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- PDB-5ibv: Crystal Structure of Human Astrovirus capsid protein -

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Basic information

Entry
Database: PDB / ID: 5ibv
TitleCrystal Structure of Human Astrovirus capsid protein
ComponentsCapsid polyprotein VP90
KeywordsVIRAL PROTEIN / Astrovirus / Capsid
Function / homologyTurkey astrovirus capsid protein / Turkey astrovirus capsid protein / Capsid, astroviral / Astrovirus capsid protein nucleoplasmin-like domain / T=3 icosahedral viral capsid / Viral coat protein subunit / clathrin-dependent endocytosis of virus by host cell / identical protein binding / Capsid polyprotein VP90
Function and homology information
Biological speciesHuman astrovirus-8
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsTao, Y.J. / Toh, Y.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103777 United States
Welch FoundationC-1565 United States
CitationJournal: J.Virol. / Year: 2016
Title: Crystal Structure of the Human Astrovirus Capsid Protein.
Authors: Toh, Y. / Harper, J. / Dryden, K.A. / Yeager, M. / Arias, C.F. / Mendez, E. / Tao, Y.J.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization ..._citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _software.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid polyprotein VP90


Theoretical massNumber of molelcules
Total (without water)37,7731
Polymers37,7731
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.983, 59.236, 56.197
Angle α, β, γ (deg.)90.00, 91.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid polyprotein VP90


Mass: 37772.746 Da / Num. of mol.: 1 / Fragment: unp residues 71-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human astrovirus-8 / Gene: ORF2 / Plasmid: HSstV-8 CP71-415 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9IFX1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.3 Å3/Da / Density % sol: 46.55 % / Description: rod shape
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: VAPOR DIFFUSION, HANGING DROP, 0.2 M ammoium phosphate, 22% PEG 4000

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 18278 / % possible obs: 99.8 % / Redundancy: 4 % / CC1/2: 0.706 / Rmerge(I) obs: 0.066 / Net I/σ(I): 17.9
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→30 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2458 3573 10.14 %0.05
Rwork0.2095 ---
obs0.2132 35248 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2437 0 0 73 2510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012512
X-RAY DIFFRACTIONf_angle_d1.2073432
X-RAY DIFFRACTIONf_dihedral_angle_d13.4791479
X-RAY DIFFRACTIONf_chiral_restr0.071402
X-RAY DIFFRACTIONf_plane_restr0.008434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1554-2.18370.3283680.3524718X-RAY DIFFRACTION57
2.1837-2.21360.39011160.35181187X-RAY DIFFRACTION95
2.2136-2.24520.38531410.32151232X-RAY DIFFRACTION98
2.2452-2.27870.3311570.3081214X-RAY DIFFRACTION98
2.2787-2.31430.30861250.28441210X-RAY DIFFRACTION99
2.3143-2.35230.3051400.28411289X-RAY DIFFRACTION99
2.3523-2.39280.31561360.24971240X-RAY DIFFRACTION100
2.3928-2.43630.30311710.25451214X-RAY DIFFRACTION100
2.4363-2.48310.28211290.26211259X-RAY DIFFRACTION100
2.4831-2.53380.29341360.22941249X-RAY DIFFRACTION100
2.5338-2.58880.29141420.23841244X-RAY DIFFRACTION100
2.5888-2.6490.26581350.22391237X-RAY DIFFRACTION100
2.649-2.71520.31431540.23141274X-RAY DIFFRACTION100
2.7152-2.78860.33871450.20911210X-RAY DIFFRACTION100
2.7886-2.87060.21311290.20951246X-RAY DIFFRACTION100
2.8706-2.96320.26061430.20741249X-RAY DIFFRACTION100
2.9632-3.0690.26521440.21991252X-RAY DIFFRACTION100
3.069-3.19170.22821450.20541231X-RAY DIFFRACTION99
3.1917-3.33680.25281140.18971274X-RAY DIFFRACTION100
3.3368-3.51240.19591460.17561246X-RAY DIFFRACTION99
3.5124-3.73210.24141440.18421259X-RAY DIFFRACTION100
3.7321-4.01960.19121380.18751221X-RAY DIFFRACTION99
4.0196-4.42290.19571480.1641221X-RAY DIFFRACTION99
4.4229-5.06020.17831520.15181226X-RAY DIFFRACTION98
5.0602-6.36490.21951420.19031235X-RAY DIFFRACTION99
6.3649-29.62080.24081330.211238X-RAY DIFFRACTION99

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