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- PDB-1hav: HEPATITIS A VIRUS 3C PROTEINASE -

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Basic information

Entry
Database: PDB / ID: 1hav
TitleHEPATITIS A VIRUS 3C PROTEINASE
Components(HEPATITIS A VIRUS 3C PROTEINASE) x 2
KeywordsHYDROLASE / POLYPROTEIN / COAT PROTEIN / CORE PROTEIN / RNA-DIRECTED RNA POLYMERASE / THIOL PROTEASE
Function / homology
Function and homology information


host cell mitochondrial outer membrane / 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 multivesicular body / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / 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 multivesicular body / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / 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 / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHepatitis A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBergmann, E.M. / James, M.N.G.
Citation
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.
#1: Journal: To be Published
Title: Hepatitis a Virus Picornain 3C
Authors: Bergmann, E.M.
#2: Journal: Nature / Year: 1994
Title: Picornaviral 3C Cysteine Proteinases Have a Fold Similar to Chymotrypsin-Like Serine Proteinases
Authors: Allaire, M. / Chernaia, M.M. / Malcolm, B.A. / James, M.N.
#3: 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.B. / Ralston, R. / Rosenberg, S.
History
DepositionOct 23, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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 1.4Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: HEPATITIS A VIRUS 3C PROTEINASE
B: HEPATITIS A VIRUS 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8933
Polymers47,8572
Non-polymers351
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEPATITIS A VIRUS 3C PROTEINASE
hetero molecules

A: HEPATITIS A VIRUS 3C PROTEINASE


Theoretical massNumber of molelcules
Total (without water)47,8933
Polymers47,8572
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2230 Å2
ΔGint-27 kcal/mol
Surface area19670 Å2
MethodPISA
3
A: HEPATITIS A VIRUS 3C PROTEINASE


Theoretical massNumber of molelcules
Total (without water)23,9051
Polymers23,9051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
B: HEPATITIS A VIRUS 3C PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9882
Polymers23,9531
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.600, 53.550, 53.200
Angle α, β, γ (deg.)99.08, 129.00, 103.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8808, -0.4661, -0.0832), (0.2512, 0.3113, 0.9165), (-0.4013, -0.8282, 0.3913)
Vector: -17.5541, -26.8554, 18.584)

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Components

#1: Protein HEPATITIS A VIRUS 3C PROTEINASE / PICORNAIN 3C


Mass: 23904.564 Da / Num. of mol.: 1 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Gene: 3C / Plasmid: PHAV-3CEX / Gene (production host): 3C / Production host: Escherichia coli (E. coli) / References: UniProt: P08617, RNA-directed RNA polymerase
#2: Protein HEPATITIS A VIRUS 3C PROTEINASE / PICORNAIN 3C


Mass: 23952.562 Da / Num. of mol.: 1 / Mutation: C24S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis A virus / Genus: Hepatovirus / Gene: 3C / Plasmid: PHAV-3CEX / Gene (production host): 3C / Production host: Escherichia coli (E. coli) / References: UniProt: P08617, RNA-directed RNA polymerase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Compound detailsACTIVE SITE CYSTEINE 172 IS OXIDIZED IN MOLECULE B. MOLECULE A RESEMBLES ACTIVE PROTEINASE.

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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: 2.21 Å3/Da / Density % sol: 44.36 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
220 %mPEG20001reservoir
31.0 M1reservoirLiCl
43 mMbeta-mercaptoethanol1reservoir
50.1 MTris-HCl1reservoirpH8.5

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 30, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 25299 / % possible obs: 87 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.0673 / Net I/σ(I): 9.1
Reflection shellResolution: 2→2.15 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.2713 / Mean I/σ(I) obs: 1.4 / % possible all: 67
Reflection
*PLUS
Num. measured all: 64410
Reflection shell
*PLUS
% possible obs: 67.2 % / Num. unique obs: 3841 / Num. measured obs: 5802

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata reduction
BIOMOLdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INACTIVE DOUBLE MUTANT OF ALLAIRE ET AL. (1994), SEE REFERENCE 2.

Resolution: 2→20 Å / σ(F): 2
Details: MAXIMUM LIKELIHOOD VERSION OF X-PLOR USED INSTEAD OF CRYSTALLOGRAPHIC RESIDUAL, SEE PANNU N.S. AND READ R.J. (1996) ACTA CRYST, VOL.A50, PP.659-668 RESIDUES 147 - 151 IN BOTH MOLECULES, A ...Details: MAXIMUM LIKELIHOOD VERSION OF X-PLOR USED INSTEAD OF CRYSTALLOGRAPHIC RESIDUAL, SEE PANNU N.S. AND READ R.J. (1996) ACTA CRYST, VOL.A50, PP.659-668 RESIDUES 147 - 151 IN BOTH MOLECULES, A AND B, ARE POORLY DEFINED AND PRESUMABLY FLEXIBLE. RESIDUES 147 - 151 IN BOTH MOLECULES, A AND B, ARE POORLY DEFINED AND PRESUMABLY FLEXIBLE. ASP A 36 AND ASP B 36: UNUSUAL MAIN CHAIN CONFORMATIONAL ANGLES RESIDUE I+1 OF II' REVERSE TURN AND WELL-DEFINED IN ELECTRON DENSITY DESPITE BEING FLAGGED AN OUTLIER IN A RAMACHANDRAN PLOT.
RfactorNum. reflection% reflection
Rfree0.265 1958 11 %
Rwork0.211 --
obs0.211 20059 87 %
Displacement parametersBiso mean: 21 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 1 107 3430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.79
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 174 9 %
Rwork0.277 1504 -
obs--67 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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