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Open data
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Basic information
Entry | Database: PDB / ID: 1hav | ||||||
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Title | HEPATITIS A VIRUS 3C PROTEINASE | ||||||
![]() | (HEPATITIS A VIRUS 3C PROTEINASE) x 2 | ||||||
![]() | HYDROLASE / POLYPROTEIN / COAT PROTEIN / CORE PROTEIN / RNA-DIRECTED RNA POLYMERASE / THIOL PROTEASE | ||||||
Function / homology | ![]() 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 cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bergmann, E.M. / James, M.N.G. | ||||||
![]() | ![]() 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. #2: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.3 KB | Display | ![]() |
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PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376.8 KB | Display | ![]() |
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Full document | ![]() | 380 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 15.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.8808, -0.4661, -0.0832), Vector: |
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Components
#1: Protein | Mass: 23904.564 Da / Num. of mol.: 1 / Mutation: C24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 23952.562 Da / Num. of mol.: 1 / Mutation: C24S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
Compound details | ACTIVE SITE CYSTEINE 172 IS OXIDIZED IN MOLECULE B. MOLECULE A RESEMBLES ACTIVE PROTEINASE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 / Details: pH 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: used to seeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Oct 30, 1994 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 25299 / % possible obs: 87 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.0673 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 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
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Refinement | Method to determine structure: ![]() 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.
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Displacement parameters | Biso mean: 21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Total num. of bins used: 6
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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