[English] 日本語
Yorodumi
- PDB-8vk9: Structure of UbV.d2.3 in complex with Ube2d2-S22R -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vk9
TitleStructure of UbV.d2.3 in complex with Ube2d2-S22R
Components
  • Ubiquitin variant D2.3
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsTRANSFERASE / Ubiquitin conjugating enzyme / Ubiquitin variant / E2 enzyme / inhibitor
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling ...(E3-independent) E2 ubiquitin-conjugating enzyme / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / Peroxisomal protein import / Regulation of TNFR1 signaling / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / protein modification process / protein polyubiquitination / ubiquitin-protein transferase activity / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / ubiquitin-dependent protein catabolic process / protein ubiquitination / protein-containing complex / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 D2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiddleton, A.J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Health Research Council (HRC) New Zealand
CitationJournal: Febs J. / Year: 2024
Title: Structural and biophysical characterisation of ubiquitin variants that inhibit the ubiquitin conjugating enzyme Ube2d2.
Authors: McAlpine, J.M.R.B. / Zhu, J. / Pudjihartono, N. / Teyra, J. / Currie, M.J. / Tillett, Z.D. / Dobson, R.C.J. / Sidhu, S.S. / Day, C.L. / Middleton, A.J.
History
DepositionJan 8, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: 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 / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin variant D2.3
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin variant D2.3
E: Ubiquitin-conjugating enzyme E2 D2
F: Ubiquitin variant D2.3
G: Ubiquitin-conjugating enzyme E2 D2
H: Ubiquitin variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,90613
Polymers110,4468
Non-polymers4605
Water6,521362
1
A: Ubiquitin-conjugating enzyme E2 D2
B: Ubiquitin variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7043
Polymers27,6112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-12 kcal/mol
Surface area11770 Å2
MethodPISA
2
C: Ubiquitin-conjugating enzyme E2 D2
D: Ubiquitin variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7964
Polymers27,6112
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-11 kcal/mol
Surface area11970 Å2
MethodPISA
3
E: Ubiquitin-conjugating enzyme E2 D2
F: Ubiquitin variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7043
Polymers27,6112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area11820 Å2
MethodPISA
4
G: Ubiquitin-conjugating enzyme E2 D2
H: Ubiquitin variant D2.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7043
Polymers27,6112
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-9 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.850, 56.314, 117.499
Angle α, β, γ (deg.)86.48, 78.47, 60.32
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Ubiquitin-conjugating enzyme E2 D2 / (E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D2 / E2 ubiquitin-conjugating enzyme D2 / Ubiquitin carrier protein D2 / Ubiquitin-conjugating enzyme E2(17)KB 2 / Ubiquitin-conjugating enzyme E2-17 kDa 2 / Ubiquitin-protein ligase D2 / p53-regulated ubiquitin-conjugating enzyme 1


Mass: 17188.605 Da / Num. of mol.: 4 / Mutation: C21S, S22R, C107S, C111S
Source method: isolated from a genetically manipulated source
Details: Contains an N-terminal linker / Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B / Production host: Escherichia coli (E. coli)
References: UniProt: P62837, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#2: Protein
Ubiquitin variant D2.3


Mass: 10422.864 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Contains N-terminal linker. Obtained from phage display.
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M Sodium HEPES pH 7.0, 15% w/v PEG 20,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→41.2 Å / Num. obs: 80451 / % possible obs: 97.5 % / Redundancy: 3 % / Biso Wilson estimate: 63.7 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0528 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7996 / CC1/2: 0.678 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PHENIX1.20.1-4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.2 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2235 4061 5.05 %
Rwork0.1891 --
obs0.1908 80451 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7233 0 30 362 7625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037444
X-RAY DIFFRACTIONf_angle_d0.72210103
X-RAY DIFFRACTIONf_dihedral_angle_d6.2391003
X-RAY DIFFRACTIONf_chiral_restr0.0471125
X-RAY DIFFRACTIONf_plane_restr0.0071308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.41891590.36322606X-RAY DIFFRACTION96
2.02-2.050.35781310.32872534X-RAY DIFFRACTION97
2.05-2.070.36041430.31452651X-RAY DIFFRACTION96
2.07-2.10.33261510.30532590X-RAY DIFFRACTION97
2.1-2.130.34581290.27722617X-RAY DIFFRACTION97
2.13-2.160.29751670.25552616X-RAY DIFFRACTION96
2.16-2.190.27081250.24362616X-RAY DIFFRACTION99
2.19-2.220.27351370.23952648X-RAY DIFFRACTION97
2.22-2.260.29881510.23932637X-RAY DIFFRACTION97
2.26-2.30.30261540.23512626X-RAY DIFFRACTION99
2.3-2.340.26111430.2312609X-RAY DIFFRACTION96
2.34-2.390.271480.22682622X-RAY DIFFRACTION99
2.39-2.440.26811660.22352658X-RAY DIFFRACTION97
2.44-2.490.26141440.22782613X-RAY DIFFRACTION98
2.49-2.550.26341230.23222682X-RAY DIFFRACTION97
2.55-2.610.2801940.22522661X-RAY DIFFRACTION99
2.61-2.680.27071430.23022664X-RAY DIFFRACTION97
2.68-2.760.25561160.22372656X-RAY DIFFRACTION99
2.76-2.850.24071390.2142663X-RAY DIFFRACTION97
2.85-2.950.27261440.21762669X-RAY DIFFRACTION98
2.95-3.070.27971470.22172616X-RAY DIFFRACTION99
3.07-3.210.25041510.21342628X-RAY DIFFRACTION98
3.21-3.380.25131420.21162624X-RAY DIFFRACTION97
3.38-3.590.23531220.19272659X-RAY DIFFRACTION97
3.59-3.870.21431320.17432620X-RAY DIFFRACTION97
3.87-4.250.20241660.1532685X-RAY DIFFRACTION99
4.25-4.870.1751530.13442620X-RAY DIFFRACTION98
4.87-6.130.17551160.15422691X-RAY DIFFRACTION98
6.13-41.20.13651250.14922609X-RAY DIFFRACTION96
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)
13.6061-2.0042.00914.2829-0.42264.62150.5103-0.336-0.51950.1925-0.12160.12380.3891-0.2732-0.07380.6790.06470.04270.35370.02380.4512-31.4994-31.6864-34.0816
22.1847-2.32460.49824.6736-0.63482.39670.26020.33010.0709-0.3953-0.4506-0.0696-0.0418-0.13240.01840.65120.05670.03210.3775-0.02610.3599-35.5509-19.3007-37.3316
33.1782-2.62410.00424.5144-0.04842.29370.075-0.06510.11770.1286-0.16740.2126-0.2806-0.2180.04160.59030.07410.02040.3724-0.05960.3944-45.1253-11.2159-33.6384
43.2442-0.8994-0.89723.5779-0.043.51050.24550.5907-0.0958-0.5247-0.2327-0.77480.58470.5142-0.02320.67990.22130.07350.50280.03640.5061-15.9359-38.5443-40.9437
53.0852-1.06680.4671.2606-0.36342.87660.40130.50251.2052-0.4464-0.1548-1.5943-0.90750.61170.11250.95450.27930.40570.9130.31451.1227-9.0925-30.7785-47.9046
62.9048-1.0867-0.51411.0368-1.27683.70650.39310.49650.4209-0.6629-0.1874-0.9718-0.16410.2947-0.08890.66810.11290.19890.57750.15430.8083-14.0485-31.2856-44.1701
72.57230.031-0.17662.46480.34946.1640.0056-0.04680.34310.71190.1106-0.5839-0.05190.99440.01330.4916-0.1693-0.03420.3708-0.01090.4635-20.8978-16.4905-2.0167
81.64541.07890.20643.424-0.52693.0978-0.0343-0.0139-0.1314-0.01920.07860.08160.0839-0.0716-0.01220.2754-0.06890.00930.32130.01840.359-29.9079-28.1937-7.9912
91.43520.162-0.01521.2511-0.20672.29410.1077-0.0533-0.32960.1273-0.0817-0.20390.36130.076-0.04620.3305-0.07230.00190.3710.03190.4164-27.4009-37.607-2.5635
101.0215-0.78520.98374.01711.6894.56970.2601-0.2914-1.52830.2765-0.29850.44090.8042-0.2039-0.07140.6566-0.1639-0.06870.4230.08530.6848-36.3666-52.6381-6.0795
111.8538-0.76610.70624.1658-0.77032.6059-0.20890.694-0.0571-1.32140.20130.32850.2827-0.0756-0.14280.5927-0.1649-0.05370.3797-0.02660.5101-38.5504-44.7413-16.8212
123.2918-0.5232-0.45172.78821.00713.8262-0.04280.25250.37380.72160.0432-0.1938-0.0724-0.01620.14020.7524-0.1307-0.05420.2943-0.04120.4995-24.1283-8.5658-3.2374
131.9011-1.37150.58291.71031.00863.0739-0.2168-0.56791.49811.9693-0.0207-0.568-1.83180.6906-0.97171.3271-0.2522-0.150.1565-0.09550.6625-24.03090.8081-2.7571
143.06770.92580.66550.68890.05762.7738-0.12530.60951.03780.67040.17920.31-1.45850.42620.17010.7377-0.0228-0.02020.2620.09820.6218-26.45983.638-13.0809
152.12350.0780.50853.39950.13632.32240.25630.42550.2776-0.00530.76560.769-1.6834-1.0810.31721.21750.19910.2850.5380.14861.0807-37.15910.8065-5.6327
164.9609-3.50.69913.7799-0.08030.20910.0858-0.77230.88931.12820.34750.7071-1.1763-1.09940.34721.02140.20620.34770.591-0.06790.8517-35.6237-4.31041.3004
175.24812.561-1.71346.1724-4.08172.78270.00010.22760.60730.57540.73851.6503-0.5182-0.61460.03080.5428-0.0542-0.03910.34620.04260.6522-30.4585-2.6631-13.3117
184.0216-1.49541.0813.3214-0.25273.9121-0.12860.3473-0.1995-0.21240.05250.03160.26530.4391-0.02230.40430.01040.02250.51020.00040.4731-14.5074-35.366621.9789
193.5313-0.4580.83751.1293-0.533.0685-0.2209-0.10850.17580.20320.20290.0607-0.145-0.1717-0.01560.35650.00710.02260.45660.02540.3613-27.0695-31.412919.933
202.56420.25170.66551.392-0.01693.22360.0211-0.52430.47530.8720.31120.0184-0.54130.0578-0.06510.4147-0.01640.10090.70810.05160.496-38.8873-30.523722.8309
213.2287-0.16892.30881.1672-0.54324.0425-0.1171-0.6688-0.2887-0.04940.05120.34680.2713-0.743-0.02490.4520.04830.03880.70180.07060.4342-27.5997-36.682732.3826
222.53750.19290.6821.3154-0.86451.374-0.2744-0.5525-0.3330.25420.38430.36840.2195-0.537-0.08840.3862-0.03890.07580.68470.10570.4624-40.2479-38.698924.1604
231.9321-0.0078-0.77021.3095-0.51622.9608-0.1260.2096-0.0969-0.17270.1780.29170.0528-0.1532-0.09810.4053-0.12850.03890.61650.07090.5067-44.8-36.377211.1124
243.5855-0.14080.13914.2753-0.78072.9734-0.1494-0.16620.32140.18180.0559-0.3960.05720.21610.12230.3724-0.0562-0.02970.59970.00720.5416-5.6813-26.254920.7138
254.4404-0.7582-3.84830.54971.61955.5467-0.1806-0.40220.40920.059-0.2529-0.6963-0.59420.85680.19270.8738-0.2751-0.28750.8421-0.25581.39070.9101-15.206926.2901
260.3093-0.61150.63871.6358-0.20163.7991-0.26360.28820.722-0.55710.2925-0.48340.22110.78410.2560.3734-0.19260.06030.81910.21911.00483.6208-22.84914.6385
271.614-0.51760.74215.7275-1.75476.9077-0.20530.32590.6550.06080.13740.07360.1256-0.48880.14620.6223-0.1439-0.18880.76620.29661.3096-9.7-13.61612.6852
283.1655-0.3242-0.42833.30320.46530.44450.34370.55741.2917-0.40440.0366-1.2211-1.24640.99370.24720.6137-0.2813-0.05940.5820.12041.3857-1.2559-10.486218.2644
292.94761.24291.22122.7064-1.67055.3499-0.4273-1.25782.06680.83290.0357-0.1234-1.1184-0.47910.14360.48760.0092-0.13240.57880.0271.1289-9.9969-16.062424.2498
304.88460.8824-0.39325.1244-1.33865.8101-0.14410.69351.1583-0.9734-0.4543-0.328-0.24690.45490.09040.5423-0.0655-0.05220.63890.28340.7648-3.6721-22.24528.9324
311.7418-1.2979-0.12642.94830.80463.8197-0.4486-0.79160.47570.4960.6481-0.139-0.1982-0.0041-0.03020.68780.247-0.05740.6967-0.10030.4454-23.5058-28.978950.3391
321.15360.59110.34513.13810.49292.8924-0.4257-0.39090.50120.83880.4927-0.2101-0.1878-0.252-0.24930.63770.3878-0.06390.6876-0.09440.3023-17.1698-37.887450.98
337.2014-0.1831-1.1541.75221.88942.402-0.9752-0.3229-1.30421.44921.06240.52440.78020.13940.08580.72540.35330.00280.70530.07980.3923-17.3121-46.762848.6951
343.1953-1.9282-0.50423.26530.45235.0586-0.2438-1.1553-1.15160.94920.53780.04790.6026-0.2161-0.0480.82580.2869-0.02450.86630.050.4835-14.1171-48.915252.827
350.17820.16760.18770.99240.14210.3363-0.3707-0.8750.2131.04850.2174-0.23140.0564-0.0323-1.24981.19550.622-0.35291.1562-0.39280.5647-13.0482-35.343261.459
362.5164-0.6121-0.52840.4254-0.67082.256-1.0245-1.3780.48571.40411.0489-1.16740.2460.37140.31780.83850.3156-0.28010.9752-0.19260.6294-8.4211-40.544753.0795
374.5443-0.653-0.77733.37551.80550.9970.1027-0.7158-0.80681.3410.4719-0.6320.88080.26370.16690.85250.477-0.25150.967-0.08880.7157-2.1123-55.492352.2696
383.7529-2.01121.72272.712-1.08313.41450.12261.0514-0.316-0.8474-0.04510.03750.2810.5362-0.03160.71050.2433-0.05850.6797-0.18040.5723-7.841-52.017840.3818
390.98940.7756-0.13581.35540.69451.3943-1.0702-1.04250.81380.87771.11460.4805-0.8466-0.9537-0.46560.82220.67360.08551.1097-0.04360.64-39.7029-19.225250.6575
401.09531.36130.18832.733-0.66921.9539-0.2656-0.4275-0.8419-0.11250.20720.5679-0.0182-0.6955-0.15750.66220.1950.0541.01990.23691.0134-44.2762-29.142144.0561
411.72080.0326-0.62040.96040.87181.5985-0.5736-0.9503-0.60670.10890.54940.88570.0893-0.3307-0.1850.70570.26710.16350.95650.19030.8465-44.5688-26.688448.8785
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 147 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 45 )
5X-RAY DIFFRACTION5chain 'B' and (resid 46 through 56 )
6X-RAY DIFFRACTION6chain 'B' and (resid 57 through 72 )
7X-RAY DIFFRACTION7chain 'C' and (resid -3 through 15 )
8X-RAY DIFFRACTION8chain 'C' and (resid 16 through 74 )
9X-RAY DIFFRACTION9chain 'C' and (resid 75 through 120 )
10X-RAY DIFFRACTION10chain 'C' and (resid 121 through 130 )
11X-RAY DIFFRACTION11chain 'C' and (resid 131 through 147 )
12X-RAY DIFFRACTION12chain 'D' and (resid -3 through 12 )
13X-RAY DIFFRACTION13chain 'D' and (resid 13 through 34 )
14X-RAY DIFFRACTION14chain 'D' and (resid 35 through 44 )
15X-RAY DIFFRACTION15chain 'D' and (resid 45 through 56 )
16X-RAY DIFFRACTION16chain 'D' and (resid 57 through 65 )
17X-RAY DIFFRACTION17chain 'D' and (resid 66 through 72 )
18X-RAY DIFFRACTION18chain 'E' and (resid -2 through 24 )
19X-RAY DIFFRACTION19chain 'E' and (resid 25 through 74 )
20X-RAY DIFFRACTION20chain 'E' and (resid 75 through 84 )
21X-RAY DIFFRACTION21chain 'E' and (resid 85 through 98 )
22X-RAY DIFFRACTION22chain 'E' and (resid 99 through 130 )
23X-RAY DIFFRACTION23chain 'E' and (resid 131 through 147 )
24X-RAY DIFFRACTION24chain 'F' and (resid -1 through 17 )
25X-RAY DIFFRACTION25chain 'F' and (resid 18 through 22 )
26X-RAY DIFFRACTION26chain 'F' and (resid 23 through 44 )
27X-RAY DIFFRACTION27chain 'F' and (resid 45 through 49 )
28X-RAY DIFFRACTION28chain 'F' and (resid 50 through 59 )
29X-RAY DIFFRACTION29chain 'F' and (resid 60 through 65 )
30X-RAY DIFFRACTION30chain 'F' and (resid 66 through 73 )
31X-RAY DIFFRACTION31chain 'G' and (resid -1 through 38 )
32X-RAY DIFFRACTION32chain 'G' and (resid 39 through 65 )
33X-RAY DIFFRACTION33chain 'G' and (resid 66 through 74 )
34X-RAY DIFFRACTION34chain 'G' and (resid 75 through 84 )
35X-RAY DIFFRACTION35chain 'G' and (resid 85 through 98 )
36X-RAY DIFFRACTION36chain 'G' and (resid 99 through 120 )
37X-RAY DIFFRACTION37chain 'G' and (resid 121 through 130 )
38X-RAY DIFFRACTION38chain 'G' and (resid 131 through 147 )
39X-RAY DIFFRACTION39chain 'H' and (resid -2 through 40 )
40X-RAY DIFFRACTION40chain 'H' and (resid 41 through 49 )
41X-RAY DIFFRACTION41chain 'H' and (resid 50 through 72 )

+
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