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- PDB-4jmy: Crystal structure of HCV NS3/NS4A protease complexed with DDIVPC ... -

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Basic information

Entry
Database: PDB / ID: 4jmy
TitleCrystal structure of HCV NS3/NS4A protease complexed with DDIVPC peptide
Components
  • HCV non-structural protein 4A
  • Polyprotein
  • substrate peptide
KeywordsHYDROLASE/PROTEIN BINDING / Hepatitis C Virus / serine protease / DDIVPC / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


RNA stabilization / DNA/DNA annealing activity / RNA strand annealing activity / RNA folding chaperone / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint ...RNA stabilization / DNA/DNA annealing activity / RNA strand annealing activity / RNA folding chaperone / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated transformation of host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 / ribonucleoside triphosphate phosphatase activity / protein-DNA complex / viral capsid / nucleoside-triphosphate phosphatase / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / 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 core protein, chain A superfamily ...Thrombin, subunit H - #120 / 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 core protein, chain A superfamily / : / 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 / NS3 RNA helicase, C-terminal helical domain / 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 / Trypsin-like serine proteases / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / 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 genotype 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLemke, C.T.
CitationJournal: To be Published
Title: Importance of the peptide scaffold of drugs that target the hepatitis C virus NS3 protease and its crucial bioactive conformation and dynamic factors.
Authors: LaPlante, S. / Lemke, C.T.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_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: Polyprotein
B: Polyprotein
C: HCV non-structural protein 4A
D: HCV non-structural protein 4A
E: substrate peptide
F: substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,45610
Polymers44,2796
Non-polymers1774
Water3,927218
1
A: Polyprotein
C: HCV non-structural protein 4A
E: substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2285
Polymers22,1403
Non-polymers882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-65 kcal/mol
Surface area9050 Å2
MethodPISA
2
B: Polyprotein
D: HCV non-structural protein 4A
F: substrate peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2285
Polymers22,1403
Non-polymers882
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-63 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.123, 94.123, 83.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Polyprotein


Mass: 19663.635 Da / Num. of mol.: 2 / Fragment: NS3 protease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus genotype 2 / Strain: Isolate Japanes, Taxonomy ID: 11116 / Gene: POLG_HCVJA / Production host: Escherichia coli (E. coli) / References: UniProt: Q81817, hepacivirin

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Protein/peptide , 2 types, 4 molecules CDEF

#2: Protein/peptide HCV non-structural protein 4A


Mass: 1815.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P26662*PLUS
#3: Protein/peptide substrate peptide


Mass: 660.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized

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Non-polymers , 3 types, 222 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3M NaCl, 0.1M Na Citrate pH6.0, 2.5% T-butanol, 20mM OBG, 5mM DTT, 3mM sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Details: VariMax-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→58.24 Å / Num. all: 30601 / Num. obs: 30448 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.59 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.331 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→58.238 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1507 5.07 %Random
Rwork0.2161 ---
obs0.2179 29721 97.1 %-
all-30601 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.388 Å2 / ksol: 0.425 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4814 Å20 Å20 Å2
2---0.4814 Å20 Å2
3---0.9629 Å2
Refinement stepCycle: LAST / Resolution: 1.95→58.238 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 4 218 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082980
X-RAY DIFFRACTIONf_angle_d1.1344062
X-RAY DIFFRACTIONf_dihedral_angle_d12.3311078
X-RAY DIFFRACTIONf_chiral_restr0.074486
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0130.46511280.39762409X-RAY DIFFRACTION91
2.013-2.08490.43721360.37792468X-RAY DIFFRACTION94
2.0849-2.16840.36921450.31322465X-RAY DIFFRACTION95
2.1684-2.26710.35551450.28312530X-RAY DIFFRACTION96
2.2671-2.38660.31221460.25192548X-RAY DIFFRACTION97
2.3866-2.53610.30681400.24872585X-RAY DIFFRACTION98
2.5361-2.73190.31581220.23712631X-RAY DIFFRACTION99
2.7319-3.00690.26381440.21952599X-RAY DIFFRACTION99
3.0069-3.44190.24551460.19492624X-RAY DIFFRACTION100
3.4419-4.33620.19611380.18142665X-RAY DIFFRACTION100
4.3362-58.26390.21541170.19542690X-RAY DIFFRACTION99

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