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

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Basic information

Entry
Database: PDB / ID: 5ymu
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 speciesPorcine rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSun, X. / Duan, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81472003; 31500139 China
CitationJournal: J. Virol. / Year: 2018
Title: Glycan Binding Specificity and Mechanism of Human and Porcine P[6]/P[19] Rotavirus VP8*s.
Authors: Sun, X. / Li, D. / Qi, J. / Chai, W. / Wang, L. / Wang, L. / Peng, R. / Wang, H. / Zhang, Q. / Pang, L. / Kong, X. / Wang, H. / Jin, M. / Gao, G.F. / Duan, Z.
History
DepositionOct 22, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3317
Polymers74,0544
Non-polymers2763
Water12,466692
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6062
Polymers18,5141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6062
Polymers18,5141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6062
Polymers18,5141
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,5141
Polymers18,5141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.396, 131.396, 123.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-417-

HOH

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Components

#1: Protein
Outer capsid protein VP4 / P[6] VP8*


Mass: 18513.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine rotavirus A
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A2U8JDD5*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES monohydrate pH 6.0, 25% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97775 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. obs: 74097 / % possible obs: 100 % / Redundancy: 10.5 % / Net I/σ(I): 21.895

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GJ6

5gj6


Resolution: 1.8→41.86 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 19.03
RfactorNum. reflection% reflection
Rfree0.189 3701 5.03 %
Rwork0.166 --
obs0.168 73566 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5236 0 18 692 5946
Refinement TLS params.Method: refined / Origin x: 36.3251 Å / Origin y: -37.9375 Å / Origin z: 25.8261 Å
111213212223313233
T0.0558 Å20.0033 Å20.006 Å2-0.0714 Å20.0079 Å2--0.0777 Å2
L0.2469 °2-0.0235 °20.0128 °2-0.1279 °20.1143 °2--0.2605 °2
S0.0308 Å °0.0166 Å °0.0013 Å °-0.032 Å °-0.0068 Å °0.0106 Å °-0.0154 Å °-0.0381 Å °0.0578 Å °
Refinement TLS groupSelection details: ALL

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