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- PDB-5zhg: Human group C rotavirus VP8*s recognize type A histo-blood group ... -

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Basic information

Entry
Database: PDB / ID: 5zhg
TitleHuman group C rotavirus VP8*s recognize type A histo-blood group antigens as ligands
ComponentsOuter capsid protein VP8*
KeywordsVIRAL PROTEIN / group C rotavirus / VP8* / galactin-like / histo-blood group antigen.
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / 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
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus C
MethodX-RAY DIFFRACTION / Resolution: 1.799 Å
AuthorsSun, X. / Duan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81472003; 31500139;81601813 China
CitationJournal: J. Virol. / Year: 2018
Title: Human Group C Rotavirus VP8*s Recognize Type A Histo-Blood Group Antigens as Ligands.
Authors: Sun, X. / Wang, L. / Qi, J. / Li, D. / Wang, M. / Cong, X. / Peng, R. / Chai, W. / Zhang, Q. / Wang, H. / Wen, H. / Gao, G.F. / Tan, M. / Duan, Z.
History
DepositionMar 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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 VP8*


Theoretical massNumber of molelcules
Total (without water)18,7391
Polymers18,7391
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8490 Å2
Unit cell
Length a, b, c (Å)38.065, 40.070, 124.014
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer capsid protein VP8* / Hemagglutinin


Mass: 18738.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus C
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q82040
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: 0.1 M Sodium chloride, 0.1 M BIS-TRIS pH 6.5, 1.5 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SEALED TUBE / Type: Xenocs GeniX 3D Cu HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.799→50 Å / Num. obs: 18290 / % possible obs: 99.4 % / Redundancy: 10.3 % / Biso Wilson estimate: 20.43 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 21.019
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.565

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 1.799→38.129 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93
RfactorNum. reflection% reflection
Rfree0.204 930 5.1 %
Rwork0.1798 --
obs0.181 18222 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.49 Å2 / Biso mean: 23.6151 Å2 / Biso min: 10.07 Å2
Refinement stepCycle: final / Resolution: 1.799→38.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1320 0 0 208 1528
Biso mean---35.38 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041374
X-RAY DIFFRACTIONf_angle_d0.6971877
X-RAY DIFFRACTIONf_chiral_restr0.055199
X-RAY DIFFRACTIONf_plane_restr0.004241
X-RAY DIFFRACTIONf_dihedral_angle_d16.621482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7988-1.89360.37671220.35672355247796
1.8936-2.01220.21271470.1962404255199
2.0122-2.16760.1513980.166924552553100
2.1676-2.38570.19131410.161124722613100
2.3857-2.73080.21591390.179924592598100
2.7308-3.44020.19291290.169225232652100
3.4402-38.13760.1991540.170126242778100
Refinement TLS params.Method: refined / Origin x: 39.6356 Å / Origin y: 55.8409 Å / Origin z: 139.6974 Å
111213212223313233
T0.1256 Å20.0063 Å2-0.0006 Å2-0.1232 Å2-0.0046 Å2--0.1326 Å2
L0.4528 °2-0.1053 °2-0.0914 °2-0.4681 °20.189 °2--0.8616 °2
S0.0041 Å °0.0163 Å °-0.0043 Å °0.0336 Å °-0.0021 Å °-0.0015 Å °0.0232 Å °0.0086 Å °-0 Å °
Refinement TLS groupSelection details: all

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