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- PDB-6ut9: Crystal structure of the carbohydrate-binding domain VP8* of huma... -

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Basic information

Entry
Database: PDB / ID: 6ut9
TitleCrystal structure of the carbohydrate-binding domain VP8* of human P[4] rotavirus strain BM5265
ComponentsOuter capsid protein VP4
KeywordsVIRUS / Rotavirus / host receptor interaction
Function / homology
Function and homology information


host cytoskeleton / viral outer capsid / symbiont entry into host cell via permeabilization of host membrane / host cell endoplasmic reticulum / virion attachment to host cell / host cell plasma membrane
Similarity search - Function
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 speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsXu, S. / Stuckert, M. / Burnside, R. / McGinnis, K. / Jiang, X. / Kennedy, M.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Structural basis of P[II] rotavirus evolution and host ranges under selection of histo-blood group antigens.
Authors: Xu, S. / McGinnis, K.R. / Liu, Y. / Huang, P. / Tan, M. / Stuckert, M.R. / Burnside, R.E. / Jacob, E.G. / Ni, S. / Jiang, X. / Kennedy, M.A.
History
DepositionOct 29, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 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 VP4


Theoretical massNumber of molelcules
Total (without water)18,4811
Polymers18,4811
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.040, 32.448, 50.997
Angle α, β, γ (deg.)90.000, 94.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Outer capsid protein VP4


Mass: 18481.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Gene: VP4 / Production host: Escherichia coli (E. coli) / References: UniProt: E9BVI9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
PH range: 7.4-7.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2019
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.21→50.83 Å / Num. obs: 44980 / % possible obs: 95.1 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Rrim(I) all: 0.063 / Net I/σ(I): 10.5 / Num. measured all: 148616 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.21-1.270.4342199166920.850.2820.5212.597.6
3.82-50.830.034480814780.9980.0220.0427.193.7

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NIW

6niw


Resolution: 1.21→50.83 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.715 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.049
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2113 2356 5.2 %RANDOM
Rwork0.1873 ---
obs0.1886 42612 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 90.69 Å2 / Biso mean: 11.746 Å2 / Biso min: 6.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å2-0 Å2-0.56 Å2
2---0.34 Å2-0 Å2
3----0.34 Å2
Refinement stepCycle: final / Resolution: 1.21→50.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 0 138 1435
Biso mean---20.84 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131331
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181129
X-RAY DIFFRACTIONr_angle_refined_deg1.471.6461809
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5732634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3265160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57223.41879
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.31615210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.205157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021517
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02296
LS refinement shellResolution: 1.21→1.239 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.259 146 -
Rwork0.25 3229 -
obs--97.23 %

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