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- PDB-6gmn: pVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-car... -

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Basic information

Entry
Database: PDB / ID: 6gmn
TitlepVHL:EloB:EloC in complex with methyl 4H-furo[3,2-b]pyrrole-5-carboxylate
Components
  • (Elongin-B) x 2
  • (von Hippel-Lindau disease tumor ...) x 2
  • Elongin-C
KeywordsONCOPROTEIN / E3 ubiquitin ligase / tumor supressor / PROTAC / fragment-based drug discovery
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / target-directed miRNA degradation / transcription elongation factor activity / VCB complex / elongin complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / intracellular membraneless organelle / Cul2-RING ubiquitin ligase complex / 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 / Tat-mediated elongation of the HIV-1 transcript / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV-1 elongation complex containing HIV-1 Tat / negative regulation of signal transduction / 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 / protein serine/threonine kinase binding / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / 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 / cell morphogenesis / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / 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 / Replication of the SARS-CoV-2 genome / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / cellular response to hypoxia / molecular adaptor activity / 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 / negative regulation of transcription by RNA polymerase II / 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-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 / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / 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
ACETATE ION / methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsVan Molle, I. / Lucas, X. / Ciulli, A.
Funding support United Kingdom, 5items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460
European CommissionH2020-MSCA-IF-2015-806323
European CommissionEC PIEF-GA-2010-275683
Welcome Trust 100476/Z/12/Z United Kingdom
Welcome Trust 094090/Z/10/Z United Kingdom
CitationJournal: J. Med. Chem. / Year: 2018
Title: Surface Probing by Fragment-Based Screening and Computational Methods Identifies Ligandable Pockets on the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase.
Authors: Lucas, X. / Van Molle, I. / Ciulli, A.
History
DepositionMay 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,36719
Polymers166,74112
Non-polymers6267
Water15,115839
1
A: Elongin-B
B: Elongin-C
C: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9176
Polymers41,6333
Non-polymers2833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-39 kcal/mol
Surface area15750 Å2
MethodPISA
2
D: Elongin-B
E: Elongin-C
F: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7964
Polymers41,7373
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-36 kcal/mol
Surface area15920 Å2
MethodPISA
3
G: Elongin-B
H: Elongin-C
I: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6924
Polymers41,6333
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-39 kcal/mol
Surface area16400 Å2
MethodPISA
4
J: Elongin-B
K: Elongin-C
L: von Hippel-Lindau disease tumor suppressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9615
Polymers41,7373
Non-polymers2242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-37 kcal/mol
Surface area16210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.710, 93.710, 364.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
43

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'C' and (resid 63 or (resid 64 and (name...C1 - 58
121(chain 'C' and (resid 63 or (resid 64 and (name...C60 - 80
131(chain 'C' and (resid 63 or (resid 64 and (name...C83 - 87
141(chain 'C' and (resid 63 or (resid 64 and (name...C90 - 98
151(chain 'C' and (resid 63 or (resid 64 and (name...C101
211(chain 'F' and (resid 63 through 76 or resid 78...F1 - 58
221(chain 'F' and (resid 63 through 76 or resid 78...F60 - 80
231(chain 'F' and (resid 63 through 76 or resid 78...F83 - 87
241(chain 'F' and (resid 63 through 76 or resid 78...F90 - 98
251(chain 'F' and (resid 63 through 76 or resid 78...F101
311(chain 'I' and (resid 63 or (resid 64 and (name...I1 - 58
321(chain 'I' and (resid 63 or (resid 64 and (name...I60 - 80
331(chain 'I' and (resid 63 or (resid 64 and (name...I83 - 87
341(chain 'I' and (resid 63 or (resid 64 and (name...I90 - 98
351(chain 'I' and (resid 63 or (resid 64 and (name...I101
411(chain 'L' and (resid 63 or (resid 64 and (name...L1 - 58
421(chain 'L' and (resid 63 or (resid 64 and (name...L60 - 80
431(chain 'L' and (resid 63 or (resid 64 and (name...L83 - 87
441(chain 'L' and (resid 63 or (resid 64 and (name...L90 - 98
451(chain 'L' and (resid 63 or (resid 64 and (name...L101
112(chain 'B' and (resid 17 through 46 or resid 58...B17 - 45
122(chain 'B' and (resid 17 through 46 or resid 58...B58 - 80
132(chain 'B' and (resid 17 through 46 or resid 58...B83 - 112
212(chain 'E' and (resid 17 through 33 or (resid 34...E17 - 45
222(chain 'E' and (resid 17 through 33 or (resid 34...E58 - 80
232(chain 'E' and (resid 17 through 33 or (resid 34...E83 - 112
312(chain 'H' and (resid 17 through 33 or (resid 34...H17 - 45
322(chain 'H' and (resid 17 through 33 or (resid 34...H58 - 80
332(chain 'H' and (resid 17 through 33 or (resid 34...H83 - 112
412(chain 'K' and (resid 17 through 33 or (resid 34...K17 - 45
422(chain 'K' and (resid 17 through 33 or (resid 34...K58 - 80
432(chain 'K' and (resid 17 through 33 or (resid 34...K83 - 112
113(chain 'A' and (resid 1 through 35 or (resid 36...A63 - 75
123(chain 'A' and (resid 1 through 35 or (resid 36...A78 - 107
133(chain 'A' and (resid 1 through 35 or (resid 36...A109 - 118
143(chain 'A' and (resid 1 through 35 or (resid 36...A121 - 140
153(chain 'A' and (resid 1 through 35 or (resid 36...A146 - 189
163(chain 'A' and (resid 1 through 35 or (resid 36...A192 - 200
213(chain 'D' and (resid 1 through 35 or (resid 36...D63 - 75
223(chain 'D' and (resid 1 through 35 or (resid 36...D78 - 107
233(chain 'D' and (resid 1 through 35 or (resid 36...D109 - 118
243(chain 'D' and (resid 1 through 35 or (resid 36...D121 - 140
253(chain 'D' and (resid 1 through 35 or (resid 36...D146 - 189
263(chain 'D' and (resid 1 through 35 or (resid 36...D192 - 200
313(chain 'G' and ((resid 1 and (name N or name...G63 - 75
323(chain 'G' and ((resid 1 and (name N or name...G78 - 107
333(chain 'G' and ((resid 1 and (name N or name...G109 - 118
343(chain 'G' and ((resid 1 and (name N or name...G121 - 140
353(chain 'G' and ((resid 1 and (name N or name...G146 - 189
363(chain 'G' and ((resid 1 and (name N or name...G192 - 200
413(chain 'J' and ((resid 1 and (name N or name...J63 - 75
423(chain 'J' and ((resid 1 and (name N or name...J78 - 107
433(chain 'J' and ((resid 1 and (name N or name...J109 - 118
443(chain 'J' and ((resid 1 and (name N or name...J121 - 140
453(chain 'J' and ((resid 1 and (name N or name...J146 - 189
463(chain 'J' and ((resid 1 and (name N or name...J192 - 200

NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 8 molecules ABEHKDGJ

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


Mass: 11852.390 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#2: Protein
Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: additional M at N-terminus due to cloning / Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11956.372 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370

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Von Hippel-Lindau disease tumor ... , 2 types, 4 molecules CFLI

#3: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18806.273 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#5: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18702.291 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: S-(DIMETHYLARSENIC)CYSTEINE modification / Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337

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Non-polymers , 3 types, 846 molecules

#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-F4E / methyl 4~{H}-furo[3,2-b]pyrrole-5-carboxylate


Mass: 165.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 839 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Na cacodylate pH 6.0, 0.2 M Mg acetate, 15% PEG3350, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 226893 / % possible obs: 99.4 % / Redundancy: 7 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.077 / Net I/σ(I): 13.75
Reflection shellResolution: 1.94→2.06 Å / Redundancy: 7 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 36190 / CC1/2: 0.902 / Rrim(I) all: 0.798 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
BUSTER-TNTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.94→46.47 Å / SU ML: 0.2323 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.6969 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2439 6006 5.02 %
Rwork0.2027 113595 -
obs0.2048 119601 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.21 Å2
Refinement stepCycle: LAST / Resolution: 1.94→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10504 0 44 839 11387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009310841
X-RAY DIFFRACTIONf_angle_d1.155514729
X-RAY DIFFRACTIONf_chiral_restr0.06491684
X-RAY DIFFRACTIONf_plane_restr0.00831904
X-RAY DIFFRACTIONf_dihedral_angle_d10.74327315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.970.31011850.27593581X-RAY DIFFRACTION95.1
1.97-1.990.2831870.25933714X-RAY DIFFRACTION98.58
1.99-2.010.28452060.25333699X-RAY DIFFRACTION98.64
2.01-2.040.28921890.23713733X-RAY DIFFRACTION98.79
2.04-2.070.27132060.23023657X-RAY DIFFRACTION98.8
2.07-2.090.25851920.23293740X-RAY DIFFRACTION98.92
2.09-2.120.26652090.2193707X-RAY DIFFRACTION98.91
2.12-2.160.2541920.22413713X-RAY DIFFRACTION99.04
2.16-2.190.25571820.21643751X-RAY DIFFRACTION98.87
2.19-2.230.2372120.21243741X-RAY DIFFRACTION99.1
2.23-2.260.26742090.21533691X-RAY DIFFRACTION99.09
2.26-2.310.28561920.20873762X-RAY DIFFRACTION99.17
2.31-2.350.25841730.20773796X-RAY DIFFRACTION99.18
2.35-2.40.26441960.21833749X-RAY DIFFRACTION99.27
2.4-2.450.2662080.21333757X-RAY DIFFRACTION99.37
2.45-2.510.24771900.21933756X-RAY DIFFRACTION99.35
2.51-2.570.28791800.22753764X-RAY DIFFRACTION99.27
2.57-2.640.28141910.2293798X-RAY DIFFRACTION99.55
2.64-2.720.26061910.22443806X-RAY DIFFRACTION99.45
2.72-2.80.27892140.23043760X-RAY DIFFRACTION99.55
2.8-2.90.30462340.23853782X-RAY DIFFRACTION99.55
2.9-3.020.3112070.22073823X-RAY DIFFRACTION99.63
3.02-3.160.25232010.21353808X-RAY DIFFRACTION99.68
3.16-3.320.25212070.20883825X-RAY DIFFRACTION99.83
3.32-3.530.26272020.20493837X-RAY DIFFRACTION99.78
3.53-3.80.22982020.1933879X-RAY DIFFRACTION99.9
3.8-4.190.19372150.16553881X-RAY DIFFRACTION99.88
4.19-4.790.19762200.1533907X-RAY DIFFRACTION99.93
4.79-6.040.21422000.18463993X-RAY DIFFRACTION99.86
6.04-46.490.22242140.20864185X-RAY DIFFRACTION98.68
Refinement TLS params.Method: refined / Origin x: 11.7633091726 Å / Origin y: 29.7986885431 Å / Origin z: 24.2286485321 Å
111213212223313233
T0.475046264842 Å2-0.00138228913604 Å20.068489329445 Å2-0.249600369202 Å20.00364935982214 Å2--0.261715835551 Å2
L0.0511821826919 °20.00722425445689 °20.0551502396389 °2-0.0700837062555 °2-0.00865946599993 °2---0.0795382623171 °2
S0.0170418176691 Å °-0.0104047081863 Å °-0.0170029147508 Å °-0.0258839126563 Å °-0.0210487483316 Å °-0.00610919012667 Å °0.0150425571942 Å °0.00938252618232 Å °0.00356263288507 Å °
Refinement TLS groupSelection details: all

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