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- PDB-1a1q: HEPATITIS C VIRUS NS3 PROTEINASE -

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Basic information

Entry
Database: PDB / ID: 1a1q
TitleHEPATITIS C VIRUS NS3 PROTEINASE
ComponentsNS3 PROTEINASE
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / : ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / SH3 domain binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / ribonucleoprotein complex / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b ...Hepatitis C virus core protein, chain A superfamily / Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / HEAVY ATOMS: ISOMORPHOUS, ANOMALOUS SIGNALS / Resolution: 2.4 Å
AuthorsLove, R.A. / Parge, H.E. / Wickersham, J.A. / Hostomsky, Z. / Habuka, N. / Moomaw, E.W. / Adachi, T. / Hostomska, Z.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1996
Title: The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site.
Authors: Love, R.A. / Parge, H.E. / Wickersham, J.A. / Hostomsky, Z. / Habuka, N. / Moomaw, E.W. / Adachi, T. / Hostomska, Z.
History
DepositionDec 12, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3 PROTEINASE
B: NS3 PROTEINASE
C: NS3 PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8806
Polymers59,6843
Non-polymers1963
Water0
1
A: NS3 PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9602
Polymers19,8951
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS3 PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9602
Polymers19,8951
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NS3 PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9602
Polymers19,8951
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.000, 133.000, 223.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.95206, 0.305556, -0.014748), (-0.305663, -0.952124, 0.005574), (-0.012339, 0.009815, 0.999876)-22.67001, 73.03197, 0.78307
2given(-0.919307, -0.392193, 0.032539), (-0.388774, 0.917892, 0.079553), (-0.061068, 0.060484, -0.9963)27.04836, 2.94648, -2.43504

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Components

#1: Protein NS3 PROTEINASE / Coordinate model: Cα atoms only


Mass: 19894.604 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: TYPE 1B / Description: EXPRESSED AS SOLUBLE PROTEIN / Gene: CDNA / Variant: BK ISOLATE / Plasmid: CDNA DERIVED FROM VIRAL RNA ISOLATED FROM PAT / Gene (production host): CDNA DERIVED FROM / Production host: Escherichia coli (E. coli) / References: UniProt: P26663
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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: 3.18 Å3/Da / Density % sol: 62 %
Crystal growpH: 6.5
Details: VAPOR DIFFUSION. PROTEIN MIXED WITH WELL SOLUTION OF: 3.5M NACL, 150MM TRIS-HCL (PH 6.0), 5% PEG400., pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
225 mMsodium acetate1drop
35 mMdithiothreitol1drop
41.9 M1dropNaCl
52.5 %PEG4001drop
675 mMTris-HCl1drop
75 %PEG4001reservoir
83.5 M1reservoirNaCl
9150 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 30000 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.079 / Net I/σ(I): 10
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.29 / % possible all: 98
Reflection
*PLUS
Num. measured all: 96285 / Rmerge(I) obs: 0.079

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: HEAVY ATOMS: ISOMORPHOUS, ANOMALOUS SIGNALS
Resolution: 2.4→8 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT, THE CONFORMATION OF N TERMINAL REGION IS TRULY REPRESENTED BY CHAINS A AND C AND SHOWS A STRAND EXCHANGE PHENOMENON. HOWEVER, THIS COULD NOT BE ...Details: OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT, THE CONFORMATION OF N TERMINAL REGION IS TRULY REPRESENTED BY CHAINS A AND C AND SHOWS A STRAND EXCHANGE PHENOMENON. HOWEVER, THIS COULD NOT BE CLEARLY SEEN IN CHAIN B SINCE THERE ARE SOME MISSING RESIDUES. FOR COMPLETE DESCRIPTION PLEASE SEE THE REFERENCED JOURNAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.32 2000 8 %RANDOM
Rwork0.225 ---
obs0.225 25000 98 %-
Displacement parametersBiso mean: 17 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms531 0 3 0 534
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it55
X-RAY DIFFRACTIONx_mcangle_it55
X-RAY DIFFRACTIONx_scbond_it55
X-RAY DIFFRACTIONx_scangle_it55
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 10 Å2 / Rms dev position: 1.5 Å / Weight Biso : 2 / Weight position: 200
LS refinement shellResolution: 2.4→2.5 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.38 200 8 %
Rwork0.28 2000 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.32
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2

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