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- PDB-4wb4: wt SA11 NSP4_CCD -

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Basic information

Entry
Database: PDB / ID: 4wb4
Titlewt SA11 NSP4_CCD
ComponentsNon-structural glycoprotein NSP4
KeywordsVIRAL PROTEIN / Nonstructural protein / enterotoxin / Ca2+-binding protein
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 speciesSimian rotavirus A/SA11
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 ...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 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7113
Polymers12,6712
Non-polymers401
Water70339
1
A: Non-structural glycoprotein NSP4
B: Non-structural glycoprotein NSP4
hetero molecules

A: Non-structural glycoprotein NSP4
B: Non-structural glycoprotein NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4226
Polymers25,3424
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area7720 Å2
ΔGint-112 kcal/mol
Surface area8750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.970, 35.720, 178.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-201-

CA

21A-312-

HOH

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Components

#1: Protein Non-structural glycoprotein NSP4


Mass: 6335.458 Da / Num. of mol.: 2 / Fragment: UNP residues 95-146
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 38.95 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 25% w/v PEG 1500, 0.1M MIB buffer (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.03→44.71 Å / Num. obs: 6998 / % possible obs: 99.3 % / Redundancy: 2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 13.4

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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: 2.03→44.71 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2764 330 4.72 %
Rwork0.234 --
obs0.2361 6985 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms628 0 1 39 668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008626
X-RAY DIFFRACTIONf_angle_d0.93839
X-RAY DIFFRACTIONf_dihedral_angle_d15.95241
X-RAY DIFFRACTIONf_chiral_restr0.037109
X-RAY DIFFRACTIONf_plane_restr0.004103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.55760.2651630.21143239X-RAY DIFFRACTION99
2.5576-44.72080.27961670.24093416X-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)
12.0812-0.1619-0.15874.6824-3.70792.9575-0.1435-0.2204-0.1210.14230.0195-0.31060.00130.17950.09520.3326-0.01050.02370.2647-0.0090.3503-10.08291.0813-34.9245
21.76471.0922-1.6763.0406-1.79537.28170.1035-0.29950.12630.19350.2907-0.01580.3181-0.0744-0.36910.29830.0694-0.010.2779-0.00750.3558-14.6027-5.9432-33.4822
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 136 )
2X-RAY DIFFRACTION2chain 'B' and (resid 95 through 135 )

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