[English] 日本語
Yorodumi
- PDB-5gj6: Functional and structural characterization of P[19] rotavirus VP8... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gj6
TitleFunctional and structural characterization of P[19] rotavirus VP8* interaction with histo-blood group antigens
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / Rotavirus / P[19] VP8*
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.388 Å
AuthorsSun, X. / Duan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81472003; 31500139 China
CitationJournal: J. Virol. / Year: 2016
Title: Functional and Structural Characterization of P[19] Rotavirus VP8* Interaction with Histo-blood Group Antigens.
Authors: Sun, X. / Li, D. / Peng, R. / Guo, N. / Jin, M. / Zhou, Y. / Xie, G. / Pang, L. / Zhang, Q. / Qi, J. / Duan, Z.J.
History
DepositionJun 28, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
D: Outer capsid protein VP4
E: Outer capsid protein VP4
F: Outer capsid protein VP4
G: Outer capsid protein VP4
H: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,36112
Polymers144,9778
Non-polymers3844
Water6,521362
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2182
Polymers18,1221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2182
Polymers18,1221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2182
Polymers18,1221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2182
Polymers18,1221
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,1221
Polymers18,1221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.904, 129.782, 86.818
Angle α, β, γ (deg.)90.000, 115.900, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Outer capsid protein VP4


Mass: 18122.115 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 64-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Plasmid: pET3oa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Q2P6
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.2M ammonium sulfate, 0.1M MES pH 6.5, 30% w/v polyethylene glycol MME 5000

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 0.97944 Å
DetectorType: Nonius Kappa CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 2.388→50 Å / Num. obs: 70312 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.15 / Rsym value: 0.15 / Net I/σ(I): 10.73
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.974 / % possible all: 100

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DWR

2dwr


Resolution: 2.388→33.822 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.27
RfactorNum. reflection% reflection
Rfree0.2594 3413 4.86 %
Rwork0.2155 --
obs0.2176 70272 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 105.21 Å2 / Biso mean: 40.1406 Å2 / Biso min: 16.27 Å2
Refinement stepCycle: final / Resolution: 2.388→33.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10232 0 20 362 10614
Biso mean--29.38 42.12 -
Num. residues----1280
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)
10.37870.0825-0.11030.056-0.19270.85240.2618-0.00920.2337-0.275-0.19960.055-0.1044-0.5056-0.0340.2944-0.02340.00990.16820.02350.2434183.7097-3.5863102.2183
20.4346-0.0833-0.55090.7449-0.23760.8271-0.1581-0.02040.05250.04580.14420.0638-0.4195-0.0361-0.0030.2827-0.03920.00570.16780.01410.2402180.4526-0.9093120.3156
30.9404-0.15280.21410.65190.19181.5601-0.05440.068-0.01810.10910.06580.0363-0.1084-0.0265-00.2725-0.03490.03310.16190.00460.2217180.7692-8.0937116.6612
40.2798-0.10840.06970.09830.02690.12510.1940.1612-0.1371-0.1393-0.1973-0.1342-0.02640.4957-00.27960.0037-0.02340.30540.00790.2074191.6415-10.2403104.3606
50.49520.34330.56190.9362-0.45141.17810.0620.0231-0.1120.0628-0.09430.09950.1298-0.2461-0.00210.2712-0.04750.04040.23780.05010.2542169.434117.4587135.2435
60.94810.47850.0451.36460.08060.6617-0.11660.0003-0.1665-0.09790.1007-0.0635-0.0841-0.046900.22370.00670.05070.14910.03140.1911179.638819.6583123.7943
70.5821-0.4734-0.23790.47660.50481.2749-0.1619-0.01530.10150.14990.1240.008-0.0298-0.0712-0.00180.2441-0.01630.01180.14530.01580.2227171.592326.4981129.8752
80.32480.04930.11280.3038-0.1980.1623-0.1464-0.3688-0.0320.1956-0.01850.10070.12850.051400.221-0.02940.01530.30790.01380.2702173.252525.4755142.7577
90.11660.1392-0.24030.2056-0.27970.45530.48930.09690.1708-0.0001-0.3133-0.5928-0.56870.241-0.00770.26520.0030.0210.29850.02910.357202.423446.0805112.3966
100.56660.3402-0.33520.48920.09260.43780.09780.30610.1531-0.116-0.205-0.3587-0.02320.4738-0.00230.3708-0.05920.03710.2394-0.03890.4096194.851943.9539115.526
110.65420.1597-0.22210.56270.5240.7135-0.0649-0.17070.12560.14650.0995-0.1317-0.19410.136100.2195-0.0175-0.00230.249-0.02610.3002191.608640.9483131.187
120.2882-0.00340.18860.3674-0.28530.3237-0.068-0.1097-0.0085-0.0139-0.10440.07770.0398-0.145600.2233-0.0455-0.00090.26-0.00950.3456183.65541.361129.1507
130.24370.05130.00170.0414-0.08480.1202-0.07770.22760.3823-0.2291-0.0445-0.0977-0.0189-0.16240.00250.2123-0.01720.02360.1750.08430.2882192.99338.1593116.7582
141.3418-0.34280.41772.73560.45420.2437-0.04650.5237-0.5303-0.04640.2778-0.3642-0.1960.24390.02230.19860.01650.01510.1167-0.00810.2699183.984738.3443115.9383
150.29650.23090.20280.17710.15650.1245-0.04510.1887-0.3659-0.01850.15820.45910.0706-0.0619-00.21230.0267-0.01850.2510.00490.2477186.30831.4983118.6764
160.08570.03980.07210.0150.03250.0582-0.15840.3553-0.2242-0.5888-0.0714-0.3811-0.415-0.1534-00.387-0.00460.05840.31940.00140.4387181.032351.4633115.3323
170.7487-0.7276-0.43511.2064-0.01890.65560.00810.64340.2729-0.0048-0.1046-0.2185-0.48130.2762-0.03070.1481-0.0471-0.01690.2173-0.02350.3774197.583748.0542120.9474
180.184-0.0707-0.10240.1481-0.12480.2386-0.08310.1561-0.1163-0.35930.0027-0.19110.01570.039-00.3058-0.01490.04020.2743-0.01020.3153195.892235.163109.9912
190.21620.20490.29990.31420.01350.7670.0240.2678-0.1955-0.06380.1451-0.13860.05920.0334-00.4117-0.02330.00860.298-0.04170.2938156.447734.429792.8141
200.4757-0.4781-0.01160.42720.29991.44760.15180.2739-0.1641-0.2337-0.21780.16350.1087-0.1977-00.2995-0.0052-0.04210.27810.00130.3232144.679137.6123106.8752
210.14470.16250.30970.56640.32660.5818-0.0679-0.16980.07660.0850.12420.0971-0.101-0.408200.25920.0006-0.01010.28710.02660.2385144.115441.3816109.0417
220.2916-0.4135-0.07480.41790.09390.07450.0666-0.1488-0.04950.4141-0.2407-0.1996-0.10420.1777-00.3966-0.0465-0.01180.34320.01260.2748151.251338.6894113.4038
230.66980.0569-0.01720.0271-0.20280.58430.17330.08190.2551-0.1299-0.1323-0.3926-0.15580.0898-0.00010.25860.01520.02170.1641-0.01570.2331158.091244.3377102.8548
240.1924-0.0483-0.09750.0390.00540.2185-0.36360.274-0.0471-0.01290.1712-0.0611-0.10970.169200.4496-0.027-0.00970.2879-0.01750.2994157.468429.6726103.3964
250.0825-0.1252-0.10810.24450.08050.21380.11810.25210.0594-0.3138-0.0228-0.1470.0304-0.121-00.43220.03990.06180.3045-0.00450.2615158.163844.434891.9377
260.6994-0.3718-0.10190.5041-0.38020.54790.37320.49950.1633-0.0654-0.05220.0633-0.1874-0.28770.01620.43240.01770.00610.60870.01680.2479157.0288-2.15145.3368
270.5204-0.38940.57560.2715-0.42730.6227-0.11190.08160.1445-0.08650.09390.0864-0.1385-0.246100.2397-0.0448-0.00240.3416-0.06660.2349156.0849-3.8645159.8813
280.463-0.1089-0.20680.3494-0.26820.6881-0.00240.0977-0.0318-0.04570.0266-0.1232-0.040.0985-00.2581-0.04150.01540.30460.00250.2394164.0924-1.8915167.5489
290.4811-0.6512-0.05160.8952-0.06370.39060.0964-0.0187-0.0165-0.0225-0.00730.0992-0.04330.0081-00.3296-0.05140.0090.3609-0.03770.2332159.8922-9.3322159.8259
301.10760.65681.16830.46780.47791.31550.02930.2754-0.185-0.0647-0.0401-0.06540.0657-0.0132-0.00020.3212-0.08390.01510.36-0.00020.2385158.9865-11.163153.4948
310.56150.03890.06670.4568-0.10390.15220.03850.648-0.1925-0.6223-0.1139-0.24690.11890.1983-0.01250.4818-0.06470.0070.496-0.05510.2558166.5904-6.5109143.8556
321.40060.5231-0.36250.52030.62684.2107-0.287-0.2984-0.14420.1249-0.08030.26730.9022-0.6076-0.15730.1919-0.10230.00130.6217-0.04020.3847146.056917.7007168.4625
330.8190.0675-0.83981.08430.53511.8644-0.0363-0.0626-0.1509-0.07690.0813-0.04510.1273-0.260500.2239-0.00750.02310.28320.01470.2068163.658919.609159.0038
340.7993-0.0966-0.25940.863-0.58040.9183-0.106-0.18160.22520.16150.04620.0479-0.0632-0.4969-0.00310.19910.04760.02380.3347-0.00870.2169153.991225.9964165.8724
350.6009-0.14840.38850.1050.07440.4713-0.128-0.55390.42160.36430.12820.2941-0.0333-0.68080.00260.3471-0.01880.05060.63430.02810.4417150.925321.2114176.4854
360.76230.2170.00110.67120.3590.2151-0.15370.22720.0489-0.33820.0186-0.3831-0.12790.4387-00.3142-0.05870.00260.37880.04560.4156184.242644.6035163.7726
370.15210.147-0.15780.1861-0.14810.1267-0.09180.1255-0.09650.07280.1049-0.1909-0.0686-0.120900.3140.0616-0.05850.28950.01040.4091172.063245.037171.4555
380.27790.291-0.01080.2642-0.05750.5608-0.1068-0.14080.1117-0.18830.03460.1101-0.34750.0076-00.2790.0214-0.07190.2818-0.00820.3922174.516532.2788182.2894
390.1567-0.15730.02891.64090.65640.3854-0.04790.05110.06680.0071-0.0746-0.0072-0.073-0.1941-00.25280.0472-0.02830.30040.0130.3023171.168238.152168.0999
400.3795-0.1440.17970.3354-0.3460.3568-0.05410.25330.0441-0.4938-0.0304-0.1731-0.1680.215100.3274-0.03420.01710.38270.03740.4034183.416138.97160.1167
410.60530.28020.64090.16780.33890.6142-0.07830.3272-0.0215-0.2391-0.00470.1380.3088-0.1924-00.47660.0308-0.09970.5576-0.08520.4486123.704235.5293134.4852
420.3749-0.11180.34290.1330.09740.5273-0.0749-0.0222-0.21650.3341-0.03470.35290.1332-0.0449-00.32360.0229-0.0010.34980.04910.407120.242340.1708152.2721
430.38360.38330.40770.33560.36110.3704-0.065-0.2669-0.0601-0.0035-0.13550.24990.28960.040900.35650.0464-0.01470.31780.04720.3496122.869948.3689148.6717
440.46230.36980.08351.05860.58540.94520.0338-0.1695-0.1970.038-0.0629-0.1106-0.04260.3512-0.00260.24840.0826-0.02840.30350.06290.276131.768440.5076145.3427
450.4030.018-0.01030.31450.18360.4417-0.00380.2933-0.2148-0.09860.02480.0430.25380.0948-00.51010.036-0.09480.4636-0.06290.3823127.077641.1022132.8974
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 22 )A1 - 22
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 58 )A23 - 58
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 140 )A59 - 140
4X-RAY DIFFRACTION4chain 'A' and (resid 141 through 160 )A141 - 160
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 33 )B1 - 33
6X-RAY DIFFRACTION6chain 'B' and (resid 34 through 106 )B34 - 106
7X-RAY DIFFRACTION7chain 'B' and (resid 107 through 140 )B107 - 140
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 160 )B141 - 160
9X-RAY DIFFRACTION9chain 'C' and (resid 1 through 10 )C1 - 10
10X-RAY DIFFRACTION10chain 'C' and (resid 11 through 26 )C11 - 26
11X-RAY DIFFRACTION11chain 'C' and (resid 27 through 81 )C27 - 81
12X-RAY DIFFRACTION12chain 'C' and (resid 82 through 96 )C82 - 96
13X-RAY DIFFRACTION13chain 'C' and (resid 97 through 106 )C97 - 106
14X-RAY DIFFRACTION14chain 'C' and (resid 107 through 114 )C107 - 114
15X-RAY DIFFRACTION15chain 'C' and (resid 115 through 126 )C115 - 126
16X-RAY DIFFRACTION16chain 'C' and (resid 127 through 133 )C127 - 133
17X-RAY DIFFRACTION17chain 'C' and (resid 134 through 140 )C134 - 140
18X-RAY DIFFRACTION18chain 'C' and (resid 141 through 160 )C141 - 160
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 22 )D1 - 22
20X-RAY DIFFRACTION20chain 'D' and (resid 23 through 58 )D23 - 58
21X-RAY DIFFRACTION21chain 'D' and (resid 59 through 81 )D59 - 81
22X-RAY DIFFRACTION22chain 'D' and (resid 82 through 96 )D82 - 96
23X-RAY DIFFRACTION23chain 'D' and (resid 97 through 126 )D97 - 126
24X-RAY DIFFRACTION24chain 'D' and (resid 127 through 139 )D127 - 139
25X-RAY DIFFRACTION25chain 'D' and (resid 140 through 160 )D140 - 160
26X-RAY DIFFRACTION26chain 'E' and (resid 1 through 22 )E1 - 22
27X-RAY DIFFRACTION27chain 'E' and (resid 23 through 45 )E23 - 45
28X-RAY DIFFRACTION28chain 'E' and (resid 46 through 81 )E46 - 81
29X-RAY DIFFRACTION29chain 'E' and (resid 82 through 106 )E82 - 106
30X-RAY DIFFRACTION30chain 'E' and (resid 107 through 140 )E107 - 140
31X-RAY DIFFRACTION31chain 'E' and (resid 141 through 160 )E141 - 160
32X-RAY DIFFRACTION32chain 'F' and (resid 1 through 22 )F1 - 22
33X-RAY DIFFRACTION33chain 'F' and (resid 23 through 96 )F23 - 96
34X-RAY DIFFRACTION34chain 'F' and (resid 97 through 139 )F97 - 139
35X-RAY DIFFRACTION35chain 'F' and (resid 140 through 160 )F140 - 160
36X-RAY DIFFRACTION36chain 'G' and (resid 1 through 26 )G1 - 26
37X-RAY DIFFRACTION37chain 'G' and (resid 27 through 45 )G27 - 45
38X-RAY DIFFRACTION38chain 'G' and (resid 46 through 58 )G46 - 58
39X-RAY DIFFRACTION39chain 'G' and (resid 59 through 133 )G59 - 133
40X-RAY DIFFRACTION40chain 'G' and (resid 134 through 160 )G134 - 160
41X-RAY DIFFRACTION41chain 'H' and (resid 1 through 26 )H1 - 26
42X-RAY DIFFRACTION42chain 'H' and (resid 27 through 67 )H27 - 67
43X-RAY DIFFRACTION43chain 'H' and (resid 68 through 81 )H68 - 81
44X-RAY DIFFRACTION44chain 'H' and (resid 82 through 133 )H82 - 133
45X-RAY DIFFRACTION45chain 'H' and (resid 134 through 160 )H134 - 160

+
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