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- PDB-4wba: Q/E mutant SA11 NSP4_CCD -

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Basic information

Entry
Database: PDB / ID: 4wba
TitleQ/E mutant SA11 NSP4_CCD
ComponentsNon-structural glycoprotein NSP4
KeywordsVIRAL PROTEIN / Nonstructural protein / Enterotoxin / CCD / Ca2+-binding mutant
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
PHOSPHATE ION / Non-structural glycoprotein 4
Similarity search - Component
Biological speciesSimian rotavirus A/SA11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsViskovska, M. / Sastri, N.P. / Hyser, J.M. / Tanner, M.R. / Horton, L.B. / Sankaran, B. / Prasad, B.V.V. / Estes, M.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080656 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI36040 United States
CitationJournal: J.Virol. / Year: 2014
Title: Structural Plasticity of the Coiled-Coil Domain of Rotavirus NSP4.
Authors: Sastri, N.P. / Viskovska, M. / Hyser, J.M. / Tanner, M.R. / Horton, L.B. / Sankaran, B. / Prasad, B.V. / Estes, M.K.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural glycoprotein NSP4
B: Non-structural glycoprotein NSP4
C: Non-structural glycoprotein NSP4
D: Non-structural glycoprotein NSP4
E: Non-structural glycoprotein NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3818
Polymers31,1025
Non-polymers2793
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11530 Å2
ΔGint-123 kcal/mol
Surface area10600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.857, 53.469, 52.543
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Non-structural glycoprotein NSP4


Mass: 6220.371 Da / Num. of mol.: 5 / Fragment: UNP residues 95-146 / Mutation: E120A, Q123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A/SA11 / Plasmid: pET46Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O92323
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 1.79 Å3/Da / Density % sol: 31.32 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.2 / Details: 10%w/v PEG 8000, 0.2M NaCl, 0.1M Na/K PO4 (pH 6.2)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.799→28.24 Å / Num. obs: 20053 / % possible obs: 99.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.21

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O1K

2o1k


Resolution: 1.799→28.24 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2369 1029 5.14 %
Rwork0.1874 --
obs0.1899 20035 97.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.799→28.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 17 330 1985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061652
X-RAY DIFFRACTIONf_angle_d0.9232204
X-RAY DIFFRACTIONf_dihedral_angle_d11.892659
X-RAY DIFFRACTIONf_chiral_restr0.034275
X-RAY DIFFRACTIONf_plane_restr0.004270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.89350.25471490.20192328X-RAY DIFFRACTION85
1.8935-2.01220.24731320.19662733X-RAY DIFFRACTION99
2.0122-2.16750.23871410.18232784X-RAY DIFFRACTION100
2.1675-2.38550.21831640.17272755X-RAY DIFFRACTION100
2.3855-2.73040.22051450.17072772X-RAY DIFFRACTION100
2.7304-3.43910.25051520.18812799X-RAY DIFFRACTION100
3.4391-28.24670.23861460.19842835X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.11250.9228-4.60320.6602-1.32045.37880.0357-0.19970.18370.12120.0777-0.0609-0.0370.3726-0.07280.1603-0.0002-0.05570.1293-0.010.1498-11.73773.1428-16.304
26.0251-0.6571-5.63950.55710.78275.8572-0.26160.0657-0.09550.12610.12570.04010.32810.00670.06120.1652-0.0049-0.03870.0688-0.00890.1422-16.4454-9.9614-22.1161
37.53480.8685-6.6390.75-0.3416.9385-0.2342-0.4739-0.10260.07610.0725-0.07520.35570.6190.10980.13230.0593-0.06020.12840.01270.1228-10.7207-5.7644-16.0649
42.8911-0.1553-4.11520.6641-0.13068.32030.16130.08960.28170.06610.1966-0.0448-0.0715-0.2717-0.28950.15990.0059-0.05410.01180.00970.1558-18.28925.1579-23.3798
53.5089-1.3895-4.17870.67750.98694.3932-0.08720.25510.02210.02740.01990.02560.1616-0.34210.08370.144-0.0023-0.04910.1376-0.01520.1473-21.5704-2.9539-26.0146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 95 through 136 )
2X-RAY DIFFRACTION2chain 'B' and (resid 95 through 135 )
3X-RAY DIFFRACTION3chain 'C' and (resid 95 through 135 )
4X-RAY DIFFRACTION4chain 'D' and (resid 95 through 135 )
5X-RAY DIFFRACTION5chain 'E' and (resid 95 through 136 )

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