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- PDB-1qa7: CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ... -

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Basic information

Entry
Database: PDB / ID: 1qa7
TitleCRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV
ComponentsHAV 3C PROTEINASE
Keywordshydrolase/hydrolase inhibitor / CHYMOTRYPSIN-LIKE CYSTEINE PROTEINASE VIRAL PROTEASE P'-SITE INHIBITOR / HYDROLASE / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / virion assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid ...negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / host cell mitochondrial outer membrane / RNA-protein covalent cross-linking / : / virion assembly / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / membrane => GO:0016020 / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / 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 ...: / 2B protein soluble domain / Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
N-(iodoacetyl)-L-valyl-L-phenylalaninamide / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBergmann, E.M. / Cherney, M.M. / Mckendrick, J. / Vederas, J.C. / James, M.N.G.
Citation
Journal: Virology / Year: 1999
Title: Crystal structure of an inhibitor complex of the 3C proteinase from hepatitis A virus (HAV) and implications for the polyprotein processing in HAV.
Authors: Bergmann, E.M. / Cherney, M.M. / Mckendrick, J. / Frormann, S. / Luo, C. / Malcolm, B.A. / Vederas, J.C. / James, M.N.
#1: Journal: J.Virol. / Year: 1997
Title: The refined crystal structure of the 3C gene product from hepatitis A virus: specific proteinase activity and RNA recognition
Authors: Bergmann, E.M. / Mosimann, S.C. / Chernaia, M.M. / Malcolm, B.A. / James, M.N.G.
#2: Journal: Handbook of Proteolytic Enzymes / Year: 1998
Title: Hepatitis A virus picornain 3C
Authors: Bergmann, E.M.
#3: Journal: Handbook of Exp. Pharmacol., Vol. Proteases as Targets for Therapy
Year: 1999
Title: The 3C proteinases of picornaviruses and other positive-sense, single-stranded RNA viruses
Authors: Bergmann, E.M. / James, M.N.G.
#4: Journal: Biochemistry / Year: 1992
Title: Expression and characterization of recombinant hepatitis A virus 3C proteinase
Authors: Malcolm, B.A. / Chin, S.M. / Jewell, D.A. / Stratton-Thomas, J.R. / Thudium, K.
History
DepositionApr 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 16, 2012Group: Non-polymer description
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HAV 3C PROTEINASE
B: HAV 3C PROTEINASE
C: HAV 3C PROTEINASE
D: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,20910
Polymers95,3144
Non-polymers1,8956
Water9,260514
1
A: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2602
Polymers23,8281
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2602
Polymers23,8281
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2602
Polymers23,8281
Non-polymers4311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4304
Polymers23,8281
Non-polymers6013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-43 kcal/mol
Surface area35940 Å2
MethodPISA
6
A: HAV 3C PROTEINASE
B: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5194
Polymers47,6572
Non-polymers8632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-16 kcal/mol
Surface area18710 Å2
MethodPISA
7
C: HAV 3C PROTEINASE
D: HAV 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6906
Polymers47,6572
Non-polymers1,0334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-19 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.562, 78.357, 105.287
Angle α, β, γ (deg.)90.00, 97.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HAV 3C PROTEINASE


Mass: 23828.469 Da / Num. of mol.: 4 / Fragment: HAV 3C PROTEINASE / Mutation: C24S, F82A
Source method: isolated from a genetically manipulated source
Details: PROTEINASE CHEMICALLY BONDED TO INHIBITOR ACE-VAL-NFA. IT WAS CHEMICALLY SYNTHESIZED AS IODOACETYL-VALYL-PHENYLALANYL AMIDE
Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Plasmid: PHAV3-CEX / Production host: Escherichia coli (E. coli) / References: UniProt: P26582, UniProt: P08617*PLUS
#2: Chemical
ChemComp-IVF / N-(iodoacetyl)-L-valyl-L-phenylalaninamide / iodoacetyl-valyl-phenylalanyl-amide


Type: peptide-like / Mass: 431.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H22IN3O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS, 5% DMSO, 18% PEG 8000 , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
210 mMTris1drop
3100 mMTris1reservoir
45 %DMSO1reservoir
518 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 64826 / Num. obs: 59384 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 4.8
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.157 / Num. unique all: 4001 / % possible all: 74.7
Reflection
*PLUS
Num. measured all: 494113
Reflection shell
*PLUS
% possible obs: 74.7 % / Num. unique obs: 4001 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1hav

1hav


Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: no non-crystallographic restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.298 3902 6.5 %random
Rwork0.204 ---
all0.214 55982 --
obs0.214 55982 92.3 %-
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6616 0 98 514 7228
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.42
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / σ(F): 0 / % reflection Rfree: 6.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg1.42
X-RAY DIFFRACTIONt_plane_restr0.025

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