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- PDB-5mz4: Crystal Structure of full-lengh CSFV NS3/4A -

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Basic information

Entry
Database: PDB / ID: 5mz4
TitleCrystal Structure of full-lengh CSFV NS3/4A
ComponentsGenome polyprotein,Genome polyprotein
KeywordsVIRAL PROTEIN / Flaviviridae / NS3/NS4A / Protease/Helicase
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm ...pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / viral protein processing / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / GTP binding / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
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 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 / : / 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. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.048 Å
AuthorsTortorici, M.A. / Rey, F.A.
CitationJournal: PLoS Pathog. / Year: 2017
Title: A positive-strand RNA virus uses alternative protein-protein interactions within a viral protease/cofactor complex to switch between RNA replication and virion morphogenesis.
Authors: Dubrau, D. / Tortorici, M.A. / Rey, F.A. / Tautz, N.
History
DepositionJan 30, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 15, 2017ID: 5LKL
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Genome polyprotein,Genome polyprotein
B: Genome polyprotein,Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)167,3392
Polymers167,3392
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint0 kcal/mol
Surface area63750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.211, 168.839, 98.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Genome polyprotein,Genome polyprotein


Mass: 83669.328 Da / Num. of mol.: 2 / Fragment: UNP residues 2293-2329,UNP residues 1590-2280 / Mutation: S163A,S163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus (strain Alfort)
Strain: Alfort / Production host: Escherichia coli (E. coli)
References: UniProt: P19712, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, pestivirus NS3 polyprotein peptidase, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.16 Å3/Da / Density % sol: 61.07 % / Description: Two molecules in the asymmetric unit
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.6
Details: 12% PEG 3350 250 mM Tri-sodium citrate 100 mM 2-aminoethanesulfonic acid

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.95367 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95367 Å / Relative weight: 1
ReflectionResolution: 3.05→38.95 Å / Num. obs: 40242 / % possible obs: 98.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.2
Reflection shellResolution: 3.05→3.21 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5483 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on 1CU1

1cu1


Resolution: 3.048→38.948 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.06
RfactorNum. reflection% reflection
Rfree0.2327 1975 4.91 %
Rwork0.1934 --
obs0.1954 40185 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.048→38.948 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10788 0 0 10 10798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410992
X-RAY DIFFRACTIONf_angle_d0.71314864
X-RAY DIFFRACTIONf_dihedral_angle_d14.2886682
X-RAY DIFFRACTIONf_chiral_restr0.0481670
X-RAY DIFFRACTIONf_plane_restr0.0051920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0482-3.12440.3527560.32192371X-RAY DIFFRACTION84
3.1244-3.20890.32511950.28632664X-RAY DIFFRACTION98
3.2089-3.30320.294610.27222808X-RAY DIFFRACTION99
3.3032-3.40980.31481780.24472709X-RAY DIFFRACTION100
3.4098-3.53160.26822030.21942691X-RAY DIFFRACTION99
3.5316-3.67290.278560.20852885X-RAY DIFFRACTION100
3.6729-3.83990.28261940.19512716X-RAY DIFFRACTION100
3.8399-4.04220.21341440.17882746X-RAY DIFFRACTION99
4.0422-4.29510.19141580.17042765X-RAY DIFFRACTION99
4.2951-4.62630.19261410.14892772X-RAY DIFFRACTION99
4.6263-5.09090.19932080.1542716X-RAY DIFFRACTION99
5.0909-5.82550.20191590.17632770X-RAY DIFFRACTION98
5.8255-7.33150.22911060.19762830X-RAY DIFFRACTION98
7.3315-38.95080.2281660.18442767X-RAY DIFFRACTION93
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)
14.9875-0.11821.03023.87831.62213.5523-0.05950.7338-0.0161-0.2552-0.07220.37570.1377-0.60630.16660.413-0.16050.040.94940.00310.413-45.970929.2355-12.1019
22.948-1.1781.36554.0717-1.35393.1045-0.035-0.441-0.28641.60290.0193-0.45950.02920.4302-0.04991.2859-0.2028-0.22270.8025-0.04450.7526-33.597-1.1632.4804
35.70560.53560.66614.89090.99385.03520.0341-0.2960.24520.30910.2367-0.4357-0.13480.6797-0.22820.321-0.0760.00490.5131-0.07740.3805-18.496242.760117.4044
41.98770.18790.53891.6065-0.16621.2534-0.06340.12710.1804-0.01480.13510.3463-0.1001-0.3027-0.05220.3927-0.04180.02940.49240.11590.5657-82.43588.28165.8147
56.4865-0.2849-2.20933.46012.05327.7864-0.329-0.55460.27461.7361-0.2778-0.3717-0.81850.76410.36691.4606-0.0191-0.34950.806-0.04950.7535-34.337435.800449.891
65.355-2.05290.15033.5673-3.92486.34570.4663-0.0635-0.2349-0.0925-0.09780.56110.6256-0.3937-0.34481.1557-0.3874-0.16341.0776-0.14040.7314-32.90662.6782-30.891
74.86180.3879-2.16941.0809-0.34123.2718-0.12890.4729-0.2243-0.11630.1263-0.19980.3468-0.0834-0.01150.3772-0.07730.01210.4443-0.13160.4503-14.789124.2889-10.5552
85.3384-1.8648-0.9332.58620.63072.5088-0.0902-0.02520.17340.1391-0.042-0.01960.0168-0.23720.11350.321-0.1113-0.04070.45280.01050.329-49.824137.549420.3757
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 244:399)
2X-RAY DIFFRACTION2chain B and (resid 1:236 or resid 724:731)
3X-RAY DIFFRACTION3chain B and (resid 247:392)
4X-RAY DIFFRACTION4chain A and (resid 1:236 or resid 724:731)
5X-RAY DIFFRACTION5chain B and (resid 407:512 or resid 534:565)
6X-RAY DIFFRACTION6chain A and (resid 405:512 or resid 534:565)
7X-RAY DIFFRACTION7chain A and (resid 513:533 or resid 566:723)
8X-RAY DIFFRACTION8chain B and (resid 513:533 or resid 566:723)

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