[English] 日本語
Yorodumi
- PDB-6hpr: Crystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a n... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hpr
TitleCrystal structure of cIAP1 RING domain bound to UbcH5B-Ub and a non-covalent Ub
Components
  • Baculoviral IAP repeat-containing protein 2
  • Polyubiquitin-B
  • Ubiquitin-conjugating enzyme E2 D2
KeywordsLIGASE / Ubiquitin / E3 / cIAP1 / UbcH5B / ubiquitin ligase
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / FBXO family protein binding / positive regulation of protein monoubiquitination / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / (E3-independent) E2 ubiquitin-conjugating enzyme / XY body / negative regulation of necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / symbiont entry into host cell via disruption of host cell glycocalyx / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of reactive oxygen species metabolic process / E2 ubiquitin-conjugating enzyme / symbiont entry into host cell via disruption of host cell envelope / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / virus tail / necroptotic process / ubiquitin conjugating enzyme activity / regulation of cell differentiation / response to cAMP / canonical NF-kappaB signal transduction / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / IKK complex recruitment mediated by RIP1 / TNFR1-induced NF-kappa-B signaling pathway / PINK1-PRKN Mediated Mitophagy / Negative regulators of DDX58/IFIH1 signaling / TNFR2 non-canonical NF-kB pathway / Peroxisomal protein import / placenta development / Regulation of TNFR1 signaling / ubiquitin binding / tumor necrosis factor-mediated signaling pathway / NOD1/2 Signaling Pathway / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of necroptotic cell death / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / RING-type E3 ubiquitin transferase / protein modification process / cytoplasmic side of plasma membrane / 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 / regulation of cell population proliferation / protein-folding chaperone binding / transferase activity / regulation of inflammatory response / ubiquitin-dependent protein catabolic process / response to ethanol / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / protein ubiquitination / regulation of cell cycle / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / protein-containing complex / extracellular exosome / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Zinc/RING finger domain, C3HC4 (zinc finger) / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Herpes Virus-1 / Ubiquitin-conjugating enzyme/RWD-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Ubiquitin-conjugating enzyme E2 D2 / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPatel, A. / Huang, D.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA23278 United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2019
Title: Structural insights into non-covalent ubiquitin activation of the cIAP1-UbcH5B∼ubiquitin complex.
Authors: Patel, A. / Sibbet, G.J. / Huang, D.T.
History
DepositionSep 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.4May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_validate_close_contact ...diffrn_source / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Jan 24, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
B: Polyubiquitin-B
C: Ubiquitin-conjugating enzyme E2 D2
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0626
Polymers41,9314
Non-polymers1312
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance, Other biochemical assays, NMR
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-19 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.190, 53.600, 78.540
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / ...Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / hIAP2 / RING finger protein 48 / RING-type E3 ubiquitin transferase BIRC2 / TNFR2-TRAF-signaling complex protein 2


Mass: 7305.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: cIAP1 residues 556-C with N-terminal GS resulted from TEV cleavage
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, MIHB, RNF48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13490, RING-type E3 ubiquitin transferase
#2: Protein Polyubiquitin-B


Mass: 8922.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Ubiquitin residues 1-76 contains N-terminal GSGGS after TEV cleavage. Chain D Gly76 forms isopeptide linkage with Chain C Lys85.
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: 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: 16781.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: UbcH5B residues 1-147. Cys85 is mutated to Lys and forms isopeptide linkage with ubiquitin's Gly76 in chain D.
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
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium fluoride and 15% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→23.52 Å / Num. obs: 34206 / % possible obs: 98.8 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Net I/σ(I): 13.8
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2 / CC1/2: 0.632 / % possible all: 94.7

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2142: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EB6, 3ZNI

3eb6

3zni


Resolution: 1.7→23.515 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.46
RfactorNum. reflection% reflection
Rfree0.1972 1744 5.1 %
Rwork0.1704 --
obs0.1718 34206 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 2 222 3008
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072851
X-RAY DIFFRACTIONf_angle_d0.9223880
X-RAY DIFFRACTIONf_dihedral_angle_d16.1671758
X-RAY DIFFRACTIONf_chiral_restr0.06457
X-RAY DIFFRACTIONf_plane_restr0.006500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.29951400.25582578X-RAY DIFFRACTION95
1.75-1.80650.26091330.22872663X-RAY DIFFRACTION98
1.8065-1.8710.23711520.20612681X-RAY DIFFRACTION98
1.871-1.94590.22371490.20072688X-RAY DIFFRACTION99
1.9459-2.03440.23431480.1952686X-RAY DIFFRACTION99
2.0344-2.14160.21231340.18012728X-RAY DIFFRACTION99
2.1416-2.27570.24431490.16892700X-RAY DIFFRACTION99
2.2757-2.45120.22031340.1752737X-RAY DIFFRACTION99
2.4512-2.69760.19131540.16942723X-RAY DIFFRACTION99
2.6976-3.08720.18731420.16662741X-RAY DIFFRACTION100
3.0872-3.88670.17971640.15352732X-RAY DIFFRACTION100
3.8867-23.51760.15211450.14652805X-RAY DIFFRACTION99
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)
12.37813.39362.59356.84874.58593.2009-0.76051.0463-0.4041-0.44660.9886-0.5349-1.09940.7152-0.16030.7581-0.26830.08820.4848-0.12440.3938-8.30434.688733.4518
25.00420.5566-1.60294.1905-1.52524.5867-0.0265-0.0785-0.0134-0.03050.00640.316-0.0268-0.45850.01960.1156-0.0287-0.00350.1787-0.02490.0971-11.3224-15.576828.6709
37.8282-7.53593.04032.1048-4.58042.1223-0.6008-0.12580.46540.84430.334-0.3488-0.17820.20090.17090.31350.0302-0.06250.321-0.09130.41537.035515.83622.0174
42.0362-0.53851.99922.0224-0.00924.0627-0.3089-0.57271.2232-0.03240.496-0.7479-0.6120.2218-0.16920.3354-0.02760.03280.2593-0.11080.63819.290822.737814.5544
55.12874.99461.29946.1381-0.02134.5975-0.3624-0.48850.2254-0.59080.2441-1.4109-0.42291.01170.08920.2541-0.09580.08230.3249-0.12230.623416.490315.445511.9651
65.8583-1.5190.25812.0432-0.15363.41480.16690.31790.465-1.07130.0669-0.1921-0.43860.1665-0.20.2937-0.05480.04560.1708-0.00280.2784.695314.40117.0938
74.65561.7546-2.08924.28510.28722.00530.2988-0.09450.6198-0.07250.16750.2707-0.4507-0.54-0.5360.18040.06150.020.2632-0.0130.2757-2.146815.93213.1253
85.418-2.5476-0.55565.82270.64992.66110.0079-0.24270.7364-0.22920.2695-1.0683-0.00770.9336-0.26060.2044-0.0042-0.02110.3988-0.10180.414715.29810.435814.283
98.81483.9388-1.78072.0526-0.76548.4831-0.2078-0.36021.16980.69090.14790.9979-0.6643-0.44310.15740.26340.0879-0.01690.1816-0.02220.3281-7.13581.169817.6806
102.1046-3.90737.58617.6492-2.34355.98210.2133-0.21990.56270.3748-0.2412-0.31980.4386-0.28990.09220.1709-0.03930.01390.32680.03690.18412.0663.63413.827
112.0416-0.71956.62152.8349-0.79217.4844-0.44180.13650.7384-0.04330.01090.1356-0.1443-0.04830.48890.1628-0.0119-0.0120.1093-0.01480.1403-0.40270.34988.3637
122.0345-4.6766-3.44139.8284-1.55544.2868-0.2428-0.60440.11170.38510.1203-0.4264-0.23120.42920.14910.1337-0.0263-0.03420.1993-0.00670.157421.0745-1.171914.0071
138.07717.4184-2.10649.4101-1.02292.1728-0.46980.3050.3598-0.7590.28150.2214-0.0027-0.09070.18860.1448-0.0001-0.00420.070.01070.09325.8132-1.78156.4637
143.7499-2.6436-2.69295.8448-3.03692.041-0.19750.3935-0.4692-0.1055-0.00530.48090.3547-0.66010.13380.1495-0.05060.00650.1877-0.03240.1368-7.7191-10.586611.6642
159.7785-3.56071.64832.1501-0.33990.33460.07420.49770.1611-0.0979-0.2101-0.2341-0.0001-0.00290.12630.1731-0.016-0.01010.14910.00250.117111.5442-6.13573.8525
164.2667-0.1472-2.20570.7850.07012.06030.01670.0889-0.1268-0.0644-0.0507-0.0108-0.0074-0.11360.02770.14230.0054-0.02070.07330.01210.08136.6881-11.446112.3047
177.5817-0.30540.47631.81470.77343.4644-0.00150.0999-0.77640.1248-0.00340.01860.38620.0304-0.01190.17640.01080.01910.0927-0.01780.175921.0971-17.79718.3946
188.6721-6.66833.41487.6831-5.02315.4945-0.10180.27470.6281-0.0614-0.1-0.7275-0.18920.23580.17690.1267-0.03830.02670.1387-0.0170.14724.6545-4.52335.4611
192.10623.17998.33855.42262.89169.3064-0.4005-0.98250.6050.1379-0.02930.0391-0.4866-0.43940.37680.1767-0.00370.02230.362-0.12490.19927.1575-3.177833.9148
208.1227-2.85834.36682.4952-0.88852.6294-0.4292-0.73610.44390.18530.0547-0.1191-0.628-0.56990.34860.2239-0.03240.01110.4701-0.10560.20168.0933-3.703237.5422
213.8833.63113.17882.00242.00958.9525-0.1991-0.3699-0.19890.58890.7506-0.70460.16940.4177-0.59750.16660.0107-0.01010.2829-0.04750.262120.1035-8.009938.6956
229.26671.069-3.87674.97011.20749.17320.0312-0.9443-0.40730.3746-0.25750.08580.4861-0.12480.24040.209-0.0709-0.03620.270.03410.11119.5931-13.179435.9903
233.94442.3161-1.87614.3453-1.23974.50170.0301-0.4195-0.12310.0486-0.17780.02690.0350.06180.14050.1143-0.0183-0.00130.18510.00320.10037.8959-14.677727.994
246.978-3.87237.06057.1078-6.392.06440.20630.212-0.2514-0.4462-0.2431-0.24430.3550.4034-0.01440.20620.01410.04310.19130.00380.157818.666-9.193326.6194
256.03392.3452.60145.44792.13743.944-0.0749-0.57460.7050.0224-0.1048-0.1018-0.32840.01290.19310.1598-0.03640.01450.154-0.03640.165514.9378-3.259329.9188
268.1604-8.8541.98539.91312.00772.0006-0.40890.1979-0.32980.39640.10130.3491.5685-0.53920.46190.2055-0.04480.03280.0794-0.03160.11399.4386-17.674917.0306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 556 through 569 )
2X-RAY DIFFRACTION2chain 'A' and (resid 570 through 618 )
3X-RAY DIFFRACTION3chain 'B' and (resid 0 through 17 )
4X-RAY DIFFRACTION4chain 'B' and (resid 18 through 34 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 74 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 15 )
10X-RAY DIFFRACTION10chain 'C' and (resid 16 through 28 )
11X-RAY DIFFRACTION11chain 'C' and (resid 29 through 38 )
12X-RAY DIFFRACTION12chain 'C' and (resid 39 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 55 )
14X-RAY DIFFRACTION14chain 'C' and (resid 56 through 65 )
15X-RAY DIFFRACTION15chain 'C' and (resid 66 through 74 )
16X-RAY DIFFRACTION16chain 'C' and (resid 75 through 110 )
17X-RAY DIFFRACTION17chain 'C' and (resid 111 through 130 )
18X-RAY DIFFRACTION18chain 'C' and (resid 131 through 147 )
19X-RAY DIFFRACTION19chain 'D' and (resid -1 through 11 )
20X-RAY DIFFRACTION20chain 'D' and (resid 12 through 17 )
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 22 )
22X-RAY DIFFRACTION22chain 'D' and (resid 23 through 34 )
23X-RAY DIFFRACTION23chain 'D' and (resid 35 through 44 )
24X-RAY DIFFRACTION24chain 'D' and (resid 45 through 56 )
25X-RAY DIFFRACTION25chain 'D' and (resid 57 through 71 )
26X-RAY DIFFRACTION26chain 'D' and (resid 72 through 76 )

+
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