[English] 日本語
Yorodumi
- PDB-2o25: Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conj... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2o25
TitleUbiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9
Components
  • SUMO-1-conjugating enzyme UBC9
  • Ubiquitin-conjugating enzyme E2-25 kDa
KeywordsLIGASE / Ubl conjugation pathway / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / free ubiquitin chain polymerization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / regulation of proteasomal ubiquitin-dependent protein catabolic process / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex ...positive regulation of SUMO transferase activity / SUMO conjugating enzyme activity / RING-like zinc finger domain binding / SUMO ligase complex / free ubiquitin chain polymerization / SUMOylation of nuclear envelope proteins / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / regulation of proteasomal ubiquitin-dependent protein catabolic process / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / transferase complex / mitotic nuclear membrane reassembly / filopodium tip / Vitamin D (calciferol) metabolism / synaptonemal complex / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / SUMOylation of SUMOylation proteins / positive regulation of tumor necrosis factor-mediated signaling pathway / Maturation of nucleoprotein / positive regulation of type I interferon-mediated signaling pathway / Transferases; Acyltransferases; Aminoacyltransferases / SUMOylation of RNA binding proteins / nuclear export / SUMO transferase activity / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / ubiquitin-ubiquitin ligase activity / E2 ubiquitin-conjugating enzyme / SUMOylation of ubiquitinylation proteins / ubiquitin conjugating enzyme activity / SUMOylation of DNA replication proteins / transcription factor binding / SUMOylation of transcription factors / protein sumoylation / cellular response to interferon-beta / protein K48-linked ubiquitination / SUMOylation of DNA damage response and repair proteins / nuclear pore / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Meiotic synapsis / SUMOylation of chromatin organization proteins / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / SUMOylation of transcription cofactors / positive regulation of peptidyl-threonine phosphorylation / transcription coregulator binding / chromosome segregation / Negative regulators of DDX58/IFIH1 signaling / SUMOylation of intracellular receptors / protein modification process / PKR-mediated signaling / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin-protein transferase activity / Antigen processing: Ubiquitination & Proteasome degradation / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / nuclear envelope / Processing of DNA double-strand break ends / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of cell migration / cell division / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site ...Vertebrate ubiquitin-conjugating enzyme E2 K, UBA domain / Ubiquitin-associated (UBA) domain / UBA/TS-N domain / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Helicase, Ruva Protein; domain 3 / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 K / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWalker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: A Novel and Unexpected Complex Between the SUMO-1-Conjugating Enzyme UBC9 and the Ubiquitin-Conjugating Enzyme E2-25 kDa
Authors: Walker, J.R. / Avvakumov, G.V. / Xue, S. / Newman, E.M. / Mackenzie, F. / Weigelt, J. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Dhe-Paganon, S.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2-25 kDa
B: Ubiquitin-conjugating enzyme E2-25 kDa
C: SUMO-1-conjugating enzyme UBC9
D: SUMO-1-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)81,4994
Polymers81,4994
Non-polymers00
Water70339
1
A: Ubiquitin-conjugating enzyme E2-25 kDa
D: SUMO-1-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)40,7502
Polymers40,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2-25 kDa
C: SUMO-1-conjugating enzyme UBC9


Theoretical massNumber of molelcules
Total (without water)40,7502
Polymers40,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.874, 68.498, 91.277
Angle α, β, γ (deg.)85.05, 80.85, 75.83
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Ubiquitin-conjugating enzyme E2-25 kDa / Ubiquitin-protein ligase / Ubiquitin carrier protein / E225K / Huntingtin-interacting protein 2 / HIP-2


Mass: 22574.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP2, LIG / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61086, ubiquitin-protein ligase
#2: Protein SUMO-1-conjugating enzyme UBC9 / SUMO-1-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin ...SUMO-1-protein ligase / Ubiquitin-conjugating enzyme E2 I / Ubiquitin-protein ligase I / Ubiquitin carrier protein I / Ubiquitin carrier protein 9 / p18


Mass: 18174.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2I, UBC9, UBCE9 / Plasmid: pET28-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P63279, ubiquitin-protein ligase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, ...Details: The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91841 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 7, 2006
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 27651 / Num. obs: 27651 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.051 / Net I/σ(I): 13.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.17 / Num. unique all: 1028 / Rsym value: 0.293 / % possible all: 70.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1YLA and 1A3S

1yla

1a3s


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 28.352 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.783 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29091 1398 5.1 %RANDOM
Rwork0.22775 ---
obs0.23105 26281 92.92 %-
all-27651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.036 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å20.79 Å21.94 Å2
2---2.91 Å2-1.17 Å2
3---4.42 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5628 0 0 39 5667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225792
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9717876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4375709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07424.708257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.218151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6151532
X-RAY DIFFRACTIONr_chiral_restr0.10.2861
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024410
X-RAY DIFFRACTIONr_nbd_refined0.2080.22570
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23917
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.25
X-RAY DIFFRACTIONr_mcbond_it0.41.53691
X-RAY DIFFRACTIONr_mcangle_it0.63625815
X-RAY DIFFRACTIONr_scbond_it1.06832438
X-RAY DIFFRACTIONr_scangle_it1.6934.52061
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 62 -
Rwork0.304 1352 -
obs--65.4 %
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)
110.00760.34891.30236.2029-0.16774.3253-0.0091-0.47860.56770.13280.01561.2579-0.4948-1.2335-0.00640.17850.05080.01460.3625-0.04570.473-18.91390.356312.2941
27.6106-3.73651.919914.56010.72176.2498-0.1831-0.09550.58450.2689-0.20170.3029-0.6657-0.08780.38480.0618-0.01-0.02850.1799-0.03410.1921-10.38520.45896.4906
39.3865-2.6427-0.1383.82060.12853.1464-0.10110.0456-0.2515-0.32010.02770.62710.1224-0.25830.07340.1493-0.0221-0.10120.1176-0.01590.2105-11.2066-8.3845-2.9601
43.26290.0299-2.56691.13890.8543.9932-0.14890.5311-0.9744-0.3597-0.02330.40750.5098-0.30860.17220.2490.0152-0.08250.2237-0.00590.4518-8.2594-16.1943-4.2951
59.7375-0.7461-1.349911.1613-2.14446.1648-0.76380.1199-0.3634-0.30850.6307-1.0262-0.04210.67860.13310.57640.00620.05390.4283-0.110.33619.5444-12.5188-15.9706
67.4483-5.4215-7.543526.3061-9.006725.1974-1.14012.6621-1.0077-2.45571.2741.03132.6105-1.1302-0.13381.053-0.2647-0.00830.7562-0.13080.42476.0767-14.1931-26.4423
76.411-0.5415-4.95811.76843.20844.4981-0.1576-1.7714-0.2392.10970.23370.1560.0949-3.2382-0.0761.7659-0.59150.57771.4326-0.15590.8903-31.9067-32.030651.2295
86.07511.30992.275414.8221-16.81821.45741.1729-1.053-0.25680.8499-0.45280.6181.1934-0.0342-0.72011.2804-0.17110.42030.6504-0.04390.4423-25.7198-32.512542.995
94.35011.3614-1.05818.61371.05349.0602-0.0153-1.3051-0.60152.3614-0.22780.1181.03990.40470.24311.1995-0.05110.13030.45190.0460.2268-17.7879-28.211443.1084
103.5691-1.025-2.26392.28341.898412.11950.2345-1.1570.37072.0978-0.43240.1349-0.00280.2420.19791.187-0.17330.00270.5346-0.17680.3716-16.1103-19.29343.1297
117.95863.09660.91715.79191.91496.1324-0.25410.42670.781-0.11270.27080.6139-0.6025-0.2733-0.01660.1217-0.01390.0370.0785-0.04120.191-19.5182-20.537824.3753
129.1091-6.1026-1.936613.08630.24796.0216-0.09280.0801-0.18720.16360.0109-0.55940.0870.21610.0818-0.0382-0.0030.04570.08360.04960.2069-7.4312-24.772518.3986
1316.063-0.70394.79125.01280.732513.3567-0.12680.15161.2919-0.2055-0.05130.0473-0.1287-0.19640.17820.06690.04960.13030.03570.06760.33854.5427-27.940110.1841
146.31020.8834-1.19854.00451.070210.6489-0.09621.30060.772-0.69770.17590.0527-1.7650.5161-0.07960.1559-0.03280.05470.13130.09510.284614.0044-30.61585.7743
156.8645-1.9832-0.12136.987-2.41380.93710.0148-0.22430.50870.05140.0533-0.4534-0.41940.0283-0.0681-0.0214-0.00920.03660.0497-0.03760.161817.6024-39.721213.2537
166.8439-4.6888-0.47485.98120.52851.18830.15280.2273-0.5164-0.26430.08810.3294-0.0536-0.086-0.2408-0.0459-0.0057-0.00970.05160.00720.12479.4993-46.59449.566
1711.1516-3.2340.68256.7333-2.48241.24480.0686-0.3779-0.52770.46320.00850.43090.2795-0.1024-0.07710.0213-0.0230.04970.11030.01810.03096.499-43.642918.0312
1810.50192.5198-0.67659.3203-0.19945.64330.2533-0.5682-0.73670.6622-0.22-0.8690.19260.1117-0.03330.02190.0565-0.13160.2112-0.01530.187323.3954-54.662217.6672
198.5253-4.6355-0.23623.5988-3.346111.2021-0.8210.6989-0.1451-0.781-0.3707-0.10231.08670.34651.19170.9902-0.1530.31540.6807-0.09840.42614.8628-9.8162-33.079
2017.34597.9775-5.40338.63442.500611.69770.1482-0.4664-1.3644-0.7267-0.3528-0.64361.34530.06220.20451.1288-0.0220.05350.629-0.14440.487115.9998-8.3-42.5902
210.9682-2.29371.78518.6238-3.06584.702-0.83741.4950.23-1.020.4710.86440.4263-1.050.36641.4112-0.2296-0.05291.16430.02550.59014.1571.7429-47.5915
228.1168-5.7887-4.12867.0313-3.20815.13890.24070.06160.4261-0.4221-0.4569-0.27980.32070.58380.21620.7562-0.12180.13250.4837-0.00730.395616.8042.9317-37.3355
234.3794-0.0713-2.249311.2472-1.8034.38460.1440.51190.4148-0.3108-0.18120.8529-0.4149-0.70930.03720.89420.017-0.01410.69620.00060.43998.18468.622-37.7472
248.85032.9524.16861.04820.98094.6038-0.11610.9912-0.15010.6363-0.57391.0667-0.589-0.16620.691.6440.1373-0.11071.48910.20190.60112.825216.7122-50.8278
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 213 - 23
2X-RAY DIFFRACTION2AA22 - 4424 - 46
3X-RAY DIFFRACTION3AA45 - 9447 - 96
4X-RAY DIFFRACTION4AA95 - 15697 - 158
5X-RAY DIFFRACTION5AA157 - 188159 - 190
6X-RAY DIFFRACTION6AA189 - 199191 - 201
7X-RAY DIFFRACTION7BB3 - 265 - 28
8X-RAY DIFFRACTION8BB27 - 5029 - 52
9X-RAY DIFFRACTION9BB51 - 8553 - 87
10X-RAY DIFFRACTION10BB86 - 13888 - 140
11X-RAY DIFFRACTION11BB139 - 161141 - 163
12X-RAY DIFFRACTION12BB162 - 199164 - 201
13X-RAY DIFFRACTION13CC2 - 194 - 21
14X-RAY DIFFRACTION14CC20 - 3722 - 39
15X-RAY DIFFRACTION15CC38 - 6340 - 65
16X-RAY DIFFRACTION16CC64 - 9666 - 98
17X-RAY DIFFRACTION17CC97 - 12499 - 126
18X-RAY DIFFRACTION18CC125 - 158127 - 160
19X-RAY DIFFRACTION19DD2 - 184 - 20
20X-RAY DIFFRACTION20DD19 - 3921 - 41
21X-RAY DIFFRACTION21DD40 - 5742 - 59
22X-RAY DIFFRACTION22DD58 - 7760 - 79
23X-RAY DIFFRACTION23DD78 - 12580 - 127
24X-RAY DIFFRACTION24DD126 - 157128 - 159

+
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://pdbjlvh1.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