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

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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 / permeabilization of host organelle membrane involved in viral entry into host cell / host cytoskeleton / viral outer capsid / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
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 / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...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 / Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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