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- PDB-6ae6: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 6ae6
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-672, Y471A mutant, form 2)
ComponentsRdRp catalytic
KeywordsTRANSFERASE / Polymerase
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing ...serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / GTP binding / virion attachment to host cell / virion membrane / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.856 Å
AuthorsLiu, W. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670154 China
Ministry of Science and Technology (China)2018YFA0507200 China
Ministry of Science and Technology (China)2018YFD0500100 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase.
Authors: Liu, W. / Shi, X. / Gong, P.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Nov 22, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RdRp catalytic
B: RdRp catalytic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5429
Polymers156,1292
Non-polymers4137
Water1086
1
A: RdRp catalytic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2414
Polymers78,0641
Non-polymers1773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-0 kcal/mol
Surface area27150 Å2
MethodPISA
2
B: RdRp catalytic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3015
Polymers78,0641
Non-polymers2364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-0 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.501, 115.501, 293.335
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 13 through 233 or (resid 234...
21(chain B and (resid 13 through 43 or (resid 44...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNILEILE(chain A and (resid 13 through 233 or (resid 234...AA13 - 23314 - 234
12LEULEULEULEU(chain A and (resid 13 through 233 or (resid 234...AA234235
13ASNASNGLNGLN(chain A and (resid 13 through 233 or (resid 234...AA13 - 67014 - 671
14ASNASNGLNGLN(chain A and (resid 13 through 233 or (resid 234...AA13 - 67014 - 671
15ASNASNGLNGLN(chain A and (resid 13 through 233 or (resid 234...AA13 - 67014 - 671
16ASNASNGLNGLN(chain A and (resid 13 through 233 or (resid 234...AA13 - 67014 - 671
21ASNASNALAALA(chain B and (resid 13 through 43 or (resid 44...BB13 - 4314 - 44
22GLNGLNGLNGLN(chain B and (resid 13 through 43 or (resid 44...BB4445
23ASNASNGLNGLN(chain B and (resid 13 through 43 or (resid 44...BB13 - 67014 - 671
24ASNASNGLNGLN(chain B and (resid 13 through 43 or (resid 44...BB13 - 67014 - 671
25ASNASNGLNGLN(chain B and (resid 13 through 43 or (resid 44...BB13 - 67014 - 671
26ASNASNGLNGLN(chain B and (resid 13 through 43 or (resid 44...BB13 - 67014 - 671

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Components

#1: Protein RdRp catalytic


Mass: 78064.328 Da / Num. of mol.: 2 / Mutation: Y471A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Strain: Shimen / Gene: NS5B / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5U8X5
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.62 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: SOKALAN CP42

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 22116 / % possible obs: 99.8 % / Redundancy: 7.9 % / Biso Wilson estimate: 106.46 Å2 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.055 / Rrim(I) all: 0.157 / Χ2: 1.035 / Net I/σ(I): 4.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.85-3.998.30.52321610.890.1920.5581.019100
3.99-4.158.20.39121510.9390.1440.4181.025100
4.15-4.3480.3121720.960.1150.3311.015100
4.34-4.567.40.23221730.9760.090.2491.058100
4.56-4.858.10.19821940.9840.0740.2111.045100
4.85-5.228.40.19122100.9870.0690.2041.029100
5.22-5.758.30.17822140.9840.0660.1911.048100
5.75-6.587.70.14822130.9870.0570.1591.04100
6.58-8.287.80.09422770.9970.0360.1011.00899.9
8.28-507.20.05823510.9980.0230.0631.06798.5

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJQ

2cjq


Resolution: 3.856→41.319 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.2472 1177 5.34 %
Rwork0.209 --
obs0.2111 22045 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.46 Å2 / Biso mean: 95.2619 Å2 / Biso min: 52.95 Å2
Refinement stepCycle: final / Resolution: 3.856→41.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9522 0 28 6 9556
Biso mean--94.42 76.77 -
Num. residues----1294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039759
X-RAY DIFFRACTIONf_angle_d0.68213331
X-RAY DIFFRACTIONf_chiral_restr0.0431537
X-RAY DIFFRACTIONf_plane_restr0.0041734
X-RAY DIFFRACTIONf_dihedral_angle_d9.2515712
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5808X-RAY DIFFRACTION1.749TORSIONAL
12B5808X-RAY DIFFRACTION1.749TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8564-4.03180.27791320.262625352667100
4.0318-4.24410.28871620.23825612723100
4.2441-4.50970.21471450.204125662711100
4.5097-4.85740.26831470.197725882735100
4.8574-5.34530.2571580.217325872745100
5.3453-6.11670.25821470.229926262773100
6.1167-7.69820.27011400.228226682808100
7.6982-41.32130.2081460.17162737288398

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