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- PDB-2b4h: Crystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Dimer -

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Basic information

Entry
Database: PDB / ID: 2b4h
TitleCrystal Structure of the Rhesus Rotavirus VP5 Antigen Domain Dimer
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / BETA SANDWICH / GREEK KEY / MEMBRANE PENETRATION PROTEIN / NON-ENVELOPED VIRUS / SPIKE PROTEIN / REARRANGEMENT
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
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Outer capsid protein VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYoder, J.D. / Dormitzer, P.R.
CitationJournal: Embo J. / Year: 2006
Title: Alternative intermolecular contacts underlie the rotavirus VP5(*) two- to three-fold rearrangement
Authors: Yoder, J.D. / Dormitzer, P.R.
History
DepositionSep 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6447
Polymers57,0502
Non-polymers5955
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-48 kcal/mol
Surface area20490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.356, 54.805, 65.734
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Outer capsid protein VP4


Mass: 28524.771 Da / Num. of mol.: 2 / Fragment: VP5* Antigen Domain
Source method: isolated from a genetically manipulated source
Details: see remark 400 / Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Gene: GENOME SEGMENT 4 / Plasmid: pFastBac-1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q91HI9, UniProt: P12473*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2.33 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Tris, sodium chloride, EDTA, MPD, Glycerol, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9998 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2004
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.6→70 Å / Num. all: 73654 / Num. obs: 73654 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 19.767 Å2 / Rsym value: 0.04 / Net I/σ(I): 28.36
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 4.36 % / Mean I/σ(I) obs: 4.54 / Num. unique all: 3601 / Rsym value: 0.294 / % possible all: 69.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Residues 267-470 of VP5CT (1SLQ)

1slq


Resolution: 1.6→45.5 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2245 3727 -RANDOM
Rwork0.2028 ---
all0.2039 73654 --
obs0.2039 73654 93.6 %-
Displacement parametersBiso mean: 32.0273 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.6→45.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3535 0 40 418 3993
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012039
X-RAY DIFFRACTIONc_angle_deg1.61123
LS refinement shellResolution: 1.6→1.66 Å
RfactorNum. reflection% reflection
Rfree0.3021 293 -
Rwork0.2837 --
obs-5515 70.9 %

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