[English] 日本語
Yorodumi
- PDB-8vlb: Crystal structure of EloBC-VHL-CDO1 complex bound to compound 4 m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vlb
TitleCrystal structure of EloBC-VHL-CDO1 complex bound to compound 4 molecular glue
Components
  • Cysteine dioxygenase type 1
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsAPOPTOSIS / VHL / CDO1 / VHL-small molecule-CDO1 ternary complex / degradation
Function / homology
Function and homology information


sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle ...sulfur amino acid biosynthetic process / Degradation of cysteine and homocysteine / taurine biosynthetic process / cysteine dioxygenase / cysteine dioxygenase activity / response to azide / L-cysteine catabolic process / cysteine metabolic process / 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 / response to glucagon / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / nickel cation binding / 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 / response to cAMP / response to amino acid / 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 / lactation / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / protein serine/threonine kinase binding / negative regulation of autophagy / response to glucocorticoid / 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 / ferrous iron binding / 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 / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / response to ethanol / protein-macromolecule adaptor activity / cellular response to hypoxia / DNA-binding transcription factor binding / molecular adaptor activity / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / inflammatory response / 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 / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / 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 ...Cysteine dioxygenase type I / Cysteine dioxygenase type I / 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 / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / RmlC-like cupin domain superfamily / SKP1/BTB/POZ domain superfamily / RmlC-like jelly roll fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-3JF / CITRIC ACID / : / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B / Cysteine dioxygenase type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsShu, W. / Ma, X. / Tutter, A. / Buckley, D. / Golosov, A. / Michaud, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Chem.Biol. / Year: 2025
Title: A small-molecule VHL molecular glue degrader for cysteine dioxygenase 1.
Authors: Tutter, A. / Buckley, D. / Golosov, A.A. / Ma, X. / Shu, W. / McKay, D.J.J. / Darsigny, V. / Dovala, D. / Beckwith, R. / Solomon, J. / Rao, P. / Xu, L. / Fazal, A. / Lingel, A. / Wartchow, C. ...Authors: Tutter, A. / Buckley, D. / Golosov, A.A. / Ma, X. / Shu, W. / McKay, D.J.J. / Darsigny, V. / Dovala, D. / Beckwith, R. / Solomon, J. / Rao, P. / Xu, L. / Fazal, A. / Lingel, A. / Wartchow, C. / Cobb, J.S. / Hachey, A. / Tullai, J. / Michaud, G.A.
History
DepositionJan 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 5, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: von Hippel-Lindau disease tumor suppressor
B: Elongin-B
C: Elongin-C
D: Cysteine dioxygenase type 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4857
Polymers65,7644
Non-polymers7213
Water905
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.440, 178.116, 104.166
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 4 types, 4 molecules ABCD

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


Mass: 18712.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#2: 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: 13147.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#3: 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: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#4: Protein Cysteine dioxygenase type 1 / Cysteine dioxygenase type I / CDO / CDO-I


Mass: 23060.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16878, cysteine dioxygenase

-
Non-polymers , 4 types, 8 molecules

#5: Chemical ChemComp-3JF / N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-[4-(4-methyl-1,3-thiazol-5-yl)benzyl]-L-prolinamide


Mass: 472.600 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N4O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.11 Å3/Da / Density % sol: 70.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2M SODIUM CITRATE, 0.1M BIS-TRIS-PROPANE PH 6.5, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→97.46 Å / Num. obs: 23239 / % possible obs: 95.3 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Net I/σ(I): 8.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.397 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3885 / CC1/2: 0.411 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→58.22 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2581 1181 5.09 %
Rwork0.208 --
obs0.2105 23190 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→58.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 47 5 4348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054455
X-RAY DIFFRACTIONf_angle_d0.8336043
X-RAY DIFFRACTIONf_dihedral_angle_d9.1223017
X-RAY DIFFRACTIONf_chiral_restr0.049660
X-RAY DIFFRACTIONf_plane_restr0.005805
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.0320.42561530.3822811X-RAY DIFFRACTION100
3.032-3.19190.36641560.32842842X-RAY DIFFRACTION100
3.1919-3.39180.30811640.28272859X-RAY DIFFRACTION100
3.3918-3.65370.33241330.24842258X-RAY DIFFRACTION82
3.6537-4.02130.26581330.2052396X-RAY DIFFRACTION87
4.0213-4.60290.19891390.16712889X-RAY DIFFRACTION100
4.6029-5.79840.21321520.17262923X-RAY DIFFRACTION100
5.7984-58.220.24391510.18683031X-RAY DIFFRACTION100
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)
10.12560.1552-0.05980.046-0.09350.07520.5259-0.5831.06270.51350.17150.5338-0.7702-0.3883-0.00410.88240.03780.1520.688-0.07260.976669.217256.179616.5856
20.49540.10170.23790.0634-0.14540.71470.0071-0.1306-0.4506-0.18270.2853-1.4415-0.12450.54310.020.6096-0.1796-0.02630.4589-0.08630.635665.254138.992225.5405
31.38570.0639-0.09610.2049-0.4051.62440.133-0.0117-0.0649-0.09430.1554-0.1756-0.08560.2958-0.00080.5577-0.03680.03890.4741-0.00180.557470.368241.297517.6766
40.29660.5982-0.02661.1069-0.86660.9913-0.15620.2762-0.19190.60980.40550.50810.4372-0.09760.0030.65520.13610.01060.6769-0.0730.571762.638140.88615.8969
50.0034-0.69610.78290.3475-0.42470.6220.3322-0.166-0.2346-0.2978-0.38740.1543-0.7028-0.4622-0.00230.6611-0.0521-0.02070.4896-0.10380.645260.163433.458613.1209
60.2070.12190.06250.37730.22930.1503-0.05740.0936-0.1163-0.01640.2507-1.0284-0.4442-0.010.00140.88240.06520.05081.0747-0.12170.784867.544426.1818-7.2191
70.48980.05710.58950.0846-0.160.88670.0581-0.08890.155-0.8790.36670.8093-0.12571.7004-0.00221.0358-0.0010.05060.79960.19780.738961.082548.02183.7383
80.826-0.32360.18360.7898-0.34760.17640.0296-0.459-0.03720.2142-0.42540.5760.3947-0.39210.00030.7719-0.11060.10290.7584-0.20790.865836.674212.752213.0816
90.4256-0.1384-0.26770.34610.39230.3740.259-0.0434-0.60130.9076-0.25370.80650.5927-0.66440.00481.1363-0.12450.15330.87690.03321.036934.78994.152316.9844
100.50560.0897-0.52390.5825-0.46920.46790.0839-0.45-0.47290.6028-0.2103-0.30730.3267-0.2058-0.00040.8441-0.14020.04240.5616-0.04480.921739.33376.09612.1041
110.09360.3583-0.13150.16880.3288-0.25530.10010.5123-0.665-0.4276-0.0554-0.33790.78820.3519-0.00140.75330.12790.06940.8506-0.06071.081959.01579.1648-2.4911
120.18550.1567-0.00590.2365-0.28650.25150.17860.4067-0.54560.2391-0.78130.95410.2364-0.5074-0.00110.8334-0.0685-0.03020.7419-0.09770.840139.122115.779-1.7715
130.04870.2807-0.09010.3203-0.17560.35210.09850.11630.11930.11270.06110.85320.0244-0.5294-0.00090.67350.0807-0.1030.5677-0.1370.708739.699425.5990.0378
140.13270.2783-0.16440.5726-0.18390.43610.5090.6893-0.0888-0.8965-0.32610.48440.0172-0.6632-0.00520.73480.1271-0.09990.9553-0.08350.915835.341121.8366-7.603
150.98190.3707-0.2662-0.04270.02140.5591-0.337-0.11580.00460.02820.26150.1719-0.08060.21220.00010.69360.0818-0.05860.5155-0.10550.722350.917623.44089.0364
160.1050.0592-0.0473-0.0086-0.11740.2658-0.32431.5002-0.20810.0644-0.372-0.2858-0.6302-0.46420.00160.68590.133-0.02510.7575-0.08840.724755.077621.5245-3.8575
17-0.01490.12740.08310.20250.07750.27810.040.70550.26-0.43960.17650.5177-0.08170.38670.00010.8696-0.13720.03280.5976-0.02760.632494.673563.119315.7359
180.0319-0.04870.06760.0775-0.17590.19340.45450.34230.4960.6253-0.44880.194-0.54190.2198-0.00271.0874-0.360.07140.9401-0.11180.8823101.56161.506423.4499
191.04870.15590.41420.1406-0.06950.24340.50630.1676-0.16380.1878-0.20810.8687-0.2120.40090.00320.7431-0.13450.01030.7417-0.05040.86283.00448.296919.6103
200.2512-0.14870.0190.1675-0.11760.01950.5532-0.0898-0.0428-0.1039-0.0120.0245-0.18170.64730.00140.5657-0.14540.08760.9904-0.0370.609894.030748.003216.487
210.14320.0650.0063-0.11640.24520.34650.57870.6337-0.72740.17740.1885-0.79040.37540.6686-0.00160.71060.056-0.05971.4831-0.01771.334795.988841.461128.3139
220.17990.0424-0.07920.13480.42610.43440.1809-1.913-0.33240.449-0.0440.2079-0.61220.15470.00370.7497-0.0602-0.02551.3775-0.08160.753492.817449.981330.2774
230.54590.0578-0.0041.42080.52260.1426-0.93351.98890.1302-0.5382-0.8335-0.56540.0865-0.29770.06280.89170.0454-0.36621.57880.24041.2202106.757135.649940.3963
240.45820.36910.29610.21270.18990.1553-0.1318-1.47440.16031.43740.71810.3799-1.38020.57780.08421.259-0.15960.03541.22040.09290.687893.425652.391834.7693
251.3581-0.8397-0.69971.98740.42640.65890.2132-0.8646-0.35250.461-0.0709-0.38770.1840.10560.53440.8165-0.1573-0.14751.2194-0.01210.73196.893741.590928.9425
260.80970.34050.04250.609-0.16520.3128-1.15991.0568-0.1135-1.04190.60280.07541.2205-0.2153-0.01771.0526-0.18560.09081.1633-0.18930.867289.448740.174512.5864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 141 )
5X-RAY DIFFRACTION5chain 'A' and (resid 142 through 167 )
6X-RAY DIFFRACTION6chain 'A' and (resid 168 through 193 )
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 208 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 35 )
9X-RAY DIFFRACTION9chain 'B' and (resid 36 through 60 )
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 89 )
11X-RAY DIFFRACTION11chain 'B' and (resid 90 through 104 )
12X-RAY DIFFRACTION12chain 'C' and (resid 17 through 27 )
13X-RAY DIFFRACTION13chain 'C' and (resid 28 through 47 )
14X-RAY DIFFRACTION14chain 'C' and (resid 48 through 66 )
15X-RAY DIFFRACTION15chain 'C' and (resid 67 through 96 )
16X-RAY DIFFRACTION16chain 'C' and (resid 97 through 112 )
17X-RAY DIFFRACTION17chain 'D' and (resid 6 through 24 )
18X-RAY DIFFRACTION18chain 'D' and (resid 25 through 39 )
19X-RAY DIFFRACTION19chain 'D' and (resid 40 through 58 )
20X-RAY DIFFRACTION20chain 'D' and (resid 59 through 77 )
21X-RAY DIFFRACTION21chain 'D' and (resid 78 through 91 )
22X-RAY DIFFRACTION22chain 'D' and (resid 92 through 107 )
23X-RAY DIFFRACTION23chain 'D' and (resid 108 through 118 )
24X-RAY DIFFRACTION24chain 'D' and (resid 119 through 133 )
25X-RAY DIFFRACTION25chain 'D' and (resid 134 through 178 )
26X-RAY DIFFRACTION26chain 'D' and (resid 179 through 190 )

+
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