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- PDB-2wv5: Crystal structure of foot-and-mouth disease virus 3C protease in ... -

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Basic information

Entry
Database: PDB / ID: 2wv5
TitleCrystal structure of foot-and-mouth disease virus 3C protease in complex with a decameric peptide corresponding to the VP1-2A cleavage junction with a GLN to Glu substitution at P1
Components
  • FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
  • PICORNAIN 3C
KeywordsHYDROLASE/PEPTIDE / 3C PROTEASE / HYDROLASE / VIRAL PROTEIN / HYDROLASE PEPTIDE COMPLEX / HYDROLASE-PEPTIDE complex
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / regulation of translation / host cell / nucleoside-triphosphate phosphatase ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / regulation of translation / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Picornavirus coat protein / Papain-like cysteine peptidase superfamily / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Insights Into Cleavage Specificity from the Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease Complexed with a Peptide Substrate.
Authors: Zunszain, P.A. / Knox, S.R. / Sweeney, T.R. / Yang, J. / Roque-Rosell, N. / Belsham, G.J. / Leatherbarrow, R.J. / Curry, S.
History
DepositionOct 13, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -4-STRANDED BARREL THIS IS REPRESENTED BY A -3-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY A -1-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PICORNAIN 3C
B: PICORNAIN 3C
C: PICORNAIN 3C
D: PICORNAIN 3C
E: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
F: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
G: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN
H: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)96,7768
Polymers96,7768
Non-polymers00
Water93752
1
A: PICORNAIN 3C
E: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-11.7 kcal/mol
Surface area8750 Å2
MethodPISA
2
D: PICORNAIN 3C
H: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-11.1 kcal/mol
Surface area9140 Å2
MethodPISA
3
B: PICORNAIN 3C
F: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-11.3 kcal/mol
Surface area8830 Å2
MethodPISA
4
C: PICORNAIN 3C
G: FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,1942
Polymers24,1942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-11.2 kcal/mol
Surface area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.033, 75.105, 86.303
Angle α, β, γ (deg.)90.00, 99.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9735, -0.1553, 0.168), (-0.0738, 0.9082, 0.4119), (-0.2166, 0.3886, -0.8956)64.9036, -0.8716, 23.1669
2given(0.9999, -0.0025, 0.0136), (0.0027, 0.9999, -0.016), (-0.0135, 0.0161, 0.9998)-25.8601, -3.0141, -42.1898
3given(0.9709, -0.155, -0.1828), (0.0731, 0.9179, -0.39), (0.2283, 0.3653, 0.9025)-19.1516, 40.4574, -22.696

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Components

#1: Protein
PICORNAIN 3C / FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE / PROTEASE 3C / P3C / PROTEASE P20B


Mass: 23049.654 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: A10-61 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03306, picornain 3C
#2: Protein/peptide
FOOT AND MOUTH DISEASE VIRUS (SEROTYPE A) VARIANT VP1 CAPSID PROTEIN


Mass: 1144.297 Da / Num. of mol.: 4 / Fragment: VP1-2A CLEAVAGE JUNCTION (P5-P5'), RESIDUES 29-38 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) FOOT-AND-MOUTH DISEASE VIRUS / References: UniProt: Q65050, UniProt: P03306*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS1791 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN A, CYS1812 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN B, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN B, CYS1812 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN C, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN C, CYS1812 TO ALA ENGINEERED RESIDUE IN CHAIN D, CYS1744 TO LYS ENGINEERED RESIDUE IN CHAIN D, CYS1791 TO LEU ENGINEERED RESIDUE IN CHAIN D, CYS1812 TO ALA ENGINEERED RESIDUE IN CHAIN E, GLN 33 TO GLU ENGINEERED RESIDUE IN CHAIN F, GLN 33 TO GLU ENGINEERED RESIDUE IN CHAIN G, GLN 33 TO GLU ENGINEERED RESIDUE IN CHAIN H, GLN 33 TO GLU
Has protein modificationY
Sequence detailsCONTAINS ADDITIONAL GLY AS RESIDUE 1. LAST 6 RESIDUES AT C- TERM MISSING FROM OUR STRUCTURE. ...CONTAINS ADDITIONAL GLY AS RESIDUE 1. LAST 6 RESIDUES AT C- TERM MISSING FROM OUR STRUCTURE. SEQUENCE DATABASE ENTRY FOR THIS PROTEIN CONTAINS KNOWN ERRORS.

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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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 8 / Details: SEE PAPER, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→63.2 Å / Num. obs: 16981 / % possible obs: 76.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.2 / % possible all: 60.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J92

2j92


Resolution: 2.7→56.33 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 666675.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 831 4.9 %RANDOM
Rwork0.236 ---
obs0.236 16981 75.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.132 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--8.07 Å20 Å28.34 Å2
2---7.05 Å20 Å2
3---15.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.7→56.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 0 52 6096
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.42.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 118 5.3 %
Rwork0.334 2107 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CAPPING.PARAMCAPPING.TOP

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