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- PDB-3rc6: Molecular mechanisms of viral and host-cell substrate recognition... -

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Basic information

Entry
Database: PDB / ID: 3rc6
TitleMolecular mechanisms of viral and host-cell substrate recognition by HCV NS3/4A protease
ComponentsNS3/4A
KeywordsVIRAL PROTEIN / HYDROLASE / drug resistance / drug design / Protease inhibitors / serine protease
Function / homology
Function and homology information


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 / channel activity / viral nucleocapsid ...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 / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / 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 / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / 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
Biological speciesHepatitis C virus subtype 1a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSchiffer, C.A. / Romano, K.P.
CitationJournal: J.Virol. / Year: 2011
Title: Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease.
Authors: Romano, K.P. / Laine, J.M. / Deveau, L.M. / Cao, H. / Massi, F. / Schiffer, C.A.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Jul 26, 2023Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 1.6Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NS3/4A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5532
Polymers21,4871
Non-polymers651
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.850, 58.581, 60.901
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NS3/4A


Mass: 21487.330 Da / Num. of mol.: 1
Fragment: NS4A (UNP residues 1678-1688), NS3 (UNP residues 1027-1208)
Mutation: A1027S, P1028G, I1029D, L1039E, L1040E, I1043Q, I1044E, L1047Q, A1066T, C1073S, C1078L, I1098T, P1112Q, S1165A, C1185S, C1679S, V1686I, I1687N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus subtype 1a / Gene: NS3 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8DG50
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY ...THE COFACTOR 4A RESIDUES 990-1000 (GLY SER VAL VAL ILE VAL GLY ARG ILE ASN LEU) IN THIS ENTRY CORRESPOND TO RESIDUES NUMBERING 1678-1688 OF DATABASE SEQUENCE REFERENCE (UNP A8DG50). THIS PEPTIDE IS COVALENTLY LINKED TO THE N-TERMINUS OF NS3. C1679S MUTATION WAS ENGINEERED TO PREVENT DISULFIDE FORMATION. THE V1686I AND I1687N WERE ENGINEERED TO OPTIMIZE THE LINKER BETWEEN THE COFACTOR 4A AND NS3.

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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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 295 K / Method: hanging drop, vapor diffusion / pH: 6.2
Details: 20-25% PEG 3350, 0.1M MES (pH 6.5), 4% ammonium sulfate, hanging drop, vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F
DetectorDate: Jul 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 45595 / % possible obs: 93.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Χ2: 1.004 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.3540.37746791.001197.1
1.35-1.44.10.28646471.006196.6
1.4-1.464.10.21446591.007196.1
1.46-1.544.20.15346300.999195.5
1.54-1.644.20.11246031.006195.2
1.64-1.764.30.08445871.003194.2
1.76-1.944.30.06945441.003193.1
1.94-2.224.10.06344961.004191.3
2.22-2.84.10.05244691.008190
2.8-504.30.03242811.005182.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M5M

3m5m


Resolution: 1.3→26.62 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.2099 / WRfactor Rwork: 0.1794 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8976 / SU B: 1.419 / SU ML: 0.028 / SU R Cruickshank DPI: 0.0533 / SU Rfree: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2301 5.1 %RANDOM
Rwork0.1608 ---
obs0.1623 45433 92.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.72 Å2 / Biso mean: 11.9581 Å2 / Biso min: 3.15 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.88 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1465 0 1 166 1632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211531
X-RAY DIFFRACTIONr_bond_other_d0.0010.021022
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9552091
X-RAY DIFFRACTIONr_angle_other_deg0.80732500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.14422.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.37915242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6231513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211749
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
X-RAY DIFFRACTIONr_mcbond_it1.0051.51014
X-RAY DIFFRACTIONr_mcbond_other0.2731.5422
X-RAY DIFFRACTIONr_mcangle_it1.65121634
X-RAY DIFFRACTIONr_scbond_it2.2863517
X-RAY DIFFRACTIONr_scangle_it3.3474.5451
X-RAY DIFFRACTIONr_rigid_bond_restr0.84432553
LS refinement shellResolution: 1.3→1.333 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 172 -
Rwork0.194 3169 -
all-3341 -
obs--93.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6005-2.9165-3.37118.478411.656411.59550.1573-0.05850.1258-0.66480.0407-0.0602-0.95840.244-0.1980.20860.02150.04340.13320.03790.09666.2002-21.6156-2.5018
20.7032-0.3198-0.8094.46730.53231.01120.04590.02520.0187-0.02310.0008-0.1499-0.04020.0597-0.04670.07420.0014-0.00070.07340.00740.09515.2642-4.865516.1121
3-1.6534-1.904-2.184612.094-6.98868.7589-0.0417-0.45180.08230.7352-0.0806-0.5253-0.4985-0.18020.12230.1484-0.05290.04280.2079-0.11060.1249-0.3665.943128.9734
43.5297-1.054-3.30321.78580.52473.26130.0915-0.11260.14690.01360.0181-0.0775-0.06760.1967-0.10960.0931-0.00720.0030.06420.00540.1034.99394.468118.1807
53.8115-1.79180.37276.0976-0.12593.36280.11160.20860.0052-0.5102-0.1661-0.1723-0.06620.05510.05450.10690.0070.03810.0660.01520.083610.1158-5.47738.6752
613.57950.2962-9.70610.14291.653413.52560.0774-0.39170.01210.02670.0729-0.1572-0.3480.6756-0.15030.0815-0.0402-0.02360.0821-0.00130.169311.8753-2.233922.1915
71.6332-0.3307-0.78061.62260.0196.03390.14710.10980.0443-0.089-0.0017-0.04990.0095-0.2508-0.14540.07150.0066-0.00140.07980.01760.085-0.1724-4.759515.8803
81.0601-0.1161-0.27060.54970.16890.26340.0019-0.0197-0.03390.0025-0.0101-0.00740.00340.00760.00810.08050.0008-0.00170.07080.00460.0833-1.945-11.87121.5539
92.08160.9793-0.43791.072-0.17671.3389-0.0006-0.0376-0.1162-0.0446-0.0873-0.08730.05560.13060.08780.07130.00890.0090.07960.01160.108410.2189-13.295516.2357
101.39010.5577-0.03250.91560.49450.7296-0.0011-0.0436-0.11010.0257-0.0453-0.03070.03970.01190.04630.08210.0026-0.00040.06840.00830.0931-0.6166-17.929321.5944
111.6894-0.0774-1.60010.51220.09631.37170.0429-0.28650.05820.062-0.0442-0.0059-0.03620.17070.00130.0787-0.0161-0.00340.1094-0.01530.0731-4.0834-7.038334.7578
124.10451.7335-3.37211.6466-2.43295.2866-0.0202-0.09150.5717-0.1434-0.03770.32680.07470.02160.05790.08930.014-0.01820.0367-0.030.2427-8.42181.719323.6642
1313.73677.9437-7.48745.951-3.78323.57040.2030.07670.64390.02720.21630.093-0.0698-0.1749-0.41940.07620.01450.04230.0614-0.01610.1658-15.24841.465928.5889
142.8382-0.6685-1.35823.0622-0.5461.94450.01750.0056-0.0501-0.0410.04440.14080.003-0.1442-0.0620.07320.00390.00910.09850.01120.0789-20.308-9.242629.162
152.0370.03271.8623-1.4275-3.39818.08650.08630.1030.7780.0967-0.0695-0.1445-0.41420.2361-0.01680.09840.03120.08280.07710.050.2442-20.50283.190723.7366
162.6337-3.12040.39.6465-1.59570.7822-0.08050.03760.09350.05810.2476-0.0291-0.0195-0.1102-0.1670.08720.0152-0.00150.10210.04650.0785-14.71692.10815.4285
170.43680.1613-1.28250.2170.8596.2820.0772-0.06220.1432-0.0089-0.0440.1191-0.15880.0355-0.03330.08490.00070.01180.0934-0.01950.1071-8.4915-3.714628.8877
182.4673-0.7228-0.06870.28120.72612.70130.0155-0.05030.06450.0258-0.00520.0140.05310.0325-0.01030.0833-0.00360.00890.07820.00170.0862-9.7676-8.5327.8481
194.30543.37261.68352.6004-5.19758.3494-0.06290.58970.18410.04150.520.61340.2052-0.3252-0.45710.06950.0092-0.02240.19510.08090.1194-22.0678-3.608716.0334
204.2418-2.29081.10112.2512-1.18491.5127-0.0178-0.1313-0.16960.05320.05040.07430.0638-0.0076-0.03260.088-0.00580.00230.08250.01310.0799-9.7691-14.924228.956
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A980 - 989
2X-RAY DIFFRACTION2A990 - 997
3X-RAY DIFFRACTION3A998 - 1005
4X-RAY DIFFRACTION4A1006 - 1012
5X-RAY DIFFRACTION5A1013 - 1025
6X-RAY DIFFRACTION6A1026 - 1031
7X-RAY DIFFRACTION7A1032 - 1042
8X-RAY DIFFRACTION8A1043 - 1061
9X-RAY DIFFRACTION9A1062 - 1071
10X-RAY DIFFRACTION10A1072 - 1088
11X-RAY DIFFRACTION11A1089 - 1104
12X-RAY DIFFRACTION12A1105 - 1111
13X-RAY DIFFRACTION13A1112 - 1117
14X-RAY DIFFRACTION14A1118 - 1125
15X-RAY DIFFRACTION15A1126 - 1130
16X-RAY DIFFRACTION16A1131 - 1136
17X-RAY DIFFRACTION17A1137 - 1148
18X-RAY DIFFRACTION18A1149 - 1155
19X-RAY DIFFRACTION19A1156 - 1164
20X-RAY DIFFRACTION20A1165 - 1181

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