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- PDB-4qbb: Structure of the foot-and-mouth disease virus leader proteinase i... -

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Basic information

Entry
Database: PDB / ID: 4qbb
TitleStructure of the foot-and-mouth disease virus leader proteinase in complex with inhibitor (N~2~-[(3S)-4-({(2R)-1-[(4-CARBAMIMIDAMIDOBUTYL)AMINO]-4-METHYL-1-OXOPENTAN-2-YL}AMINO)-3-HYDROXY-4-OXOBUTANOYL]-L-ARGINYL-L-PROLINAMIDE)
ComponentsLeader protease
Keywordshydrolase/hydrolase inhibitor / Papain-like cysteine proteinase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / : / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell ...L-peptidase / modulation by virus of host chromatin organization / : / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / ribonucleoside triphosphate phosphatase activity / host cell endoplasmic reticulum membrane / pore formation by virus in membrane of host cell / ISG15-specific peptidase activity / suppression by virus of host ISG15-protein conjugation / nucleoside-triphosphate phosphatase / protein complex oligomerization / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / regulation of translation / positive stranded viral RNA replication / ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral protein processing / RNA helicase activity / integral to membrane of host cell / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / virion attachment to host cell / RNA-directed 5'-3' RNA polymerase activity / host cell cytoplasm / DNA-templated transcription / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / proteolysis / RNA binding / membrane / ATP binding
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth virus L-proteinase / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Viral protein VP4 subunit / Capsid protein VP4, Picornavirus / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Cysteine proteinases / Cathepsin B; Chain A ...Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth virus L-proteinase / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Viral protein VP4 subunit / Capsid protein VP4, Picornavirus / 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. / 3C cysteine protease (picornain 3C) / Peptidase C3A/C3B, picornaviral / picornavirus capsid protein / Picornavirus capsid / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / Papain-like cysteine peptidase superfamily / Viral coat protein subunit / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, C-terminal domain / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / Reverse transcriptase/Diguanylate cyclase domain / 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
Chem-E69 / : / PHOSPHATE ION / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsGrishkovskaya, I. / Steinberger, J. / Cencic, R. / Juliano, M.A. / Juliano, L. / Skern, T.
CitationJournal: Virology / Year: 2014
Title: Foot-and-mouth disease virus leader proteinase: Structural insights into the mechanism of intermolecular cleavage.
Authors: Steinberger, J. / Grishkovskaya, I. / Cencic, R. / Juliano, L. / Juliano, M.A. / Skern, T.
History
DepositionMay 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leader protease
B: Leader protease
C: Leader protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1358
Polymers57,1663
Non-polymers1,9695
Water6,774376
1
A: Leader protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7063
Polymers19,0551
Non-polymers6512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Leader protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6672
Polymers19,0551
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Leader protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7623
Polymers19,0551
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.808, 110.682, 56.774
Angle α, β, γ (deg.)90.000, 98.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Leader protease / Genome polyprotein


Mass: 19055.312 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Strain: O1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03305, L-peptidase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-E69 / N~2~-[(3S)-4-({(2R)-1-[(4-carbamimidamidobutyl)amino]-4-methyl-1-oxopentan-2-yl}amino)-3-hydroxy-4-oxobutanoyl]-L-arginyl-L-prolinamide


Type: peptide-like / Mass: 611.737 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H49N11O6
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate, 0.9M monosodium phosphate, 1.2M dipotassium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.6→56.205 Å / Num. all: 72906 / Num. obs: 72906 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 20.51 Å2 / Rsym value: 0.037 / Net I/σ(I): 29.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.692.90.1744.529409102320.17495
1.69-1.7930.1136.830544100680.11399.6
1.79-1.913.10.08952989295250.08999.5
1.91-2.073.70.0984.93268488110.09899.4
2.07-2.264.70.0896.43817281450.08999.3
2.26-2.536.40.0768.44738573730.07699.9
2.53-2.927.90.05611.95174265310.056100
2.92-3.588.10.03320.24485455510.033100
3.58-5.067.90.02229.23400742810.022100
5.06-45.3497.50.02227.91784523890.02299.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
MxCuBEdata collection
XDSdata reduction
REFMACv5.5.0110phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→45.349 Å / FOM work R set: 0.8779 / SU ML: 0.16 / σ(F): 1.37 / Phase error: 19.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2013 3679 5.05 %
Rwork0.1697 --
obs0.1713 72868 98.93 %
all-72868 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.54 Å2 / Biso mean: 25.94 Å2 / Biso min: 11.1 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.349 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 135 376 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114212
X-RAY DIFFRACTIONf_angle_d1.3995782
X-RAY DIFFRACTIONf_chiral_restr0.076610
X-RAY DIFFRACTIONf_plane_restr0.007764
X-RAY DIFFRACTIONf_dihedral_angle_d14.561526
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6001-1.62110.26431320.21152358249087
1.6211-1.64330.27321400.20312487262794
1.6433-1.66680.18311460.195926652811100
1.6668-1.69170.25641490.196326952844100
1.6917-1.71810.22441430.190226152758100
1.7181-1.74630.22951700.19492651282199
1.7463-1.77640.23111430.191226932836100
1.7764-1.80870.22061390.188526512790100
1.8087-1.84350.23911400.17862685282599
1.8435-1.88110.22971410.186126822823100
1.8811-1.92210.2291440.18372622276699
1.9221-1.96680.25371340.18622701283599
1.9668-2.01590.21441270.184826852812100
2.0159-2.07050.22831490.172226692818100
2.0705-2.13140.21151440.17212643278799
2.1314-2.20020.18971250.17472699282499
2.2002-2.27880.19021320.17242695282799
2.2788-2.370.18611450.171926562801100
2.37-2.47790.20431340.175826982832100
2.4779-2.60850.22381420.181826922834100
2.6085-2.77190.1941430.188126952838100
2.7719-2.98590.21531680.178726762844100
2.9859-3.28630.20461480.17726842832100
3.2863-3.76170.17691200.154427412861100
3.7617-4.73850.15361320.135927132845100
4.7385-45.36680.19451490.155327382887100

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