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- PDB-1qol: STRUCTURE OF THE FMDV LEADER PROTEASE -

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Basic information

Entry
Database: PDB / ID: 1qol
TitleSTRUCTURE OF THE FMDV LEADER PROTEASE
ComponentsPROTEASE (NONSTRUCTURAL PROTEIN P20A)
KeywordsHYDROLASE / SULFHYDRYL PROTEINASE / PICORNAVIRAL PROTEINASE
Function / homology
Function and homology information


L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization ...L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / regulation of translation / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane
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 / Cysteine proteinases / Cathepsin B; Chain A ...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 / Cysteine proteinases / Cathepsin B; Chain A / 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 / Picornavirus/Calicivirus coat protein / Papain-like cysteine peptidase superfamily / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGuarne, A. / Tormo, J. / Kirchweger, R. / Pfistermueller, D. / Skern, T. / Fita, I.
Citation
Journal: Embo J. / Year: 1998
Title: Structure of the Foot-and-Mouth Disease Virus Leader Protease: A Papain-Like Fold Adapted for Self-Processing and Eif4G Recognition.
Authors: Guarne, A. / Tormo, J. / Kirchweger, R. / Pfistermueller, D. / Fita, I. / Skern, T.
#1: Journal: J.Gen.Virol. / Year: 1998
Title: A Structural Model of Picornaviral Leader Proteinases Based on Papain and Bleomycin Hydrolase
Authors: Skern, T. / Fita, I. / Guarne, A.
History
DepositionNov 13, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
B: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
C: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
D: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
E: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
F: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
G: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
H: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,52614
Polymers158,2348
Non-polymers2936
Water0
1
A: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
C: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6213
Polymers39,5582
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-22.9 kcal/mol
Surface area18290 Å2
MethodPQS
2
B: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
D: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6915
Polymers39,5582
Non-polymers1333
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-23.1 kcal/mol
Surface area18230 Å2
MethodPQS
3
F: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
G: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6213
Polymers39,5582
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-7 kcal/mol
Surface area18130 Å2
MethodPQS
4
E: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
H: PROTEASE (NONSTRUCTURAL PROTEIN P20A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5943
Polymers39,5582
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-12.3 kcal/mol
Surface area18210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)65.430, 101.560, 276.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOCHEMICAL DATA INDICATES THAT LEADER PROTEASEIS ACTIVE AS A MONOMER. IN THE CRYSTAL ITASSOCIATES TO FORM A DIMER.

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Components

#1: Protein
PROTEASE (NONSTRUCTURAL PROTEIN P20A) / LEADER PROTEASE


Mass: 19779.221 Da / Num. of mol.: 8 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: O1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03305
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
Sequence detailsTHE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEIN, AND THE PROTEASE (EC 3.4.22.-) ...THE SWISSPROT ENTRY POLG_FMDVO REFERS TO A GENOME POLYPROTEIN, AND THE PROTEASE (EC 3.4.22.-) LISTED IS FOR THE RESIDUES 1650 TO 1862. THE PROTEASE STUDIED HERE WAS FOUND IN THE RESIDUES 29 TO 195 THAT ARE LISTED IN SWISSPROT AS A NONSTRUCTURAL PROTEIN P20A.

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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 Å3/Da / Density % sol: 58.9 %
Crystal growpH: 8.5
Details: 10% PEG 6000, 0.8 M MG CHLORIDE, 0.1 M TRIS/HCL PH=8.5, pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 %PEG60001reservoir
20.8 M1reservoirMgCl2
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8469
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8469 Å / Relative weight: 1
ReflectionResolution: 3→34.7 Å / Num. obs: 35080 / % possible obs: 92.5 % / Redundancy: 8.4 % / Biso Wilson estimate: 63.7 Å2 / Rsym value: 0.01 / Net I/σ(I): 9.5
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.263 / % possible all: 74.9
Reflection
*PLUS
Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.263

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→19.99 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2758596.51 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: NATIVE PATTERSON MAP PRESENT A PSEUDO-ORIGEN PEAK AT POSITION (0.5,0.5,0.225). THIS PEAK CORRESPONDS A PURE TRANSLATION THAT RELATES FOUR MOLECULES OF THE A.S.U. WITH THE OTHER FOUR
RfactorNum. reflection% reflectionSelection details
Rfree0.314 2232 6.4 %RANDOM
Rwork0.258 ---
obs0.258 34977 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 17 Å2 / ksol: 0.308148 e/Å3
Displacement parametersBiso mean: 38.8 Å2
Baniso -1Baniso -2Baniso -3
1--16.79 Å20 Å20 Å2
2--20.93 Å20 Å2
3----4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10956 0 15 0 10971
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.421.5
X-RAY DIFFRACTIONc_mcangle_it3.952
X-RAY DIFFRACTIONc_scbond_it3.282
X-RAY DIFFRACTIONc_scangle_it4.862.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 463 8.4 %
Rwork0.345 5031 -
obs--88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4ETH.PARETH.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98

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