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- PDB-5y2h: Crystal structure of the oligomerization domain of NSP4 from the ... -

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Basic information

Entry
Database: PDB / ID: 5y2h
TitleCrystal structure of the oligomerization domain of NSP4 from the rotavirus strain MF66
ComponentsNonstructural protein 4
KeywordsVIRAL PROTEIN / Antiparallel tetramer NSP4 Rotavirus Coiled-coil MF66
Function / homology
Function and homology information


host caveola / host cell rough endoplasmic reticulum membrane / protein complex oligomerization / monoatomic ion channel activity / toxin activity / induction by virus of host autophagy / extracellular region / membrane / metal ion binding
Similarity search - Function
Rotavirus non-structural protein 4 / Rotavirus non structural protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #430 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Non-structural glycoprotein 4
Similarity search - Component
Biological speciesBovine rotavirus G10
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSuguna, K. / Kumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT), Indian Institute of Science, (IISc) Partnership Program for Advanced Research in Biological Sciences and Bioengineering India
CitationJournal: Arch. Virol. / Year: 2018
Title: New tetrameric forms of the rotavirus NSP4 with antiparallel helices.
Authors: Kumar, S. / Ramappa, R. / Pamidimukkala, K. / Rao, C.D. / Suguna, K.
History
DepositionJul 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Nonstructural protein 4
A: Nonstructural protein 4
B: Nonstructural protein 4
C: Nonstructural protein 4


Theoretical massNumber of molelcules
Total (without water)24,6054
Polymers24,6054
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-88 kcal/mol
Surface area9910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.440, 87.440, 60.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

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Components

#1: Protein
Nonstructural protein 4


Mass: 6151.182 Da / Num. of mol.: 4 / Fragment: UNP residues 90-140
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine rotavirus G10 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6QT01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.8 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 299 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.1M Citric acid, pH 3.5, 3.0M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→75.73 Å / Num. obs: 8464 / % possible obs: 99.8 % / Redundancy: 5.9 % / CC1/2: 0.993 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.073 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
iMOSFLMdata processing
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→75.73 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.525 / ESU R Free: 0.299
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 430 5.1 %RANDOM
Rwork0.2348 ---
obs0.2362 8459 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 118.24 Å2 / Biso mean: 51.4056 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20.64 Å2-0 Å2
2--1.28 Å20 Å2
3----4.15 Å2
Refinement stepCycle: LAST / Resolution: 2.6→75.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1462 0 0 24 1486
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191462
X-RAY DIFFRACTIONr_bond_other_d00.021425
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.9911964
X-RAY DIFFRACTIONr_angle_other_deg3.44933270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71525.45566
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.71515305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.8821513
X-RAY DIFFRACTIONr_chiral_restr0.0680.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021573
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02244
X-RAY DIFFRACTIONr_mcbond_it6.9454.903748
X-RAY DIFFRACTIONr_mcbond_other6.9244.9747
X-RAY DIFFRACTIONr_mcangle_it9.1897.289928
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 24 -
Rwork0.325 587 -
all-611 -
obs--100 %

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