[English] 日本語
Yorodumi
- PDB-4blb: Crystal structure of a human Suppressor of fused (SUFU)-GLI1p complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4blb
TitleCrystal structure of a human Suppressor of fused (SUFU)-GLI1p complex
Components
  • MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
  • ZINC FINGER PROTEIN GLI1
KeywordsSIGNALING PROTEIN / SUGAR BINDING PROTEIN-SIGNALING PROTEIN COMPLEX / CHIMERA / FUSION PROTEIN / HEDGEHOG SIGNALING / GENE REGULATION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / pituitary gland development ...notochord regression / GLI proteins bind promoters of Hh responsive genes to promote transcription / smoothened signaling pathway involved in ventral spinal cord interneuron specification / smoothened signaling pathway involved in spinal cord motor neuron cell fate specification / positive regulation of cellular response to drug / regulation of hepatocyte proliferation / GLI-SUFU complex / ventral midline development / epidermal cell differentiation / pituitary gland development / proximal/distal pattern formation / ciliary tip / prostate gland development / positive regulation of cell cycle G1/S phase transition / cerebellar cortex morphogenesis / coronary vasculature development / regulation of smoothened signaling pathway / positive regulation of smoothened signaling pathway / dorsal/ventral pattern formation / aorta development / regulation of osteoblast differentiation / ventricular septum development / skin development / ciliary base / smoothened signaling pathway / digestive tract morphogenesis / negative regulation of protein import into nucleus / detection of maltose stimulus / maltose transport complex / heart looping / maltose binding / axoneme / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / spermatid development / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of osteoblast differentiation / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / positive regulation of cardiac muscle cell proliferation / negative regulation of ubiquitin-dependent protein catabolic process / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of DNA replication / neural tube closure / liver regeneration / Degradation of GLI1 by the proteasome / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / lung development / negative regulation of canonical Wnt signaling pathway / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / response to wounding / osteoblast differentiation / transcription corepressor activity / outer membrane-bounded periplasmic space / microtubule binding / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / periplasmic space / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA damage response / chromatin binding / positive regulation of cell population proliferation / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
C2H2-type zinc-finger protein GLI-like / Sufu, C-terminal domain / Suppressor of fused / Suppressor of fused, eukaryotic / Suppressor of fused C-terminal / Suppressor of fused, N-terminal / Suppressor of fused, C-terminal domain superfamily / Suppressor of Fused Gli/Ci N terminal binding domain / Suppressor of fused-like domain / Suppressor of fused protein (SUFU) ...C2H2-type zinc-finger protein GLI-like / Sufu, C-terminal domain / Suppressor of fused / Suppressor of fused, eukaryotic / Suppressor of fused C-terminal / Suppressor of fused, N-terminal / Suppressor of fused, C-terminal domain superfamily / Suppressor of Fused Gli/Ci N terminal binding domain / Suppressor of fused-like domain / Suppressor of fused protein (SUFU) / Zinc finger, C2H2 type / Gyrase A; domain 2 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / zinc finger / Bacterial extracellular solute-binding protein / Zinc finger C2H2 type domain profile. / Bacterial extracellular solute-binding protein / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Zinc finger protein GLI1 / Maltose/maltodextrin-binding periplasmic protein / Suppressor of fused homolog
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCherry, A.L. / Finta, C. / Karlstrom, M. / De Sanctis, D. / Toftgard, R. / Jovine, L.
Citation
#1: Journal: Nat.Cell Biol. / Year: 1999
Title: Mammalian Suppressor-of-Fused Modulates Nuclear-Cytoplasmic Shuttling of GLI-1.
Authors: Kogerman, P. / Grimm, T. / Kogerman, L. / Krause, D. / Unden, A.B. / Sandstedt, B. / Toftgard, R. / Zaphiropoulos, P.G.
#2: Journal: J.Biol.Chem. / Year: 2003
Title: Characterization of the Physical Interaction of GLI Proteins with Sufu Proteins.
Authors: Dunaeva, M. / Michelson, P. / Kogerman, P. / Toftgard, R.
#3: Journal: Mol.Cell.Biol. / Year: 2004
Title: Suppressor of Fused Regulates GLI Activity Through a Dual Binding Mechanism.
Authors: Merchant, M. / Vajdos, F.F. / Ultsch, M. / Maun, H.R. / Wendt, U. / Cannon, J. / Desmarais, W. / Lazarus, R.A. / De Vos, A.M. / De Sauvage, F.J.
#4: Journal: Dev.Cell / Year: 2006
Title: Genetic Elimination of Suppressor of Fused Reveals an Essential Repressor Function in the Mammalian Hedgehog Signaling Pathway.
Authors: Svard, J. / Heby-Henricson, K. / Persson-Lek, M. / Rozell, B. / Lauth, M. / Bergstrom, A. / Ericson, J. / Toftgard, R. / Teglund, S.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Revision 1.2Dec 18, 2013Group: Database references
Revision 1.3Mar 15, 2017Group: Source and taxonomy
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
E: ZINC FINGER PROTEIN GLI1
F: ZINC FINGER PROTEIN GLI1
G: ZINC FINGER PROTEIN GLI1
H: ZINC FINGER PROTEIN GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,76716
Polymers341,1368
Non-polymers1,6318
Water0
1
C: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
G: ZINC FINGER PROTEIN GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6924
Polymers85,2842
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-23.1 kcal/mol
Surface area30880 Å2
MethodPISA
2
A: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
E: ZINC FINGER PROTEIN GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6924
Polymers85,2842
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-24 kcal/mol
Surface area31340 Å2
MethodPISA
3
D: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
H: ZINC FINGER PROTEIN GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6924
Polymers85,2842
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-23.4 kcal/mol
Surface area31080 Å2
MethodPISA
4
B: MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG
F: ZINC FINGER PROTEIN GLI1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,6924
Polymers85,2842
Non-polymers4082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-23.7 kcal/mol
Surface area30870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.300, 137.600, 116.540
Angle α, β, γ (deg.)90.00, 105.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

-
Components

#1: Protein
MALTOSE-BINDING PERIPLASMIC PROTEIN, SUPPRESSOR OF FUSED HOMOLOG / SUFUH / LINKER / SUPPRESOR OF FUSED


Mass: 83634.141 Da / Num. of mol.: 4
Fragment: MBPP RESIDUES 29-392,SUFUH RESIDUES 32-278,361-483
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: DELETION OF RESIDUES 279-360 AND REPLACEMENT WITH PSRGEDP LINKER. DELETION OF RESIDUES 454-456. W61D, L62S, G63F, P453A, K457A
Source: (gene. exp.) ESCHERICHIA COLI (E. coli), (gene. exp.) HOMO SAPIENS (human)
Plasmid: PLJMBP4C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AEX9, UniProt: Q9UMX1
#2: Protein/peptide
ZINC FINGER PROTEIN GLI1 / / TRANSCRIPTIONAL ACTIVATOR GL1 / GLIOMA-ASSOCIATED ONCOGENE / ONCOGENE GLI


Mass: 1649.803 Da / Num. of mol.: 4 / Fragment: RESIDUES 332-338 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P08151
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Sequence detailsRESIDUES 216 AND 220 OF MALTOSE-BINDING PERIPLASMIC PROTEIN ARE MUTATED TO HISTIDINES. RESIDUES 372- ...RESIDUES 216 AND 220 OF MALTOSE-BINDING PERIPLASMIC PROTEIN ARE MUTATED TO HISTIDINES. RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32- 278. RESIDUES 61-63 OF UNIPROT Q9UMX1 HAVE BEEN MUTATED ( FROM WLG) TO DSF. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-718 REPRESENT UNIPROT Q9UMX1 RESIDUES 361-453. RESIDUES 454-456 OF UNIPROT Q9UMX1 HAVE BEEN DELETED AND RESIDUES 453 AND 457 MUTATED TO ALANINES. RESIDUES 719-745 REPRESENT UNIPROT Q9UMX1 RESIDUES 457-483. THIS MOLECULE IS A PEPTIDE CONTAINING RESIDUES 115-131

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.36 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PROTEIN (10 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS MIXED IN A 1:1 MOLAR RATIO WITH ZN(OAC)2 AND A 1:4 MOLAR RATIO WITH GLI1 PEPTIDE. THE COMPLEX WAS ...Details: PROTEIN (10 MG/ML IN 10 MM TRIS-HCL PH 7.5, 50 MM NACL, 1 MM DTT, 1 MM MALTOSE) WAS MIXED IN A 1:1 MOLAR RATIO WITH ZN(OAC)2 AND A 1:4 MOLAR RATIO WITH GLI1 PEPTIDE. THE COMPLEX WAS CRYSTALLISED BY HANGING DROP VAPOUR DIFFUSION AT 4C WITH 1:1 OR 2:1 DROPS OF PROTEIN:WELL SOLUTION (14-18% (V/V) PEG 3350, AND 0.2 M NA FORMATE)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.8→62.73 Å / Num. obs: 85233 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 79.984 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.4 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2- XDSdata reduction
xia2- XDSdata scaling
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB SUBMISSION 56660

Resolution: 2.8→19.985 Å / SU ML: 0.41 / σ(F): 1.35 / Phase error: 28.38 / Stereochemistry target values: ML
Details: RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-718 REPRESENT UNIPROT Q9UMX1 RESIDUES 361- ...Details: RESIDUES 372-618 OF THIS FUSION CONSTRUCT REPRESENT UNIPROT Q9UMX1 RESIDUES 32-278. RESIDUES 619-625 REPRESENT AN ARTIFICIAL LINKER. RESIDUES 626-718 REPRESENT UNIPROT Q9UMX1 RESIDUES 361-453. RESIDUES 719-745 REPRESENT UNIPROT Q9UMX1 RESIDUES 457-483. THEREFORE, TO OBTAIN THE CORRECT NUMBERING, 340 SHOULD BE SUBTRACTED FROM RESIDUES 372-618, 265 SHOULD BE SUBTRACTED FROM RESIDUES 626-718 AND 262 SHOULD BE SUBTRACTED FROM RESIDUES 719-745.
RfactorNum. reflection% reflection
Rfree0.2344 1963 2.3 %
Rwork0.1968 --
obs0.1977 84943 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.384 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23045 0 96 0 23141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00723782
X-RAY DIFFRACTIONf_angle_d0.99932315
X-RAY DIFFRACTIONf_dihedral_angle_d11.3788604
X-RAY DIFFRACTIONf_chiral_restr0.0413494
X-RAY DIFFRACTIONf_plane_restr0.0054193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.86990.34751510.29825887X-RAY DIFFRACTION98
2.8699-2.94720.33251250.29245945X-RAY DIFFRACTION98
2.9472-3.03370.35671390.28735908X-RAY DIFFRACTION98
3.0337-3.13120.37011650.295894X-RAY DIFFRACTION98
3.1312-3.24270.30731350.26695869X-RAY DIFFRACTION97
3.2427-3.37190.30691410.24575941X-RAY DIFFRACTION99
3.3719-3.52460.27891290.23135969X-RAY DIFFRACTION98
3.5246-3.70930.27361260.21455922X-RAY DIFFRACTION98
3.7093-3.940.25791400.20095857X-RAY DIFFRACTION97
3.94-4.24160.21761380.17625899X-RAY DIFFRACTION98
4.2416-4.66350.19571390.15695964X-RAY DIFFRACTION98
4.6635-5.32710.20021490.16015895X-RAY DIFFRACTION97
5.3271-6.66990.24631330.1936011X-RAY DIFFRACTION99
6.6699-19.98560.16951530.16916019X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.819-0.22431.15130.7546-0.19163.0528-0.1550.439-0.0697-0.0772-0.0766-0.07630.64720.7629-0.00010.83870.13370.11110.73250.06380.707970.5447-36.5125-133.0975
23.0886-1.19640.4694.57550.1731.4455-0.2287-0.01560.27290.01070.1439-0.0758-0.1997-0.004700.6248-0.0783-0.0030.5390.04680.580941.1143-9.288-127.4386
32.1984-0.57710.61771.632-0.62081.19060.0288-0.0882-0.0927-0.02020.11520.26970.2591-0.307900.8387-0.069-0.12770.78850.04450.936713.42290.0274-137.9316
42.56880.4364-0.83481.55510.81964.3785-0.16630.1374-0.08620.02840.0650.13180.0312-0.3050.00030.60070.0088-0.01260.540.0550.67176.6766-37.4142-128.5005
51.81820.0210.3253.36340.34033.3087-0.4380.24970.52110.04420.0358-0.0038-0.78620.2456-0.00120.9-0.0361-0.23530.73720.20540.87719.0906-12.7698-98.1611
60.1775-0.0151-0.30040.2639-0.23470.69930.0734-0.94190.39860.1427-0.41530.9497-1.158-0.2446-01.72460.17590.07731.3483-0.33251.6704-2.032-4.1182-71.2196
73.68730.04931.66981.12730.17322.70970.1344-0.8417-0.5070.3990.12920.21980.6746-0.62830.00261.04390.0070.03140.89610.20330.787412.2832-41.8217-64.6968
84.5584-1.0031-0.0213.45590.40433.28490.3160.22651.3968-0.2209-0.18290.0251-0.8077-0.3060.00520.96810.31590.11270.84840.08071.154839.5637-13.4074-66.7963
90.5544-0.21820.30890.1124-0.00530.49190.6388-1.69010.98690.5839-0.5434-0.3605-1.0781.22440.00011.628-0.57770.05091.7574-0.25422.110765.2094-5.6708-50.4111
102.5804-0.2982-0.77071.3602-0.49552.74560.0201-0.26930.03750.1891-0.0577-0.3054-0.19430.39530.00170.62250.0767-0.02790.78420.08980.738575.3531-39.5015-69.4405
110.90710.3886-0.54964.41780.05882.65290.027-0.10890.33140.0455-0.00440.1311-0.32520.038500.68670.10650.07410.88080.0910.767872.2508-10.4815-96.0099
120.84810.30980.07630.8733-0.10991.37150.0010.75060.1843-0.84660.1431-0.3707-0.31140.5225-01.2482-0.17550.23191.34140.17391.161783.05071.7042-122.4728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESI :371 OR RESI 900 OR RESI 748:753 OR RESI 910)
2X-RAY DIFFRACTION2(CHAIN A AND RESI 372:605) OR (CHAIN E AND RESI 333:341)
3X-RAY DIFFRACTION3CHAIN A AND RESI 606:740
4X-RAY DIFFRACTION4CHAIN B AND (RESI :371 OR RESI 900 OR RESI 747:753 OR RESI 910)
5X-RAY DIFFRACTION5(CHAIN B AND RESI 372:605) OR (CHAIN F AND RESI 333:341)
6X-RAY DIFFRACTION6CHAIN B AND RESI 606:739
7X-RAY DIFFRACTION7CHAIN C AND (RESI :371 OR RESI 900 OR RESI 746:753 OR RESI 910)
8X-RAY DIFFRACTION8(CHAIN C AND RESI 372:605) OR (CHAIN G AND RESI 333:340)
9X-RAY DIFFRACTION9CHAIN C AND RESI 606:735
10X-RAY DIFFRACTION10CHAIN D AND (RESI :371 OR RESI 900 OR RESI 747:753 OR RESI 910)
11X-RAY DIFFRACTION11(CHAIN D AND RESI 372:605) OR (CHAIN H AND RESI 333:341)
12X-RAY DIFFRACTION12CHAIN D AND RESI 606:740

+
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