[English] 日本語
Yorodumi
- PDB-6w9r: Crystal structure of an OTU deubiquitinase from Wolbachia pipient... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6w9r
TitleCrystal structure of an OTU deubiquitinase from Wolbachia pipientis wMel bound to ubiquitin
Components
  • OTU domain-containing protein wMelOTU
  • Ubiquitin
KeywordsHYDROLASE / Deubiquitinase / Bacterial effector
Function / homology
Function and homology information


Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex ...Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Hh mutants are degraded by ERAD / Recognition of DNA damage by PCNA-containing replication complex / Peroxisomal protein import / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Termination of translesion DNA synthesis / Negative regulation of FGFR4 signaling / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Stabilization of p53 / EGFR downregulation / Negative regulation of NOTCH4 signaling / Negative regulation of FGFR1 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Vif-mediated degradation of APOBEC3G
Similarity search - Function
OTU domain / OTU domain profile. / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
CITRATE ANION / Polyubiquitin-C / OTU domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Wolbachia pipientis wMel (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsSchubert, A.F. / Pruneda, J.N. / Komander, D.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)U105192732 United Kingdom
European Research Council (ERC)309456European Union
CitationJournal: Embo J. / Year: 2020
Title: Identification and characterization of diverse OTU deubiquitinases in bacteria.
Authors: Schubert, A.F. / Nguyen, J.V. / Franklin, T.G. / Geurink, P.P. / Roberts, C.G. / Sanderson, D.J. / Miller, L.N. / Ovaa, H. / Hofmann, K. / Pruneda, J.N. / Komander, D.
History
DepositionMar 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.country

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: Ubiquitin
N: Ubiquitin
O: Ubiquitin
P: Ubiquitin
Q: Ubiquitin
R: Ubiquitin
S: Ubiquitin
T: Ubiquitin
U: Ubiquitin
V: Ubiquitin
W: Ubiquitin
X: Ubiquitin
A: OTU domain-containing protein wMelOTU
B: OTU domain-containing protein wMelOTU
C: OTU domain-containing protein wMelOTU
D: OTU domain-containing protein wMelOTU
E: OTU domain-containing protein wMelOTU
F: OTU domain-containing protein wMelOTU
G: OTU domain-containing protein wMelOTU
H: OTU domain-containing protein wMelOTU
I: OTU domain-containing protein wMelOTU
J: OTU domain-containing protein wMelOTU
K: OTU domain-containing protein wMelOTU
L: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,41136
Polymers333,14124
Non-polymers2,26912
Water65,4123631
1
M: Ubiquitin
A: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-5 kcal/mol
Surface area10760 Å2
MethodPISA
2
N: Ubiquitin
B: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-6 kcal/mol
Surface area10630 Å2
MethodPISA
3
O: Ubiquitin
F: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-8 kcal/mol
Surface area10790 Å2
MethodPISA
4
P: Ubiquitin
D: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-7 kcal/mol
Surface area10980 Å2
MethodPISA
5
Q: Ubiquitin
I: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-7 kcal/mol
Surface area10680 Å2
MethodPISA
6
R: Ubiquitin
J: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-6 kcal/mol
Surface area10660 Å2
MethodPISA
7
S: Ubiquitin
E: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-5 kcal/mol
Surface area10680 Å2
MethodPISA
8
T: Ubiquitin
C: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-6 kcal/mol
Surface area10500 Å2
MethodPISA
9
U: Ubiquitin
K: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-5 kcal/mol
Surface area10510 Å2
MethodPISA
10
V: Ubiquitin
L: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-6 kcal/mol
Surface area10640 Å2
MethodPISA
11
W: Ubiquitin
G: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-8 kcal/mol
Surface area10630 Å2
MethodPISA
12
X: Ubiquitin
H: OTU domain-containing protein wMelOTU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9513
Polymers27,7622
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-6 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.925, 78.203, 280.425
Angle α, β, γ (deg.)90.000, 91.570, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Ubiquitin


Mass: 8701.014 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#2: Protein
OTU domain-containing protein wMelOTU


Mass: 19060.771 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wolbachia pipientis wMel (bacteria) / Gene: WD_0443 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73HU7
#3: Chemical
ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3631 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 6K, 0.1 M citrate pH 4.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.82→27.29 Å / Num. obs: 247996 / % possible obs: 98.3 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.056 / Rrim(I) all: 0.157 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.85-1.887.70.92493464121700.8490.3540.992.897.2
10.13-27.297.80.0591212015610.9980.0220.06318.494.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSJan 10, 2014data reduction
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ, 6W9O
Resolution: 1.82→27.29 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.47
RfactorNum. reflection% reflection
Rfree0.2081 12296 5.03 %
Rwork0.1664 --
obs0.1685 244560 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.34 Å2 / Biso mean: 24.3795 Å2 / Biso min: 6.36 Å2
Refinement stepCycle: final / Resolution: 1.82→27.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22609 0 156 3646 26411
Biso mean--29.67 34.48 -
Num. residues----2858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.840.30464170.2427889830695
1.84-1.860.29294120.22987935834795
1.86-1.890.27844210.22417867828894
1.89-1.910.23793890.21347915830494
1.91-1.930.25643940.20887878827295
1.93-1.960.25734300.20377908833895
1.96-1.990.2614190.19227868828795
1.99-2.020.24553980.18387984838294
2.02-2.050.25734030.18867864826795
2.05-2.080.22434200.18037934835495
2.08-2.120.22493990.17287925832494
2.12-2.160.21254140.16897864827894
2.16-2.20.21464180.16297869828794
2.2-2.240.20464530.16297800825393
2.24-2.290.20744320.15977753818593
2.29-2.350.23124240.15927757818193
2.35-2.40.22664010.16397759816092
2.4-2.470.2254130.17137825823893
2.47-2.540.24653950.1737796819193
2.54-2.620.2293820.16967782816493
2.62-2.720.21714420.16557737817992
2.72-2.830.20384040.1587707811192
2.83-2.960.21443850.16317651803691
2.96-3.110.19644010.15697647804891
3.11-3.310.19354040.15077596800090
3.31-3.560.18664370.15257506794389
3.56-3.920.16573680.1427535790389
3.92-4.480.15624180.14067382780088
4.48-5.640.17544140.15287293770786
5.64-27.290.18483890.16957038742781
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.3101-0.11470.53192.663-1.00341.39740.06890.03890.27220.0213-0.08910.2278-0.1547-0.03310.01770.10180.00430.010.0911-0.0060.1533-19.0794-3.748173.2665
21.3710.11960.34582.24440.19680.66660.0517-0.05780.18270.1246-0.1313-0.2312-0.07940.04540.06480.0674-0.0028-0.00280.11960.01230.151313.2418-0.7217136.6414
31.9452-0.3882-0.35251.3984-0.13441.3369-0.01350.22880.1203-0.0931-0.0752-0.24110.05510.18310.06970.0810.00260.01430.1270.04480.1516-31.3135-2.831451.3939
41.9411-0.2344-0.51531.4587-0.0511.46590.01310.13120.0567-0.1031-0.0062-0.30180.00010.2071-0.03430.07750.00180.0210.15280.01810.1601-33.11490.525121.6116
51.31940.01480.50492.8825-0.69291.4728-0.09060.03150.34970.0543-0.10180.0867-0.22430.02870.15470.19360.0036-0.07780.1349-0.01280.2477-16.9961-6.73083.3681
61.24170.13010.44061.67640.1140.95490.01040.00650.22180.0938-0.1306-0.2417-0.10660.06610.09760.0753-0.0009-0.02910.11340.02780.18315.208-3.916566.3252
73.00310.4528-0.45412.116-0.08571.6629-0.0672-0.33190.15120.08290.00680.46430.0201-0.3560.03710.16350.0175-0.00370.2295-0.03810.209728.9243-5.156518.4606
82.7517-0.0382-0.30731.65520.07071.4367-0.1435-0.33970.13410.10030.06370.36640.0581-0.22040.06640.09960.00990.00690.1499-0.02360.153727.0361-2.389188.1238
90.24180.02520.30270.0803-0.12720.7855-0.07310.1035-0.4382-0.2128-0.2822-0.6538-0.01690.88380.20240.17210.08160.09440.44390.26360.564120.77117.654545.0544
101.7408-0.17640.4481.1196-0.5931.0947-0.0410.0153-0.293-0.0016-0.0306-0.24370.06420.22170.040.08820.01710.03530.15040.03910.204319.016110.982115.4665
111.222-0.09690.58381.03280.03031.36460.2239-0.0449-0.6488-0.86840.07380.37570.9073-0.3391-0.11810.6555-0.1237-0.22260.1602-0.03110.316-21.61184.82327.4706
121.06170.44280.35162.27150.98721.2787-0.05770.1376-0.4186-0.1715-0.03310.09580.2141-0.17120.05340.1946-0.03530.00760.1243-0.04790.2587-23.20887.573697.1491
131.01340.2119-0.13231.2864-0.67310.99790.1195-0.10450.05540.2647-0.1663-0.142-0.16740.17930.0240.1552-0.0561-0.03420.1213-0.01740.1009-10.319-16.933188.7279
141.0699-0.22220.07860.9850.0291.07650.07130.0587-0.0017-0.1652-0.08120.0574-0.0037-0.06890.00040.09060.0228-0.01450.10380.00950.08843.9397-14.2748121.4627
151.15190.3446-0.26781.4756-0.31941.1838-0.0930.1188-0.1451-0.19390.0797-0.08070.1484-0.0401-0.00350.1199-0.0139-0.0010.0872-0.03380.103243.9442-3.797173.8452
160.52230.0437-0.31991.22660.08851.1739-0.0797-0.0115-0.07160.0720.03010.0330.1418-0.01740.04560.07360.00890.01050.11750.02740.1221-49.6252-0.5404136.6895
171.31020.1249-0.0151.5809-0.28111.3534-0.04760.0924-0.1447-0.22460.0292-0.09050.1361-0.03050.00290.18180.0109-0.00810.1092-0.0370.118745.6746-6.68283.8701
181.1106-0.0819-0.24731.77870.0711.3323-0.0656-0.0393-0.1460.1940.00030.06990.1553-0.0840.03540.1004-0.00730.01830.11480.04340.1239-47.6988-3.847466.441
191.8165-0.13190.61181.4239-0.49681.8029-0.0143-0.36670.02570.02840.03070.104-0.0929-0.3316-0.0190.14740.0112-0.00440.2053-0.00990.0851-16.15820.559942.2559
201.1951-0.08110.11551.0133-0.19451.58860.0157-0.1814-0.0306-0.02580.01340.1058-0.0498-0.2051-0.01570.06980.00010.01580.10720.00460.0867-18.325223.4122112.1558
211.32150.1922-0.02631.0682-0.29971.61870.0695-0.09550.06960.2138-0.1511-0.1571-0.20140.30650.05830.2294-0.0191-0.08110.196-0.02310.1752-8.3965-20.134318.7573
221.0454-0.23590.12251.15950.08141.12380.06520.15740.0149-0.1519-0.10520.06360.007-0.10710.02150.08350.0156-0.0190.11760.01440.09615.9548-17.64251.3539
231.43080.3222-0.12211.8042-0.45681.6450.00110.1572-0.0663-0.3045-0.228-0.4042-0.13810.50940.16330.31250.00430.09230.29840.10510.222613.675321.163428.9685
241.2670.12160.15071.3542-0.29171.5364-0.05470.18920.0025-0.2373-0.0453-0.1835-0.0840.28740.03420.1617-0.01110.08890.15990.03720.111612.036624.623999.2651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'M' and resid 1 through 76)M1 - 76
2X-RAY DIFFRACTION2(chain 'N' and resid 1 through 76)N1 - 76
3X-RAY DIFFRACTION3(chain 'O' and resid 1 through 76)O1 - 76
4X-RAY DIFFRACTION4(chain 'P' and resid 1 through 76)P1 - 76
5X-RAY DIFFRACTION5(chain 'Q' and resid 1 through 76)Q1 - 76
6X-RAY DIFFRACTION6(chain 'R' and resid 1 through 76)R1 - 76
7X-RAY DIFFRACTION7(chain 'S' and resid 1 through 76)S1 - 76
8X-RAY DIFFRACTION8(chain 'T' and resid 1 through 76)T1 - 76
9X-RAY DIFFRACTION9(chain 'U' and resid 1 through 76)U1 - 76
10X-RAY DIFFRACTION10(chain 'V' and resid 1 through 76)V1 - 76
11X-RAY DIFFRACTION11(chain 'W' and resid 1 through 76)W1 - 76
12X-RAY DIFFRACTION12(chain 'X' and resid 1 through 76)X1 - 76
13X-RAY DIFFRACTION13(chain 'A' and resid 39 through 200)A39 - 200
14X-RAY DIFFRACTION14(chain 'B' and resid 38 through 200)B38 - 200
15X-RAY DIFFRACTION15(chain 'C' and resid 38 through 200)C38 - 200
16X-RAY DIFFRACTION16(chain 'D' and resid 40 through 201)D40 - 201
17X-RAY DIFFRACTION17(chain 'E' and resid 39 through 200)E39 - 200
18X-RAY DIFFRACTION18(chain 'F' and resid 40 through 200)F40 - 200
19X-RAY DIFFRACTION19(chain 'G' and resid 39 through 201)G39 - 201
20X-RAY DIFFRACTION20(chain 'H' and resid 39 through 200)H39 - 200
21X-RAY DIFFRACTION21(chain 'I' and resid 40 through 200)I40 - 200
22X-RAY DIFFRACTION22(chain 'J' and resid 38 through 200)J38 - 200
23X-RAY DIFFRACTION23(chain 'K' and resid 40 through 200)K40 - 200
24X-RAY DIFFRACTION24(chain 'L' and resid 38 through 200)L38 - 200

+
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