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- PDB-7c8p: Structural and functional characterization of human group A rotav... -

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Basic information

Entry
Database: PDB / ID: 7c8p
TitleStructural and functional characterization of human group A rotavirus P[25] VP8*
ComponentsOuter capsid protein VP4
KeywordsPROTEIN BINDING / human P[25] rotavirus / glycan binding specificity / VP8* / histo-blood group antigen (HBGA)
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
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 / 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: 2.6 Å
AuthorsDuan, Z. / Dandi, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2018ZX10711-001 China
National Natural Science Foundation of China (NSFC)21934005 China
CitationJournal: Virology / Year: 2021
Title: Human group A rotavirus P[25] VP8* specifically binds to A-type histo-blood group antigen.
Authors: Li, D. / Wang, M. / Qi, J. / Zhang, Q. / Wang, H. / Pang, L. / Sun, X. / Duan, Z.
History
DepositionJun 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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

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Assembly

Deposited unit
A: Outer capsid protein VP4
B: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)36,9272
Polymers36,9272
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-5 kcal/mol
Surface area14030 Å2
Unit cell
Length a, b, c (Å)164.419, 164.419, 164.419
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Outer capsid protein VP4 / Hemagglutinin


Mass: 18463.637 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: M1GR78
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 5.02 Å3/Da / Density % sol: 75.48 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 2.0 M ammonium sulfate, 0.1 M sodium HEPES pH 7.5, and 2% v/v polyethylene glycol 400

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Data collection

DiffractionMean temperature: 118 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 23849 / % possible obs: 99.3 % / Redundancy: 8.6 % / Biso Wilson estimate: 43.79 Å2 / Rmerge(I) obs: 0.185 / Rsym value: 0.185 / Net I/σ(I): 11.968
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3.077 / Num. unique obs: 23849 / Rsym value: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DRV

4drv


Resolution: 2.6→49.574 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2156 1214 5.11 %
Rwork0.197 22551 -
obs0.198 23765 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.65 Å2 / Biso mean: 40.1347 Å2 / Biso min: 25.5 Å2
Refinement stepCycle: final / Resolution: 2.6→49.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 0 150 2744
Biso mean---41.35 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042658
X-RAY DIFFRACTIONf_angle_d0.7173626
X-RAY DIFFRACTIONf_chiral_restr0.046400
X-RAY DIFFRACTIONf_plane_restr0.004466
X-RAY DIFFRACTIONf_dihedral_angle_d16.509954
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.70380.3021170.259247799
2.7038-2.82680.30121280.24112443100
2.8268-2.97580.28881240.23472480100
2.9758-3.16220.27151480.22432474100
3.1622-3.40640.23691280.19942503100
3.4064-3.7490.191530.1872486100
3.749-4.29130.20711320.16822519100
4.2913-5.40550.16751350.1583254099
5.4055-5.40550.20021490.2002262996
Refinement TLS params.

S33: 0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41390.4063-0.02710.43050.00110.2550.0034-0.01050.0015-0.0083-0.0271-0.0181-0.02390.00970.3210.02110.00940.30380.01430.3183-22.71369.7723-6.7824
20.41090.06730.03590.35510.07010.3596-0.0049-0.04010.0607-0.05020.00290.01030.0777-0.07140.3273-0.01260.00370.31270.03730.2923-37.2507-4.202-23.955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 161 )A1 - 161
2X-RAY DIFFRACTION2chain 'B' and (resid 1 through 161 )B1 - 161

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