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- PDB-9oft: Rotavirus NSP2 WT -

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Basic information

Entry
Database: PDB / ID: 9oft
TitleRotavirus NSP2 WT
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / Rotavirus / NSP2 / viral factory
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / viral genome replication / ribonucleoside triphosphate phosphatase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / : / : / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 35, N-terminal / Rotavirus non-structural protein 2
Similarity search - Domain/homology
Non-structural protein 2
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsHollis, T.J. / Nichols, S.L. / Esstman, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other privateDM United States
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2025
Title: K294E change in the rotavirus factory forming protein NSP2 stabilizes a rare C-terminal conformation.
Authors: Nichols, S.L. / Hollis, T. / Salsbury, F.R. / Esstman, S.M.
History
DepositionApr 30, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 2


Theoretical massNumber of molelcules
Total (without water)36,2351
Polymers36,2351
Non-polymers00
Water1267
1
A: Non-structural protein 2
x 8


Theoretical massNumber of molelcules
Total (without water)289,8798
Polymers289,8798
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_565x,-y+1,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area18770 Å2
ΔGint-77 kcal/mol
Surface area118220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.673, 108.673, 153.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Non-structural protein 2 / NSP2 / NCVP3 / Non-structural RNA-binding protein 35 / NS35


Mass: 36234.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Strain: SA11 / Gene: NSP2 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: A2T3N6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl pH 7.5, 0.2M MgAc, 12% PEG6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Apr 23, 2024 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.95→35 Å / Num. obs: 10045 / % possible obs: 100 % / Redundancy: 12.1 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.051 / Rrim(I) all: 0.179 / Χ2: 1.113 / Net I/σ(I): 5.6 / Num. measured all: 121329
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.95-3.0413.30.6018220.9340.9830.170.6251.061100
3.04-3.1313.30.5828220.9580.9890.1640.6050.98100
3.13-3.2513.20.3988060.9720.9930.1130.4140.968100
3.25-3.38130.3138210.9790.9950.090.3261.28100
3.38-3.53130.2138210.9910.9980.0610.2221.109100
3.53-3.72130.178200.9930.9980.0490.1771.181100
3.72-3.9512.70.1738240.9920.9980.050.1811.168100
3.95-4.2512.40.1568320.9940.9990.0460.1631.168100
4.25-4.6811.70.1438450.9930.9980.0430.1491.214100
4.68-5.3610.10.1088430.9950.9990.0360.1141.09399.9
5.36-6.74100.1098700.9960.9990.0350.1141.07799.9
6.74-359.70.0599190.99810.0190.0631.051100

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
HKL-3000data scaling
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→34.39 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.883 / SU B: 35.13 / SU ML: 0.281 / Cross valid method: THROUGHOUT / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26608 1001 10.1 %RANDOM
Rwork0.2281 ---
obs0.23186 8873 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.251 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0 Å2
2---0.73 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.95→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 0 7 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0172600
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162511
X-RAY DIFFRACTIONr_angle_refined_deg0.8221.8193511
X-RAY DIFFRACTIONr_angle_other_deg0.3231.5685783
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5845.17323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96810487
X-RAY DIFFRACTIONr_chiral_restr0.040.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022974
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02602
X-RAY DIFFRACTIONr_mcbond_it2.0362.961251
X-RAY DIFFRACTIONr_mcbond_other2.0352.961251
X-RAY DIFFRACTIONr_mcangle_it3.4395.331562
X-RAY DIFFRACTIONr_mcangle_other3.4385.331563
X-RAY DIFFRACTIONr_scbond_it1.9853.0141349
X-RAY DIFFRACTIONr_scbond_other1.9853.0141349
X-RAY DIFFRACTIONr_scangle_other3.3785.5021950
X-RAY DIFFRACTIONr_long_range_B_refined6.8234.3510524
X-RAY DIFFRACTIONr_long_range_B_other6.81934.3510525
LS refinement shellResolution: 2.95→3.023 Å
RfactorNum. reflection% reflection
Rfree0.463 95 -
Rwork0.368 610 -
obs--98.33 %
Refinement TLS params.Method: refined / Origin x: 42.731 Å / Origin y: 20.434 Å / Origin z: 18.723 Å
111213212223313233
T0.2277 Å2-0.0114 Å20.0052 Å2-0.0626 Å20.023 Å2--0.0888 Å2
L2.2624 °20.1483 °20.1593 °2-0.5233 °2-0.079 °2--0.7487 °2
S0.0821 Å °-0.063 Å °-0.4153 Å °0.0783 Å °-0.0383 Å °0.0357 Å °0.2236 Å °-0.0614 Å °-0.0438 Å °

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