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- PDB-7rsw: Crystal structure of group B human rotavirus VP8* -

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Basic information

Entry
Database: PDB / ID: 7rsw
TitleCrystal structure of group B human rotavirus VP8*
Components
  • Outer capsid protein VP4
  • peptide
KeywordsSTRUCTURAL PROTEIN / Rotavirus / capsid / glycan-binding
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
Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus B
Rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.32 Å
AuthorsHu, L. / Salmen, W. / Sankaran, B. / Prasad, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI36040 United States
CitationJournal: Commun Biol / Year: 2022
Title: Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography.
Authors: Hu, L. / Salmen, W. / Sankaran, B. / Lasanajak, Y. / Smith, D.F. / Crawford, S.E. / Estes, M.K. / Prasad, B.V.V.
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release

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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: peptide


Theoretical massNumber of molelcules
Total (without water)37,4963
Polymers37,4963
Non-polymers00
Water5,134285
1
A: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,6111
Polymers18,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)18,6111
Polymers18,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: peptide


  • defined by author&software
  • 274 Da, 1 polymers
Theoretical massNumber of molelcules
Total (without water)2741
Polymers2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.277, 116.257, 31.312
Angle α, β, γ (deg.)90.000, 103.537, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Outer capsid protein VP4 / Hemagglutinin


Mass: 18610.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus B (isolate RVB/Human/China/ADRV/1982)
Strain: isolate RVB/Human/China/ADRV/1982 / Gene: VP4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H0USR8
#2: Protein/peptide peptide /


Mass: 274.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rotavirus
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 30% PEG 2000 MME, 0.1 M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.32→30.41 Å / Num. obs: 41757 / % possible obs: 82.69 % / Redundancy: 1.9 % / Biso Wilson estimate: 13.24 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.03
Reflection shellResolution: 1.32→1.34 Å / Rmerge(I) obs: 0.262 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 1675

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.32→30.41 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.1923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2083 2012 4.82 %
Rwork0.1573 39743 -
obs0.1598 41755 82.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 1.32→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 285 2199
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00471947
X-RAY DIFFRACTIONf_angle_d0.83472653
X-RAY DIFFRACTIONf_chiral_restr0.0805330
X-RAY DIFFRACTIONf_plane_restr0.0052331
X-RAY DIFFRACTIONf_dihedral_angle_d6.501261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.360.3463570.2287950X-RAY DIFFRACTION28.03
1.36-1.390.26931010.19511814X-RAY DIFFRACTION53.88
1.39-1.430.26931330.16482517X-RAY DIFFRACTION72.27
1.43-1.480.24831440.15782955X-RAY DIFFRACTION86.81
1.48-1.530.21741500.15043143X-RAY DIFFRACTION92.01
1.53-1.590.24671660.14993192X-RAY DIFFRACTION93.77
1.59-1.670.19291300.15083266X-RAY DIFFRACTION93.25
1.67-1.750.20611730.14843198X-RAY DIFFRACTION93.56
1.75-1.860.23781620.13993173X-RAY DIFFRACTION93.03
1.86-2.010.15441770.13393159X-RAY DIFFRACTION92.67
2.01-2.210.15821550.14123126X-RAY DIFFRACTION90.89
2.21-2.530.22691470.15373134X-RAY DIFFRACTION90.89
2.53-3.190.20661580.17343101X-RAY DIFFRACTION89.71
3.19-30.410.21531590.16773015X-RAY DIFFRACTION86.91

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