[English] 日本語
Yorodumi
- PDB-4bkt: von Hippel Lindau protein:ElonginB:ElonginC complex, in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bkt
Titlevon Hippel Lindau protein:ElonginB:ElonginC complex, in complex with (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide
Components
  • (TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ...) x 2
  • VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
KeywordsPROTEIN TRANSPORT / LIGASE / 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 / 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 initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / cell morphogenesis / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / protein-macromolecule adaptor activity / Replication of the SARS-CoV-2 genome / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor binding / 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 / 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 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
ARGININE / GLUTAMIC ACID / Chem-QD0 / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.35 Å
AuthorsVan Molle, I. / Dias, D.M. / Baud, M. / Galdeano, C. / Geraldes, C.F.G.C. / Ciulli, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2014
Title: Is NMR Fragment Screening Fine-Tuned to Assess Druggability of Protein-Protein Interactions?
Authors: Dias, D.M. / Van Molle, I. / Baud, M.G.J. / Galdeano, C. / Geraldes, C.F.G.C. / Ciulli, A.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
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)167,92518
Polymers166,53312
Non-polymers1,3916
Water7,728429
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)41,9014
Polymers41,6333
Non-polymers2671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-40.3 kcal/mol
Surface area16020 Å2
MethodPISA
2
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)42,0765
Polymers41,6333
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-39.4 kcal/mol
Surface area16360 Å2
MethodPISA
3
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)41,9014
Polymers41,6333
Non-polymers2671
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-38.2 kcal/mol
Surface area16190 Å2
MethodPISA
4
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)42,0485
Polymers41,6333
Non-polymers4142
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-34 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.180, 93.180, 364.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

-
TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE ... , 2 types, 8 molecules ADGJBEHK

#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: 11852.389 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-104
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / 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 / ...ELONGIN 15 KDA SUBUNIT / ELONGIN-C / ELOC / RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C / SIII P15 / ELONGINC


Mass: 10974.616 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15369

-
Protein , 1 types, 4 molecules CFIL

#3: Protein
VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR / PROTEIN G7 / PVHL


Mass: 18806.273 Da / Num. of mol.: 4 / Fragment: RESIDUES 54-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40337

-
Non-polymers , 4 types, 435 molecules

#4: Chemical
ChemComp-QD0 / (2S,4R)-N-methyl-1-[2-(3-methyl-1,2-oxazol-5-yl)ethanoyl]-4-oxidanyl-pyrrolidine-2-carboxamide


Mass: 267.281 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N3O4
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsGS LEFT AFTER TAG REMOVAL 2 MET AT N_TERMINUS FROM CLONING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.55 % / Description: NONE
Crystal growDetails: 0.1M NA CACODYLATE PH 6.0, 0.2 M MG ACETATE, 15% PEG3350, 5 MM DTT

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 68245 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 12.9 % / Biso Wilson estimate: 49.73 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 14.6
Reflection shellResolution: 2.35→2.45 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 15.87 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
BUSTERTNTphasing
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.35→46.59 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9268 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.312 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.214
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10903. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=64. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CAS. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10903. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=64. NUMBER TREATED BY BAD NON-BONDED CONTACTS=8.
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 3454 5.06 %RANDOM
Rwork0.1902 ---
obs0.192 68204 99.98 %-
Displacement parametersBiso mean: 54.19 Å2
Baniso -1Baniso -2Baniso -3
1--5.5367 Å20 Å20 Å2
2---5.5367 Å20 Å2
3---11.0733 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10457 0 86 429 10972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110788HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1914677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3643SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes245HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1555HARMONIC5
X-RAY DIFFRACTIONt_it10788HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion19.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1423SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11916SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2583 242 4.91 %
Rwork0.2193 4682 -
all0.2212 4924 -
obs--99.98 %
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)
14.0001-1.4693-1.87552.03911.24983.7142-0.1161-0.3247-0.19780.14050.03530.06590.26280.17250.0808-0.0455-0.0120.0453-0.09230.0355-0.1441-17.47782.097443.3091
21.57860.3491-1.52513.24340.0253.04890.02130.1025-0.1827-0.3259-0.07370.08430.01140.01330.05240.0270.01160.0135-0.1124-0.011-0.1332-14.4101-1.930526.0637
31.0291-0.71290.51194.7829-2.76563.4226-0.05870.08220.0251-0.08590.04650.11930.1533-0.07630.01220.0122-0.05380.1173-0.1301-0.0328-0.1738-7.654818.93248.9251
42.9494-1.1699-1.51272.52032.52135.3228-0.0501-0.3569-0.03080.4322-0.00060.22091.0498-0.30430.05070.1421-0.11360.0204-0.07030.0309-0.297128.9876-1.882444.0898
50.9060.6669-0.98142.74061.01314.92320.05090.0520.02430.26710.0150.02510.5581-0.2601-0.06590.1407-0.0536-0.0231-0.1299-0.007-0.198132.6555-5.918426.1473
61.4893-1.03580.71854.6444-1.7462.39190.05320.1147-0.0219-0.2979-0.0233-0.12350.158-0.0408-0.03-0.0106-0.02940.0873-0.1217-0.0406-0.179339.199113.86038.8474
71.835-1.0387-1.12793.28840.50964.1003-0.0698-0.05360.02810.4437-0.03670.3530.1394-0.26570.10650.066-0.02890.0705-0.10210.0472-0.214933.746443.420443.8003
81.31591.121-0.4813.4586-0.06673.42770.01270.1045-0.0405-0.2893-0.03860.25520.2183-0.44610.02590.1036-0.0235-0.0032-0.11210.0414-0.20235.372539.876225.8921
91.6749-1.03350.72673.4311-1.57842.5971-0.02810.053-0.0206-0.3659-0.14260.02340.27220.03270.17070.1615-0.00570.0407-0.1701-0.0113-0.241239.541360.97048.3878
102.7941-0.7921-0.80362.0843-0.12822.7005-0.0516-0.21450.04370.11990.0289-0.0080.1237-0.01230.0227-0.0517-0.03640.0399-0.0502-0.0063-0.1611-13.805247.386443.3612
111.2720.7483-0.61392.9189-0.32673.30270.00650.0870.0258-0.3879-0.05390.06050.3476-0.18020.04740.0777-0.0180.0391-0.08090.0085-0.1759-11.718444.50325.6255
121.8162-0.7640.32533.5833-1.26012.6749-0.02390.0098-0.0132-0.402-0.12510.03790.2440.02890.1490.0654-0.00860.1059-0.1567-0.0199-0.2022-7.219565.16158.1828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

+
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://pdbjlc1.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