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

+
Open data


ID or keywords:

Loading...

-
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 / 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 / target-directed miRNA degradation / transcription elongation factor activity / elongin complex / VCB complex / Replication of the SARS-CoV-1 genome / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless 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 / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / 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 / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / Replication of the SARS-CoV-2 genome / protein-macromolecule adaptor activity / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / amyloid fibril formation / molecular adaptor activity / protein stabilization / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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