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- PDB-2oin: crystal structure of HCV NS3-4A R155K mutant -

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Basic information

Entry
Database: PDB / ID: 2oin
Titlecrystal structure of HCV NS3-4A R155K mutant
Components
  • NS4A peptide
  • PolyproteinProteolysis
KeywordsHYDROLASE / HCV / protease / NS3-4A / R155K mutant
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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / 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 / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Thrombin, subunit H - #120 / 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 ...Thrombin, subunit H - #120 / 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 / 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 / Trypsin-like serine proteases / Thrombin, subunit H / 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 / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsWei, Y.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Phenotypic and structural analyses of hepatitis C virus NS3 protease Arg155 variants: sensitivity to telaprevir (VX-950) and interferon alpha.
Authors: Zhou, Y. / Muh, U. / Hanzelka, B.L. / Bartels, D.J. / Wei, Y. / Rao, B.G. / Brennan, D.L. / Tigges, A.M. / Swenson, L. / Kwong, A.D. / Lin, C.
History
DepositionJan 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 1.5Nov 15, 2023Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entity_src_syn / struct
Item: _struct.title
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
C: NS4A peptide
D: NS4A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6966
Polymers46,5664
Non-polymers1312
Water3,711206
1
A: Polyprotein
C: NS4A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3483
Polymers23,2832
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-48 kcal/mol
Surface area7890 Å2
MethodPISA, PQS
2
B: Polyprotein
D: NS4A peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3483
Polymers23,2832
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-51 kcal/mol
Surface area9880 Å2
MethodPISA, PQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-119 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.310, 225.310, 75.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Polyprotein / Proteolysis


Mass: 21205.211 Da / Num. of mol.: 2 / Fragment: HCV protease domain NS3 / Mutation: R155K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: H / Gene: NS3 / Plasmid: pBEV10 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q9ELS8, UniProt: P27958*PLUS
#2: Protein/peptide NS4A peptide


Mass: 2077.577 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P27958*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.97 Å3/Da / Density % sol: 68.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 1.4M NaCl, 0.3M KH2PO4, 0.1M MES, pH 6.2, 10.0mM PME, protein concentration 8mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 22116 / % possible obs: 86.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rmerge(I) obs: 0.09 / Χ2: 1.125 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.590.4628980.767135.5
2.59-2.690.46617540.8169.5
2.69-2.820.40522900.846190.4
2.82-2.960.29724500.884196.9
2.96-3.150.21624480.928196.5
3.15-3.390.15424570.996196.9
3.39-3.730.10524521.101196.5
3.73-4.270.07524671.281196.1
4.27-5.370.05824421.403195.2
5.37-250.04124581.436193.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
CNX2005phasing
CNX2005refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: HCV NS3-4A wild type protease

Resolution: 2.5→19.93 Å / Rfactor Rfree error: 0.007 / FOM work R set: 0.846 / Data cutoff high absF: 4536579 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1123 5.1 %RANDOM
Rwork0.2 ---
all0.208 22067 --
obs0.203 21873 86.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.077 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 42.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.22 Å22.84 Å20 Å2
2---3.22 Å20 Å2
3---6.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 2 206 2891
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.342
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.540.4100.366150160
2.54-2.590.436100.302283293
2.59-2.640.276220.287454476
2.64-2.690.31300.301630660
2.69-2.750.401470.295815862
2.75-2.810.299520.28927979
2.81-2.890.251730.23910361109
2.89-2.960.326560.24310701126
2.96-3.050.324530.23511001153
3.05-3.150.233530.22511121165
3.15-3.260.258580.22111221180
3.26-3.390.292710.22711301201
3.39-3.540.256550.20611171172
3.54-3.730.212670.18511351202
3.73-3.960.247590.18211451204
3.96-4.260.189720.14611411213
4.26-4.690.164490.12411611210
4.69-5.350.165580.14211451203
5.35-6.70.232510.17111411192
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4

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