[English] 日本語
Yorodumi
- PDB-4w9j: 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: 4w9j
TitlepVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-((S)-2-acetamido-4-methylpentanamido)-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 13)
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 / VCB complex / Replication of the SARS-CoV-1 genome / 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 / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular non-membrane-bounded organelle / SUMOylation of ubiquitinylation proteins / negative regulation of transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / ubiquitin-like ligase-substrate adaptor activity / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / negative regulation of signal transduction / 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 / transcription corepressor binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / protein-macromolecule adaptor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / regulation of gene expression / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / DNA-binding transcription factor binding / amyloid fibril formation / protein stabilization / molecular adaptor activity / protein ubiquitination / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / endoplasmic reticulum / 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 B / Elongin-C / 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 / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3JH / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

-
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)169,29216
Polymers166,94912
Non-polymers2,3434
Water8,287460
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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-39 kcal/mol
Surface area16130 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-40 kcal/mol
Surface area16160 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-38 kcal/mol
Surface area16410 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)42,3234
Polymers41,7373
Non-polymers5861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-38 kcal/mol
Surface area16260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.708, 93.708, 360.836
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

21A-217-

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-3JH / N-acetyl-L-leucyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 585.758 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H43N5O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.15 %
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: 0.986→93.708 Å / Num. all: 80705 / Num. obs: 80705 / % possible obs: 97.4 % / Redundancy: 6.8 % / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/av σ(I): 8.971 / Net I/σ(I): 15.4 / Num. measured all: 546027
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.3240.4931.640833101620.3150.4932.386.2
2.32-2.465.30.384256805108000.20.3843.696.1
2.46-2.637.50.2962.679778105980.1220.2966100
2.63-2.847.70.1864.17707299550.0750.1869.5100
2.84-3.117.70.1096.97050991670.0450.10915.2100
3.11-3.487.50.07110.46294983480.030.07122.499.9
3.48-4.027.40.05113.15507373990.0220.05129.699.9
4.02-4.927.40.04154664663300.0170.0435.699.8
4.92-6.967.30.039153669250030.0170.03930.399.9
6.96-46.8546.70.02518.11967029430.0120.02535.499.1

-
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: 2.2→93.708 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.2463 / WRfactor Rwork: 0.2054 / FOM work R set: 0.7974 / SU B: 13.28 / SU ML: 0.174 / SU R Cruickshank DPI: 0.2894 / SU Rfree: 0.2283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 4079 5.1 %RANDOM
Rwork0.2167 76517 --
obs0.2191 76517 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.97 Å2 / Biso mean: 41.7 Å2 / Biso min: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2--0.25 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 2.2→93.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 164 460 11148
Biso mean--33.74 37.42 -
Num. residues----1331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910933
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210466
X-RAY DIFFRACTIONr_angle_refined_deg1.2722.00114874
X-RAY DIFFRACTIONr_angle_other_deg0.8023.00524045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.10751313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61823.326475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.344151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3571585
X-RAY DIFFRACTIONr_chiral_restr0.0670.21705
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022427
X-RAY DIFFRACTIONr_mcbond_it1.5661.3785318
X-RAY DIFFRACTIONr_mcbond_other1.5661.3795318
X-RAY DIFFRACTIONr_mcangle_it2.6173.0836609
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1573MEDIUM POSITIONAL0.310.5
12D1573MEDIUM POSITIONAL0.250.5
13G1573MEDIUM POSITIONAL0.30.5
14J1573MEDIUM POSITIONAL0.310.5
11A1573MEDIUM THERMAL4.162
12D1573MEDIUM THERMAL3.432
13G1573MEDIUM THERMAL4.432
14J1573MEDIUM THERMAL3.182
21B1324MEDIUM POSITIONAL0.380.5
22E1324MEDIUM POSITIONAL0.420.5
23H1324MEDIUM POSITIONAL0.360.5
24K1324MEDIUM POSITIONAL0.350.5
21B1324MEDIUM THERMAL3.922
22E1324MEDIUM THERMAL4.222
23H1324MEDIUM THERMAL5.32
24K1324MEDIUM THERMAL4.042
31C1690MEDIUM POSITIONAL0.340.5
32F1690MEDIUM POSITIONAL0.40.5
33I1690MEDIUM POSITIONAL0.390.5
34L1690MEDIUM POSITIONAL0.440.5
31C1690MEDIUM THERMAL4.232
32F1690MEDIUM THERMAL4.092
33I1690MEDIUM THERMAL4.952
34L1690MEDIUM THERMAL4.632
41C245MEDIUM POSITIONAL0.380.5
42F245MEDIUM POSITIONAL0.370.5
43I245MEDIUM POSITIONAL0.330.5
41C245MEDIUM THERMAL8.672
42F245MEDIUM THERMAL6.592
43I245MEDIUM THERMAL14.872
51C228MEDIUM POSITIONAL0.630.5
52F228MEDIUM POSITIONAL0.370.5
53I228MEDIUM POSITIONAL0.370.5
54L228MEDIUM POSITIONAL0.440.5
51C228MEDIUM THERMAL4.412
52F228MEDIUM THERMAL7.22
53I228MEDIUM THERMAL4.332
54L228MEDIUM THERMAL5.862
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 258 -
Rwork0.275 4723 -
all-4981 -
obs--82.48 %
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)
11.9787-0.90380.6542.5582-0.9772.6882-0.03010.2118-0.0169-0.1769-0.0958-0.13760.01010.17590.1260.07290.00180.01540.08080.01760.118444.168665.826846.865
23.3440.31190.16770.9632-0.48033.1625-0.0375-0.09760.0478-0.0007-0.0591-0.0207-0.1070.07980.09670.00880.01690.00470.07710.04330.113647.967661.604164.2741
34.3095-0.7106-1.82031.55650.20691.94780.0194-0.1320.09020.1034-0.0172-0.0472-0.03210.0193-0.00220.0107-0.0144-0.01720.11610.05380.091327.162554.619581.3052
43.2329-0.61181.80462.2461-1.0814.4466-0.10110.67270.2413-0.1705-0.1123-0.064-0.37740.87120.21340.2672-0.05510.03330.3340.05510.156747.809119.139546.8082
53.84360.34570.86630.2613-0.75124.5046-0.0690.27450.1501-0.0193-0.0957-0.1013-0.26650.47520.16470.12050.00850.03220.20280.04520.153752.725614.754464.334
63.0616-0.8919-0.62792.02390.48731.5742-0.0292-0.08080.03090.0748-0.0641-0.007-0.028-0.18980.09330.0216-0.0195-0.03860.16320.01380.136332.11377.631680.9085
73.9505-1.44040.08922.1821-0.99423.92060.00040.36690.201-0.2947-0.0264-0.0407-0.11170.03310.0260.2258-0.03220.04230.42230.03490.24722.593113.57746.8446
84.4426-0.8701-1.49031.3302-0.50011.9899-0.0956-0.40980.20240.02730.0607-0.1354-0.17880.29170.03490.15650.01850.02310.5406-0.05330.23546.398411.786464.5382
92.6958-0.4035-0.7091.94430.1043.8283-0.0017-0.0745-0.13240.104-0.0253-0.19970.26280.66140.0270.03290.02680.00580.19320.03650.203-15.27637.625281.7076
103.1446-0.6229-0.67752.1032-0.42122.9821-0.01920.23760.1195-0.1484-0.00610.034-0.07720.18210.02530.0633-0.0097-0.00010.14790.0640.1287-1.495261.663246.9922
113.5734-0.2864-0.6761.1175-0.32292.9826-0.123-0.35970.18150.08130.0897-0.0851-0.03140.46180.03330.06040.02660.01920.28080.02140.14321.492359.437864.7299
121.9911-0.4724-1.1691.6893-0.18593.4656-0.0636-0.19220.0112-0.018-0.0519-0.05880.19230.45840.11550.0120.0166-0.00340.12850.07180.1077-20.010954.518281.7865
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