[English] 日本語
Yorodumi
- PDB-4w9k: pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4w9k
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-3-phenylpropanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 14)
Components
  • Transcription elongation factor B polypeptide 1
  • Transcription elongation factor B polypeptide 2
  • Von Hippel-Lindau disease tumor suppressor
KeywordsTRANSCRIPTION / protein complex / ubiquitin ligase / hypoxia inducible factor
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / Replication of the SARS-CoV-2 genome / protein-macromolecule adaptor activity / molecular adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain ...von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / Elongin C; Chain C, domain 1 / von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3JO / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGadd, M.S. / Galdeano, C. / van Molle, I. / Ciulli, A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460
Biotechnology and Biological Sciences Research CouncilBBSRC BB/G023123/1 United Kingdom
Marie Sklodowska-Curie ActionsEC PIEF-GA-2012-328030
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor ...Title: Structure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with in Vitro Nanomolar Affinities.
Authors: Galdeano, C. / Gadd, M.S. / Soares, P. / Scaffidi, S. / Van Molle, I. / Birced, I. / Hewitt, S. / Dias, D.M. / Ciulli, A.
History
DepositionAug 27, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
C: Von Hippel-Lindau disease tumor suppressor
D: Transcription elongation factor B polypeptide 2
E: Transcription elongation factor B polypeptide 1
F: Von Hippel-Lindau disease tumor suppressor
G: Transcription elongation factor B polypeptide 2
H: Transcription elongation factor B polypeptide 1
I: Von Hippel-Lindau disease tumor suppressor
J: Transcription elongation factor B polypeptide 2
K: Transcription elongation factor B polypeptide 1
L: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,42816
Polymers166,94912
Non-polymers2,4794
Water6,251347
1
A: Transcription elongation factor B polypeptide 2
B: Transcription elongation factor B polypeptide 1
C: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3574
Polymers41,7373
Non-polymers6201
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-39 kcal/mol
Surface area16120 Å2
MethodPISA
2
D: Transcription elongation factor B polypeptide 2
E: Transcription elongation factor B polypeptide 1
F: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3574
Polymers41,7373
Non-polymers6201
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-40 kcal/mol
Surface area16190 Å2
MethodPISA
3
G: Transcription elongation factor B polypeptide 2
H: Transcription elongation factor B polypeptide 1
I: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3574
Polymers41,7373
Non-polymers6201
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-39 kcal/mol
Surface area16290 Å2
MethodPISA
4
J: Transcription elongation factor B polypeptide 2
K: Transcription elongation factor B polypeptide 1
L: Von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3574
Polymers41,7373
Non-polymers6201
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-36 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.696, 93.696, 361.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L
14C
24F
34I
15C
25F
35I
45L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 999
2114D1 - 999
3114G1 - 999
4114J1 - 999
1124B1 - 999
2124E1 - 999
3124H1 - 999
4124K1 - 999
1134C1 - 169
2134F1 - 169
3134I1 - 169
4134L1 - 169
1144C170 - 186
2144F170 - 186
3144I170 - 186
1154C186 - 999
2154F186 - 999
3154I186 - 999
4154L186 - 999

NCS ensembles :
ID
1
2
3
4
5
DetailsThe biological unit is a trimer. There are four biological units in the asymmetric unit (chains A, B & C, chains D, E & F, chains G, H & I and chains J, K &L).

-
Components

#1: Protein
Transcription elongation factor B polypeptide 2 / Elongin 18 kDa subunit / Elongin-B / EloB / RNA polymerase II transcription factor SIII subunit B / SIII p18


Mass: 11956.372 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB2 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein
Transcription elongation factor B polypeptide 1 / Elongin 15 kDa subunit / Elongin-C / EloC / RNA polymerase II transcription factor SIII subunit C / SIII p15


Mass: 10974.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCEB1 / Plasmid: pCDFDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein
Von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18806.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Plasmid: pHAT4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40337
#4: Chemical
ChemComp-3JO / N-acetyl-L-phenylalanyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 619.774 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C33H41N5O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 3350, MgOAc, Sodium cacodylate, DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 0.988→93.696 Å / Num. all: 91790 / Num. obs: 91790 / % possible obs: 96.4 % / Redundancy: 7.2 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.077 / Rsym value: 0.066 / Net I/av σ(I): 8.239 / Net I/σ(I): 14.9 / Num. measured all: 659300
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.214.20.6681.247141111120.4070.6681.882.1
2.21-2.355.40.4711.665246120760.2430.471393.6
2.35-2.517.80.322.494790121710.1290.325.399.9
2.51-2.718.30.2013.994341114160.0780.2018.4100
2.71-2.978.20.1176.586976105470.0450.11713.4100
2.97-3.328.10.0749.67827796100.0290.07420.8100
3.32-3.8380.055126765784900.0220.05528.999.9
3.83-4.77.80.04413.75675972860.0180.04435.699.9
4.7-6.647.70.041144430557460.0170.04133.399.9
6.64-48.8617.10.03115.92380833360.0130.03134.798.8

-
Processing

Software
NameVersionClassification
SCALA3.3.21data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCB

1vcb


Resolution: 2.1→93.696 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.2532 / WRfactor Rwork: 0.21 / FOM work R set: 0.7957 / SU B: 13.048 / SU ML: 0.17 / SU R Cruickshank DPI: 0.2355 / SU Rfree: 0.1999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2596 4637 5.1 %RANDOM
Rwork0.2148 87047 --
obs0.2171 87047 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.17 Å2 / Biso mean: 50.787 Å2 / Biso min: 21.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0 Å2-0 Å2
2--0.64 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: final / Resolution: 2.1→93.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10493 0 176 347 11016
Biso mean--49.22 46.1 -
Num. residues----1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910924
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210432
X-RAY DIFFRACTIONr_angle_refined_deg1.2832.00314865
X-RAY DIFFRACTIONr_angle_other_deg0.7593.00523960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12351315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7523.305469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.535151761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1151584
X-RAY DIFFRACTIONr_chiral_restr0.0690.21702
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112083
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022437
X-RAY DIFFRACTIONr_mcbond_it2.0341.8425320
X-RAY DIFFRACTIONr_mcbond_other2.0341.8435321
X-RAY DIFFRACTIONr_mcangle_it3.2464.1236612
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1573MEDIUM POSITIONAL0.30.5
12D1573MEDIUM POSITIONAL0.250.5
13G1573MEDIUM POSITIONAL0.30.5
14J1573MEDIUM POSITIONAL0.360.5
11A1573MEDIUM THERMAL6.572
12D1573MEDIUM THERMAL6.992
13G1573MEDIUM THERMAL5.522
14J1573MEDIUM THERMAL5.592
21B1305MEDIUM POSITIONAL0.320.5
22E1305MEDIUM POSITIONAL0.430.5
23H1305MEDIUM POSITIONAL0.340.5
24K1305MEDIUM POSITIONAL0.380.5
21B1305MEDIUM THERMAL4.122
22E1305MEDIUM THERMAL4.712
23H1305MEDIUM THERMAL4.362
24K1305MEDIUM THERMAL3.852
31C1665MEDIUM POSITIONAL0.280.5
32F1665MEDIUM POSITIONAL0.310.5
33I1665MEDIUM POSITIONAL0.330.5
34L1665MEDIUM POSITIONAL0.410.5
31C1665MEDIUM THERMAL4.172
32F1665MEDIUM THERMAL6.452
33I1665MEDIUM THERMAL4.432
34L1665MEDIUM THERMAL6.562
41C233MEDIUM POSITIONAL0.240.5
42F233MEDIUM POSITIONAL0.190.5
43I233MEDIUM POSITIONAL0.260.5
41C233MEDIUM THERMAL8.32
42F233MEDIUM THERMAL4.412
43I233MEDIUM THERMAL7.652
51C228MEDIUM POSITIONAL0.340.5
52F228MEDIUM POSITIONAL0.350.5
53I228MEDIUM POSITIONAL0.310.5
54L228MEDIUM POSITIONAL0.450.5
51C228MEDIUM THERMAL4.912
52F228MEDIUM THERMAL8.192
53I228MEDIUM THERMAL5.382
54L228MEDIUM THERMAL6.982
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 285 -
Rwork0.312 5133 -
all-5418 -
obs--78.46 %
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)
12.2612-0.70190.60542.3405-0.962.84150.03540.2098-0.0785-0.2617-0.1387-0.2069-0.02750.23870.10330.09250.00920.0410.10310.05080.120844.486265.528846.964
23.9117-0.01690.17720.9947-0.90253.0279-0.0506-0.2092-0.1438-0.0431-0.0107-0.10460.02910.05980.06130.00520.00260.0040.13890.09020.125948.274661.527964.426
35.2218-0.2771-2.77751.5769-0.09562.06160.1253-0.34160.01180.0838-0.1-0.1028-0.01690.0201-0.02530.0235-0.0631-0.03570.33920.17230.121627.461754.71181.6183
42.9645-0.76872.45971.4098-0.74634.5769-0.05440.67810.1943-0.2035-0.0912-0.1983-0.53511.16510.14570.2159-0.12810.07860.33570.03740.094248.059918.802546.7133
55.41860.52951.76230.3352-0.9284.8589-0.15320.4122-0.09620.0118-0.0131-0.0606-0.17330.40940.16630.1225-0.04250.04720.25810.02590.136452.938114.503964.3909
64.03990.2924-1.37971.54910.1741.97260.0199-0.131-0.1409-0.0004-0.0413-0.1042-0.0386-0.46030.02130.0159-0.005-0.0280.3540.11260.095832.30867.661481.2021
73.9325-1.62260.40041.3777-0.8613.5072-0.01610.2440.2817-0.2272-0.1036-0.0612-0.17240.19210.11970.1747-0.03130.01550.27650.07180.12262.846313.333846.9703
85.1713-0.7074-1.5050.9868-0.61612.1482-0.3021-0.8150.24750.20290.1938-0.1133-0.09420.30930.10840.20060.0686-00.6169-0.02050.20196.497511.412664.6131
92.5404-0.3186-1.02511.3884-0.33184.4121-0.0261-0.2078-0.05990.0217-0.1350.01870.4540.79080.16110.11270.05910.03630.37040.06980.1161-15.10057.302781.7044
103.3066-0.7337-1.19862.0698-0.56922.8752-0.02650.00030.0772-0.1124-0.01290.0244-0.03780.23630.03940.0588-0.01290.00530.16350.07380.0819-1.228861.411647.1599
112.9985-0.1753-0.77240.2645-0.52583.1982-0.1968-0.55550.01980.10170.07810.01080.04840.53810.11870.07930.07130.02570.41940.0750.12291.829359.321464.9313
121.9409-0.105-0.46931.3919-0.25771.973-0.0104-0.1440.0526-0.0334-0.0927-0.03970.10690.26260.10310.04160.02170.01070.29420.13340.1245-19.494554.642482.0508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 103
2X-RAY DIFFRACTION2B17 - 112
3X-RAY DIFFRACTION3C62 - 202
4X-RAY DIFFRACTION4D1 - 102
5X-RAY DIFFRACTION5E17 - 112
6X-RAY DIFFRACTION6F63 - 204
7X-RAY DIFFRACTION7G1 - 103
8X-RAY DIFFRACTION8H17 - 112
9X-RAY DIFFRACTION9I62 - 204
10X-RAY DIFFRACTION10J1 - 103
11X-RAY DIFFRACTION11K16 - 112
12X-RAY DIFFRACTION12L62 - 204

+
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