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- PDB-7e6v: The crystal structure of foot-and-mouth disease virus(FMDV) 2C pr... -

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Basic information

Entry
Database: PDB / ID: 7e6v
TitleThe crystal structure of foot-and-mouth disease virus(FMDV) 2C protein 97-318aa
ComponentsProtein 2C
KeywordsHYDROLASE / FMDV / 2C
Function / homology
Function and homology information


modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization ...modulation by virus of host chromatin organization / RNA-protein covalent cross-linking / : / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Papain-like cysteine peptidase superfamily / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type SAT 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.832 Å
AuthorsZhang, C. / Wojdyla, J.A. / Qin, B. / Wang, M. / Gao, X. / Cui, S.
CitationJournal: Cell Rep / Year: 2022
Title: An anti-picornaviral strategy based on the crystal structure of foot-and-mouth disease virus 2C protein.
Authors: Zhang, C. / Yang, F. / Wojdyla, J.A. / Qin, B. / Zhang, W. / Zheng, M. / Cao, W. / Wang, M. / Gao, X. / Zheng, H. / Cui, S.
History
DepositionFeb 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 13, 2022Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI
Revision 1.3Jul 20, 2022Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein 2C
B: Protein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7054
Polymers50,5872
Non-polymers1182
Water5,855325
1
A: Protein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3532
Polymers25,2941
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-0 kcal/mol
Surface area12030 Å2
MethodPISA
2
B: Protein 2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3532
Polymers25,2941
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-1 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.720, 40.737, 72.937
Angle α, β, γ (deg.)77.220, 84.380, 89.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Protein 2C


Mass: 25293.627 Da / Num. of mol.: 2 / Mutation: R134A,T135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type SAT 2
Plasmid: pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B8Y0J7, RNA-directed RNA polymerase, picornain 3C, L-peptidase, nucleoside-triphosphate phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.09M Ammonium acetate, 0.045M Sodium citrate tribasic dihydrate pH 5.6, 13.5%w/v PEG 4000, 4% PEG P400, 5mM TECP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.979081 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979081 Å / Relative weight: 1
ReflectionResolution: 1.832→39.719 Å / Num. obs: 67455 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 1.69 % / Biso Wilson estimate: 30.501 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.069 / Net I/σ(I): 7.75
Reflection shellResolution: 1.84→1.94 Å / Redundancy: 1.65 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 10786 / CC1/2: 0.597 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: SAD / Resolution: 1.832→38.48 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.3
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3376 5.01 %Random
Rwork0.2007 ---
obs0.2031 67424 93.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.42 Å2 / Biso mean: 36.37 Å2 / Biso min: 10.91 Å2
Refinement stepCycle: final / Resolution: 1.832→38.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 14 325 3515
Biso mean--36.83 38.28 -
Num. residues----405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.832-1.85770.34191290.3419250491
1.8577-1.88550.33261420.3143269994
1.8855-1.91490.35841390.3172264793
1.9149-1.94630.30881390.2909268093
1.9463-1.97990.2961400.2714265995
1.9799-2.01590.28431480.25278394
2.0159-2.05460.31331450.2523269995
2.0546-2.09660.31941330.2518259592
2.0966-2.14220.29921470.2354275995
2.1422-2.1920.26361410.2278265495
2.192-2.24680.29121360.2239267293
2.2468-2.30750.29491360.2203254890
2.3075-2.37540.21441460.2069269894
2.3754-2.45210.24261430.1959275695
2.4521-2.53970.28941420.204269795
2.5397-2.64140.21141430.1905267194
2.6414-2.76160.25151280.198235483
2.7616-2.90710.23241430.1815275995
2.9071-3.08920.23961410.1813272995
3.0892-3.32760.21991410.1891267395
3.3276-3.66220.2261440.1753275494
3.6622-4.19160.19471390.1561265494
4.1916-5.27880.22391460.1562270595
5.2788-38.4770.26761450.2088269995

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