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- PDB-5gvu: crystal structure of BVDV NS3 helicase domain -

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Basic information

Entry
Database: PDB / ID: 5gvu
Titlecrystal structure of BVDV NS3 helicase domain
ComponentsNS3 helicase
KeywordsHYDROLASE / helicase / NS3 / BVDV / flavivirus / pestivirus
Function / homology
Function and homology information


dopamine receptor binding / pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle ...dopamine receptor binding / pestivirus NS3 polyprotein peptidase / ribonuclease T2 / RNA stabilization / DNA/DNA annealing activity / serine-type exopeptidase activity / ribonuclease T2 activity / RNA strand annealing activity / viral genome packaging / host cell cytoplasmic vesicle / transformation of host cell by virus / ribonucleoside triphosphate phosphatase activity / protein-DNA complex / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / symbiont entry into host cell / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / ATP binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Cleavage inducing molecular chaperone, Jiv / : / Cleavage inducing molecular chaperone / Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase ...Cleavage inducing molecular chaperone, Jiv / : / Cleavage inducing molecular chaperone / Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / : / Flavivirus NS3 helicase, C-terminal helical domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesBovine viral diarrhea virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.82 Å
AuthorsLi, S. / Mao, X.
CitationJournal: To Be Published
Title: crystal structure of BVDV NS3 helicase
Authors: Shi, J. / He, M. / Nie, Y. / Li, S. / Mao, X.
History
DepositionSep 6, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS3 helicase
B: NS3 helicase
C: NS3 helicase


Theoretical massNumber of molelcules
Total (without water)159,8633
Polymers159,8633
Non-polymers00
Water68538
1
A: NS3 helicase


Theoretical massNumber of molelcules
Total (without water)53,2881
Polymers53,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS3 helicase


Theoretical massNumber of molelcules
Total (without water)53,2881
Polymers53,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS3 helicase


Theoretical massNumber of molelcules
Total (without water)53,2881
Polymers53,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.100, 121.100, 109.721
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein NS3 helicase


Mass: 53287.805 Da / Num. of mol.: 3 / Fragment: UNP residues 1939-2414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bovine viral diarrhea virus 1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9IFH8, UniProt: P19711*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium formate, 15% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→50.01 Å / Num. obs: 41208 / % possible obs: 100 % / Redundancy: 15 % / Rsym value: 0.144 / Net I/av σ(I): 4.332 / Net I/σ(I): 17.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.82-2.9715.30.4511.61100
2.97-3.1515.30.3132.31100
3.15-3.3715.20.2123.51100
3.37-3.6415.20.1564.71100
3.64-3.99150.1385.11100
3.99-4.4614.90.1295.31100
4.46-5.1514.20.1265.51100
5.15-6.3113.80.1195.7199.9
6.31-8.9215.50.0996.21100
8.92-48.60814.30.0897.3198.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å48.61 Å
Translation3.5 Å48.61 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SCALA3.3.22data scaling
PHASER2.5.7phasing
REFMAC5.8.0124refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
REFMAC5.8.0124refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CBG

4cbg


Resolution: 2.82→50.01 Å / Cor.coef. Fo:Fc: 0.826 / Cor.coef. Fo:Fc free: 0.777 / SU B: 37.438 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.3 / ESU R Free: 0.41 / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2984 2121 4.9 %RANDOM
Rwork0.2719 ---
obs0.2732 41208 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 134.76 Å2 / Biso mean: 56.857 Å2 / Biso min: 20.59 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20.5 Å20 Å2
2--1 Å2-0 Å2
3----3.23 Å2
Refinement stepCycle: final / Resolution: 2.82→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9414 0 0 38 9452
Biso mean---41.3 -
Num. residues----1186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0199582
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.97412952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08551171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73424.065433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.873151727
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1211568
X-RAY DIFFRACTIONr_chiral_restr0.0920.21468
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217126
X-RAY DIFFRACTIONr_mcbond_it0.7834.5224729
X-RAY DIFFRACTIONr_mcangle_it1.4796.7625885
X-RAY DIFFRACTIONr_scbond_it0.3174.4274853
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 130 -
Rwork0.307 3066 -
all-3196 -
obs--100 %
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)
10.1794-0.2594-0.07340.82360.35950.25210.04250.0191-0.0314-0.1762-0.0859-0.0343-0.0922-0.08220.04330.10020.11040.00320.1545-0.03320.0882-21.9898-65.0441-47.3427
20.76860.8315-0.47981.0466-0.26210.7635-0.0199-0.0425-0.0299-0.01430.0055-0.01370.0270.08950.01440.00360.010.0080.08310.03660.1405-40.7285-29.7712-12.1173
30.39250.18320.35640.10640.05621.1706-0.08010.05080.1175-0.046-0.0280.07110.07730.28770.10810.061-0.0023-0.01460.1321-0.0050.1004-49.0259-88.4564-8.9006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A208 - 683
2X-RAY DIFFRACTION2B208 - 683
3X-RAY DIFFRACTION3C208 - 683

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