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- PDB-5y9r: Crystal structure of the oligomerization domain of NSP4 from rota... -

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Basic information

Entry
Database: PDB / ID: 5y9r
TitleCrystal structure of the oligomerization domain of NSP4 from rotavirus strain MF66
ComponentsNonstructural protein 4
KeywordsVIRAL PROTEIN / antiparallel / tetramer / coiled-coil / nickel bound
Function / homology
Function and homology information


host caveola / host cell rough endoplasmic reticulum membrane / viral process / channel activity / toxin activity / monoatomic ion transmembrane transport / symbiont-mediated activation of host autophagy / extracellular region / metal ion binding / membrane
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
: / NICKEL (II) ION / Non-structural glycoprotein 4
Similarity search - Component
Biological speciesBovine rotavirus G10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSuguna, K. / Kumar, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT)-Indian Institute of Science, Partnership program for advanced Research in Biological Science and Bioengineering India
CitationJournal: To Be Published
Title: New tetrameric forms of the rotavirus NSP4 with antiparallel helices
Authors: Suguna, K. / Kumar, S.
History
DepositionAug 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,07711
Polymers22,5994
Non-polymers4787
Water73941
1
B: Nonstructural protein 4
D: Nonstructural protein 4
C: Nonstructural protein 4
hetero molecules

A: Nonstructural protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,07711
Polymers22,5994
Non-polymers4787
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area5180 Å2
ΔGint-71 kcal/mol
Surface area12550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.120, 57.430, 62.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Nonstructural protein 4


Mass: 5649.737 Da / Num. of mol.: 4 / Fragment: UNP residues 95-139
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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 299 K / Method: microbatch / pH: 4.5
Details: 0.1M sodium acetate trihydrate, 24% PEG 2000, 10mM magnesium chloride, 10mM nickel chloride, 10mM cadmium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2015 / Details: bent collimating mirror and toroid
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→62.6 Å / Num. obs: 9675 / % possible obs: 98.8 % / Redundancy: 4.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.047 / Rrim(I) all: 0.079 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 821 / CC1/2: 0.875 / Rpim(I) all: 0.31 / Rrim(I) all: 0.52 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.595 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.06
RfactorNum. reflection% reflection
Rfree0.2384 473 4.88 %
Rwork0.2018 --
obs0.2036 9647 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1281 0 19 41 1341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051297
X-RAY DIFFRACTIONf_angle_d0.771736
X-RAY DIFFRACTIONf_dihedral_angle_d6.337908
X-RAY DIFFRACTIONf_chiral_restr0.046229
X-RAY DIFFRACTIONf_plane_restr0.004213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.33790.27031610.232792X-RAY DIFFRACTION98
2.3379-2.51830.26951630.21642767X-RAY DIFFRACTION98
2.5183-2.77170.26011450.19562808X-RAY DIFFRACTION98
2.7717-3.17260.28481470.20352800X-RAY DIFFRACTION98
3.1726-3.99660.19881040.18762844X-RAY DIFFRACTION98
3.9966-39.60140.22071420.20432782X-RAY DIFFRACTION97

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