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- PDB-7f0h: Structural and functional characterization of bovine G1P[5] rotav... -

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Basic information

Entry
Database: PDB / ID: 7f0h
TitleStructural and functional characterization of bovine G1P[5] rotavirus VP8* protein
ComponentsOuter capsid protein VP8*
KeywordsVIRAL PROTEIN / glycan binding specificity / sialic acid / histo-blood group antigen
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å
AuthorsDuan, Z. / Sun, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21934005 China
CitationJournal: Virology / Year: 2021
Title: Structural and functional characterization of bovine G1P[5] rotavirus VP8* protein.
Authors: Dang, L. / Su, Y. / Qi, J. / Wu, Z. / Li, D. / Wang, M. / Zhang, Q. / Wang, H. / Bai, R. / Duan, Z. / Sun, X.
History
DepositionJun 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein VP8*
B: Outer capsid protein VP8*


Theoretical massNumber of molelcules
Total (without water)36,1752
Polymers36,1752
Non-polymers00
Water8,629479
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-15 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.753, 102.364, 137.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

21A-394-

HOH

31A-425-

HOH

41B-206-

HOH

51B-318-

HOH

61B-414-

HOH

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Components

#1: Protein Outer capsid protein VP8*


Mass: 18087.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia phage Ecwhy_1 (virus) / References: UniProt: E2EA93
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 4.76 Å3/Da / Density % sol: 74.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.5 M ammonium sulfate, 0.1 M tri-sodium citrate dihydrate pH 5.6, 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.03923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03923 Å / Relative weight: 1
ReflectionResolution: 1.695→50 Å / Num. obs: 76163 / % possible obs: 98.54 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 24.004
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.874 / Mean I/σ(I) obs: 2.409 / Rsym value: 0.874

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDB

5jdb


Resolution: 1.695→31.806 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 3799 5.03 %
Rwork0.1667 71783 -
obs0.1678 75582 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 61.74 Å2 / Biso mean: 18.5166 Å2 / Biso min: 6.02 Å2
Refinement stepCycle: final / Resolution: 1.695→31.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 0 479 3023
Biso mean---30.65 -
Num. residues----322
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.695-1.71640.26351060.2583229485
1.7164-1.7390.26881310.2354249794
1.739-1.76280.22711140.2185258396
1.7628-1.7880.23341290.2049262297
1.788-1.81460.19731330.19260799
1.8146-1.8430.21741420.1924266199
1.843-1.87320.20441400.1917265099
1.8732-1.90550.2121400.19052675100
1.9055-1.94020.23671400.1993267999
1.9402-1.97750.19171380.1712264699
1.9775-2.01780.20071380.1661264999
2.0178-2.06170.18961420.16312687100
2.0617-2.10960.21451320.17222653100
2.1096-2.16240.18811570.1632673100
2.1624-2.22080.17291440.1652670100
2.2208-2.28620.23081250.18482706100
2.2862-2.35990.18471370.16252680100
2.3599-2.44430.2011480.16362681100
2.4443-2.54210.17961460.1657266599
2.5421-2.65770.19721550.16042699100
2.6577-2.79780.19541420.16652685100
2.7978-2.97290.18281430.16352716100
2.9729-3.20230.1661430.15172721100
3.2023-3.52420.16251690.14962698100
3.5242-4.03320.15011550.1428267499
4.0332-5.07810.16431420.1332781100
5.0781-31.8060.19281680.184283199

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