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- PDB-8got: Crystal structure of wild-type protease 3C from Seneca Valley Virus -

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Basic information

Entry
Database: PDB / ID: 8got
TitleCrystal structure of wild-type protease 3C from Seneca Valley Virus
ComponentsPeptidase C3
KeywordsVIRAL PROTEIN / Seneca Valley virus / 3C protease / phospholipid
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus ...Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-K8U / Genome polyprotein
Similarity search - Component
Biological speciesSenecavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.989 Å
AuthorsZhao, H.F. / Zhang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970152 China
CitationJournal: Plos Pathog. / Year: 2023
Title: Allosteric regulation of Senecavirus A 3Cpro proteolytic activity by an endogenous phospholipid.
Authors: Zhao, H.F. / Meng, L. / Geng, Z. / Gao, Z.Q. / Dong, Y.H. / Wang, H.W. / Zhang, H.
History
DepositionAug 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5673
Polymers22,9931
Non-polymers1,5742
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area10890 Å2
Unit cell
Length a, b, c (Å)47.303, 69.496, 75.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidase C3 / protease 3C


Mass: 22993.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Senecavirus A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9IRU2
#2: Chemical ChemComp-K8U / [(2~{S})-2-hexadecanoyloxy-3-[[(2~{R})-3-[[(2~{S})-3-[(5~{E},8~{E},11~{Z},14~{E})-icosa-5,8,11,14-tetraenoyl]oxy-2-[(9~{E},12~{Z})-octadeca-9,12-dienoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propyl] icosanoate


Mass: 1482.016 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C83H150O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 1% (w/v) tryptone, 0.05% (w/v) sodium azide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.989→50 Å / Num. obs: 25880 / % possible obs: 100 % / Redundancy: 35.9 % / Biso Wilson estimate: 44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.06 / Rrim(I) all: 0.13 / Net I/σ(I): 17
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 20.8 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4279 / CC1/2: 0.87 / Rrim(I) all: 0.766 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6L0T

6l0t


Resolution: 1.989→40.086 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 820 4.64 %
Rwork0.2131 16838 -
obs0.2151 17658 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.7 Å2 / Biso mean: 48.6087 Å2 / Biso min: 30.18 Å2
Refinement stepCycle: final / Resolution: 1.989→40.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 108 49 1753
Biso mean--77.14 49.64 -
Num. residues----208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071747
X-RAY DIFFRACTIONf_angle_d0.9192345
X-RAY DIFFRACTIONf_chiral_restr0.058248
X-RAY DIFFRACTIONf_plane_restr0.005297
X-RAY DIFFRACTIONf_dihedral_angle_d15.1471024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.9895-2.11410.33051280.27312740
2.1141-2.27730.30561220.2552773
2.2773-2.50650.30411090.24922798
2.5065-2.86910.33591700.25772757
2.8691-3.61440.26391340.21932822
3.6144-40.0860.20991570.18382948

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