal protein L31e / Ribosome


Mass: 8935.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P38618
#27: Protein 50S ribosomal protein L32e / Ribosome


Mass: 14328.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05638
#28: Protein 50S ribosomal protein L34e / Ribosome


Mass: 8993.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05981
#29: Protein 50S ribosomal protein L37Ae / Ribosome / Ribosomal protein L43e


Mass: 7536.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB29
#30: Protein 50S ribosomal protein L37e / Ribosome


Mass: 6274.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAZ9
#31: Protein/peptide 50S ribosomal protein L39e / Ribosome / L46e


Mass: 5861.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P13005
#32: Protein 50S ribosomal protein L40E / Ribosome


Mass: 6336.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP0
#33: Protein 50S ribosomal protein L44e / Ribosome


Mass: 10805.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B2
#34: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 13351.481 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8P1
#35: Protein 50S ribosomal protein L15 /


Mass: 16476.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05643
#36: Protein 50S ribosomal protein L21e / Ribosome


Mass: 11155.290 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB11
#39: Protein 50S ribosomal protein L47A / Ribosome


Mass: 9276.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: F2Z6C4
#40: Protein 50S ribosomal protein L1 /


Mass: 24416.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P35024

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30S ribosomal protein ... , 24 types, 24 molecules AS3PAS7PS10PS13PS14PS17ES19ES19PAS9PS28ES27AAS2PAS4EAS4PAS5PAS6EAS8ES11PS12PS15PS17PS24ES27ES3AE

#41: Protein 30S ribosomal protein S3 /


Mass: 22396.506 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB46
#42: Protein 30S ribosomal protein S7 /


Mass: 21862.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17198
#43: Protein 30S ribosomal protein S10 /


Mass: 11775.886 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P17199
#44: Protein 30S ribosomal protein S13 /


Mass: 17140.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39470
#45: Protein 30S ribosomal protein S14 type Z / Ribosome


Mass: 6190.371 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05635
#46: Protein 30S ribosomal protein S17e / Ribosome


Mass: 7336.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAX5
#47: Protein 30S ribosomal protein S19e / Ribosome


Mass: 17559.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J8U1
#48: Protein 30S ribosomal protein S19 /


Mass: 13800.354 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB44
#49: Protein 30S ribosomal protein S9 /


Mass: 15638.136 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39468
#50: Protein 30S ribosomal protein S28e / Ribosome


Mass: 7094.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAV1
#51: Protein 30S ribosomal protein S27ae / Ribosome


Mass: 6261.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAG0
#52: Protein 30S ribosomal protein S2 /


Mass: 22474.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39478
#53: Protein 30S ribosomal protein S4e / Ribosome


Mass: 27339.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05634
#54: Protein 30S ribosomal protein S4 /


Mass: 19440.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39467
#55: Protein 30S ribosomal protein S5 /


Mass: 22782.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: O05641
#56: Protein 30S ribosomal protein S6e / Ribosome


Mass: 11479.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI1
#57: Protein 30S ribosomal protein S8e / Ribosome


Mass: 14113.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAP5
#59: Protein 30S ribosomal protein S11 /


Mass: 13652.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P39469
#60: Protein 30S ribosomal protein S12 /


Mass: 15703.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: P11524
#61: Protein 30S ribosomal protein S15 /


Mass: 17438.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAI3
#62: Protein 30S ribosomal protein S17 /


Mass: 12602.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB49
#63: Protein 30S ribosomal protein S24e / Ribosome


Mass: 10765.213 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JAF9
#64: Protein 30S ribosomal protein S27e / Ribosome


Mass: 6576.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4J9B1
#65: Protein 30S ribosomal protein S3Ae / Ribosome / Ribosomal protein S1e


Mass: 21876.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)
References: UniProt: Q4JB17

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Protein/peptide , 1 types, 1 molecules APTP

#68: Protein/peptide PHE-PHE-PHE-PHE-PHE-PHE


Mass: 901.058 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Sulfolobus acidocaldarius DSM 639 (acidophilic)

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Non-polymers , 2 types, 58 molecules

#69: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#70: Chemical...
ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 57 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sulfolobus acidocaldarius ribosome small sbunit / Type: RIBOSOME / Entity ID: #2, #4-#38 / Source: NATURAL
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 26.7 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3841 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 229.21 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056186945
ELECTRON MICROSCOPYf_angle_d0.6581276041
ELECTRON MICROSCOPYf_chiral_restr0.038634715
ELECTRON MICROSCOPYf_plane_restr0.004917091
ELECTRON MICROSCOPYf_dihedral_angle_d16.259367612

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