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- PDB-2o1k: Structure of the extended diarrhea-inducing domain of rotavirus e... -

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Basic information

Entry
Database: PDB / ID: 2o1k
TitleStructure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein NSP4
ComponentsNon-structural glycoprotein NSP4
KeywordsVIRAL PROTEIN / Rotavirus Enterotoxin / Nonstructural protein / NSP4 / Tetrameric coiled-coil / virulence
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 / Non-structural glycoprotein 4
Similarity search - Component
Biological speciesSimian rotavirus A/SA11
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsDeepa, R. / Suguna, K. / Durga Rao, C.
CitationJournal: TO BE PUBLISHED
Title: Structure of the extended diarrhea-inducing domain of rotavirus enterotoxigenic protein
Authors: Deepa, R. / Durga Rao, C. / Suguna, K.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 25, 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 / struct_conn / struct_site
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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 / _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: Non-structural glycoprotein NSP4
B: Non-structural glycoprotein NSP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7113
Polymers12,6712
Non-polymers401
Water1,09961
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_665-x+1,-y+1,z1
Buried area8770 Å2
ΔGint-110 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.692, 38.090, 182.354
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
11B-501-

CA

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Components

#1: Protein Non-structural glycoprotein NSP4 / NS28


Mass: 6335.458 Da / Num. of mol.: 2 / Fragment: Diarrhea-inducing domain (residues 95-146)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian rotavirus A/SA11 / Species: Rotavirus A / Strain: SA11 / Gene: G10 / Plasmid: pET22(b)+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O92323, UniProt: P04512*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.5M lithium sulphate monohydrate, 0.1 HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2004 / Details: OSMIC mirror system
RadiationMonochromator: CU K alpha / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.67→15 Å / Num. obs: 12801 / % possible obs: 98.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 29.8
Reflection shellResolution: 1.67→1.76 Å / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 12.5 / Num. unique all: 1776 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1G1J

1g1j


Resolution: 1.67→15 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.9 / SU B: 2.54 / SU ML: 0.044 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23318 623 4.9 %RANDOM
Rwork0.18764 ---
obs0.18973 12178 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.67→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 1 61 762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022734
X-RAY DIFFRACTIONr_bond_other_d0.0010.02759
X-RAY DIFFRACTIONr_angle_refined_deg1.1171.998985
X-RAY DIFFRACTIONr_angle_other_deg0.76531756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.403592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.02823.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49915171
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4051510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2123
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02776
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_nbd_refined0.1990.2196
X-RAY DIFFRACTIONr_nbd_other0.1480.2760
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2359
X-RAY DIFFRACTIONr_nbtor_other0.0810.2473
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2080.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.5468
X-RAY DIFFRACTIONr_mcbond_other0.2391.5180
X-RAY DIFFRACTIONr_mcangle_it1.4462722
X-RAY DIFFRACTIONr_scbond_it2.2783300
X-RAY DIFFRACTIONr_scangle_it3.4594.5259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 46 -
Rwork0.181 812 -
obs--90.99 %
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)
12.23750.3563-2.68291.63830.916311.9687-0.03320.2073-0.0943-0.23960.0309-0.079-0.010.14980.0023-0.03230.00450.0177-0.0245-0.0054-0.026814.766813.1891125.5035
21.89620.5906-0.58322.5731-3.703112.5148-0.10190.3390.0371-0.21380.0282-0.19320.23770.07820.0737-0.0451-0.00040.0321-0.0261-0.0016-0.018221.558117.9673126.2008
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA95 - 1371 - 43
2X-RAY DIFFRACTION2BB95 - 1371 - 43

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