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- PDB-4cl1: The crystal structure of NS5A domain 1 from genotype 1a reveals n... -

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Basic information

Entry
Database: PDB / ID: 4cl1
TitleThe crystal structure of NS5A domain 1 from genotype 1a reveals new clues to the mechanism of action for dimeric HCV inhibitors
ComponentsNON-STRUCTURAL PROTEIN 5A
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


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 / host cell mitochondrion / 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 / lipid droplet / : ...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 / host cell mitochondrion / 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 / lipid droplet / : / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / ribonucleoprotein complex / symbiont entry into host cell / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Hepatitis C NS5A, domain 1B / Hepatitis C virus NS5A, 1B domain / N-terminal domain of TfIIb / 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 NS5A, domain 1B / Hepatitis C virus NS5A, 1B domain / N-terminal domain of TfIIb / 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. / Single Sheet / 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 / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHEPATITIS C VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLambert, S.M. / Langley, D.R. / Garnett, J.A. / Angell, R. / Hedgethorne, K. / Meanwell, N.A. / Matthews, S.J.
CitationJournal: Protein Sci. / Year: 2014
Title: The Crystal Structure of Ns5A Domain 1 from Genotype 1A Reveals New Clues to the Mechanism of Action for Dimeric Hcv Inhibitors.
Authors: Lambert, S.M. / Langley, D.R. / Garnett, J.A. / Angell, R. / Hedgethorne, K. / Meanwell, N.A. / Matthews, S.J.
History
DepositionJan 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: database_PDB_caveat / pdbx_struct_conn_angle ...database_PDB_caveat / pdbx_struct_conn_angle / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_biol / struct_conn / struct_conn_type
Item: _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: NON-STRUCTURAL PROTEIN 5A
B: NON-STRUCTURAL PROTEIN 5A
C: NON-STRUCTURAL PROTEIN 5A
D: NON-STRUCTURAL PROTEIN 5A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6809
Polymers79,3234
Non-polymers3585
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-20.1 kcal/mol
Surface area37080 Å2
MethodPQS
Unit cell
Length a, b, c (Å)100.230, 101.760, 149.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.844305, -0.148388, -0.514908), (-0.146974, -0.988171, 0.04378), (-0.515314, 0.038715, -0.856127)18.67724, -14.96076, 70.54702
2given(-0.992027, -0.114297, 0.053096), (0.102698, -0.977339, -0.185101), (0.073049, -0.178172, 0.981284)-37.11729, -46.66324, -3.17304

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Components

#1: Protein
NON-STRUCTURAL PROTEIN 5A / P56 / NS5A


Mass: 19830.639 Da / Num. of mol.: 4 / Fragment: DOMAIN 1, RESIDUES 2005-2174
Source method: isolated from a genetically manipulated source
Details: SULPHATE ION COORDINATED BY R 41 AND R 81 FROM CHAIN A AND R 78 FROM CHAIN B
Source: (gene. exp.) HEPATITIS C VIRUS (ISOLATE H77) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K4KA16
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 4.73 Å3/Da / Density % sol: 73.97 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M MES PH 6.0 1.6 M MAGNESIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
Details: SESO TWO STAGE DEMAGNIFICATION USING TWO K-B PAIRS OF BIMORPH TYPE MIRRORS
RadiationMonochromator: ACCEL FIXED EXIT DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3→50.12 Å / Num. obs: 17168 / % possible obs: 86 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 103.83 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.5
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 87.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAF

1gaf


Resolution: 3.5→50.115 Å / SU ML: 0.94 / σ(F): 1.34 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2664 866 5.1 %
Rwork0.2249 --
obs0.227 17136 86.05 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.302 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2---9.1493 Å20 Å2
3---6.7992 Å2
Refinement stepCycle: LAST / Resolution: 3.5→50.115 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 9 0 4462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134662
X-RAY DIFFRACTIONf_angle_d1.616395
X-RAY DIFFRACTIONf_dihedral_angle_d16.2131541
X-RAY DIFFRACTIONf_chiral_restr0.094690
X-RAY DIFFRACTIONf_plane_restr0.011843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.71930.31071410.2622678X-RAY DIFFRACTION87
3.7193-4.00630.26021580.22012701X-RAY DIFFRACTION87
4.0063-4.40930.25961500.20122711X-RAY DIFFRACTION87
4.4093-5.04680.23411200.19332733X-RAY DIFFRACTION86
5.0468-6.35640.26891610.2372690X-RAY DIFFRACTION86
6.3564-50.12010.27751360.24262757X-RAY DIFFRACTION83

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