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- PDB-2hd0: Structure of the catalytic domain of hepatitis C virus NS2 -

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Basic information

Entry
Database: PDB / ID: 2hd0
TitleStructure of the catalytic domain of hepatitis C virus NS2
ComponentsProtease NS2-3 (p23)
KeywordsHYDROLASE / Cysteine Protease / Dimer / Composite Active Site
Function / homology
Function and homology information


positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / SH3 domain binding / kinase 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 / entry receptor-mediated virion attachment to host cell / 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 / host cell plasma membrane / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2, C-terminal domain / Monooxygenase / 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 NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2, C-terminal domain / Monooxygenase / 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 / SH3 type barrels. / helicase superfamily c-terminal 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 / Roll / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsLorenz, I.C. / Rice, C.M. / Marcotrigiano, J.
CitationJournal: Nature / Year: 2006
Title: Structure of the catalytic domain of the hepatitis C virus NS2-3 protease.
Authors: Lorenz, I.C. / Marcotrigiano, J. / Dentzer, T.G. / Rice, C.M.
History
DepositionJun 19, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease NS2-3 (p23)
B: Protease NS2-3 (p23)
C: Protease NS2-3 (p23)
D: Protease NS2-3 (p23)
E: Protease NS2-3 (p23)
F: Protease NS2-3 (p23)
G: Protease NS2-3 (p23)
H: Protease NS2-3 (p23)
I: Protease NS2-3 (p23)
J: Protease NS2-3 (p23)
K: Protease NS2-3 (p23)
L: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,81524
Polymers167,11612
Non-polymers3,69912
Water3,171176
1
A: Protease NS2-3 (p23)
B: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0226
Polymers27,8532
Non-polymers1,1694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-36 kcal/mol
Surface area12830 Å2
MethodPISA
2
C: Protease NS2-3 (p23)
D: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1453
Polymers27,8532
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-34 kcal/mol
Surface area13910 Å2
MethodPISA
3
E: Protease NS2-3 (p23)
F: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4374
Polymers27,8532
Non-polymers5852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-34 kcal/mol
Surface area13610 Å2
MethodPISA
4
G: Protease NS2-3 (p23)
H: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1453
Polymers27,8532
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-39 kcal/mol
Surface area14610 Å2
MethodPISA
5
I: Protease NS2-3 (p23)
J: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9205
Polymers27,8532
Non-polymers1,0673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-34 kcal/mol
Surface area13460 Å2
MethodPISA
6
K: Protease NS2-3 (p23)
L: Protease NS2-3 (p23)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1453
Polymers27,8532
Non-polymers2921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-33 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.812, 68.819, 125.162
Angle α, β, γ (deg.)90.00, 105.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease NS2-3 (p23)


Mass: 13926.373 Da / Num. of mol.: 12 / Fragment: protease domain of NS2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P27958, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris pH 8.5 0.8 M Ammonium Acetate 0.25 M Lithium Chloride 12% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
3931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.97927
SYNCHROTRONNSLS X9A20.97939
SYNCHROTRONNSLS X29A31.1
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDNov 18, 2004
MAR CCD 165 mm2CCDNov 18, 2004
ADSC QUANTUM 3153CCDMar 2, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111MADMx-ray1
3Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979391
31.11
ReflectionResolution: 2.28→30 Å / Num. obs: 75215 / % possible obs: 99.6 % / Observed criterion σ(I): 4 / Redundancy: 3.4 % / Rsym value: 0.087 / Net I/σ(I): 13.1
Reflection shellResolution: 2.28→2.36 Å / Redundancy: 3.2 % / Rsym value: 0.175 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 7521 RANDOM
Rwork0.226 --
all-82381 -
obs-75215 -
Refinement stepCycle: LAST / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11501 0 253 176 11930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3

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