[English] 日本語
Yorodumi
- PDB-4wxr: X-ray crystal structure of NS3 Helicase from HCV with a bound inh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wxr
TitleX-ray crystal structure of NS3 Helicase from HCV with a bound inhibitor at 2.42 A resolution
ComponentsNS3
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Helicase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


transformation of host cell by virus / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / viral capsid / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane ...transformation of host cell by virus / serine-type peptidase activity / ribonucleoside triphosphate phosphatase activity / viral capsid / RNA helicase activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / symbiont entry into host cell / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / proteolysis / ATP binding / membrane
Similarity search - Function
RNA Helicase; Chain A, domain 3 / RNA Helicase Chain A , domain 3 / : / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain ...RNA Helicase; Chain A, domain 3 / RNA Helicase Chain A , domain 3 / : / NS3 RNA helicase, C-terminal helical domain / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / 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 / P-loop containing nucleotide triphosphate hydrolases / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3VZ / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsDavies, D.R. / Kim, H. / Lorimer, D.
CitationJournal: TO BE PUBLISHED
Title: crystal structure of NS3 Helicase from HCV with a bound inhibitor
Authors: Buckman, B.O. / Kossen, K. / Misialek, S. / Stevens, S. / Rajagopalan, R. / Ruhmund, D. / Hooi, L. / Snarskaya, N. / Serebryany, V. / Wang, G. / Stoycheva, A. / Nicholas, J.B. / Davies, D.R. ...Authors: Buckman, B.O. / Kossen, K. / Misialek, S. / Stevens, S. / Rajagopalan, R. / Ruhmund, D. / Hooi, L. / Snarskaya, N. / Serebryany, V. / Wang, G. / Stoycheva, A. / Nicholas, J.B. / Davies, D.R. / Brunton, S. / Montalbetti, C. / Weddell, D. / Goodwin, C. / Schonfeld, D. / Mather, O. / Cheng, R. / Blatt, L. / Beigelman, L.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS3
B: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4294
Polymers96,6022
Non-polymers8272
Water3,225179
1
A: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7142
Polymers48,3011
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7142
Polymers48,3011
Non-polymers4141
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)124.074, 112.776, 99.592
Angle α, β, γ (deg.)90.00, 126.52, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein NS3


Mass: 48300.793 Da / Num. of mol.: 2 / Fragment: UNP residues 180-630 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Production host: Escherichia coli (E. coli) / References: UniProt: A1Z092
#2: Chemical ChemComp-3VZ / {6-(3,5-diaminophenyl)-1-[4-(propan-2-yl)benzyl]-1H-indol-3-yl}acetic acid


Mass: 413.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H27N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 2.0 M NA/K PHOSPHATE (PH 10.5), 186 MM LI2SO4, 100 MM CAPS PH 10.5, VAPOR DIFFUSION, TEMPERATURE 289K
PH range: 10.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: SBC-3 / Detector: CCD / Date: Mar 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→29.7 Å / Num. obs: 38561 / % possible obs: 92.15 % / Redundancy: 2.4 % / Net I/σ(I): 15.12

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HEI

1hei


Resolution: 2.42→29.7 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.867 / SU B: 25.823 / SU ML: 0.273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.508 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.31 1931 5 %RANDOM
Rwork0.239 ---
obs0.243 38561 91.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20.06 Å2
2---0.41 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.42→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6511 0 62 179 6752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226733
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9759203
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0655858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29423.56250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075151014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2191534
X-RAY DIFFRACTIONr_chiral_restr0.0950.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215090
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.54308
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13926990
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67832425
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.74.52213
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 145 -
Rwork0.303 2616 -
obs--91.09 %
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)
10.3201-0.340.08651.39560.31320.87830.02990.07010.0202-0.09280.0231-0.0362-0.03950.0134-0.05290.08510.02830.01040.1249-0.01710.0275-20.28173.001910.6775
20.2171-0.0527-0.39980.7812-0.21420.86070.04990.0205-0.0158-0.0055-0.04410.0489-0.0195-0.0439-0.00570.07450.0313-0.0150.1254-0.01640.0622-18.0634-5.654916.3281
32.6921-0.4769-0.92272.51630.92460.45530.0667-0.14530.3194-0.27620.0787-0.3486-0.11750.0662-0.14530.051-0.01920.04180.0169-0.00230.180214.241210.939325.2031
41.91640.4607-1.12720.51950.10060.8344-0.07450.05960.0265-0.11050.0858-0.0427-0.0015-0.0061-0.01130.07930.0585-0.01070.0823-0.00680.12474.61440.461125.6004
50.40480.06040.29680.46750.6691.73050.1258-0.03550.00440.0535-0.0006-0.05990.14590.0146-0.12530.06440.00090.00950.08940.00610.0681-14.6844-3.376143.1515
60.0590.4465-0.02042.1511-0.41272.0718-0.05540.03810.0346-0.12030.01260.08220.1138-0.00160.04280.0720.0282-0.02330.15010.03360.028618.1479-26.28645.7183
70.4926-0.4415-0.15781.41560.22720.7435-0.0402-0.0139-0.0107-0.0756-0.0234-0.0556-0.02080.130.06370.04790.03180.01180.12450.03240.055722.6103-26.080314.8168
81.48830.37630.61730.77670.13860.4727-0.06330.0071-0.1619-0.05690.02630.1532-0.001-0.01020.0370.05080.03480.01760.058200.1277-7.5459-32.746925.7541
90.33950.2137-0.33570.5309-0.51211.61080.05490.0143-0.03820.0596-0.05420.0032-0.05760.0001-0.00070.06310.0251-0.03280.078-0.00880.075317.6046-24.082139.4959
101.8071.8299-2.51342.6442-0.67346.01690.2942-0.21790.06820.1339-0.24630.2412-0.80460.0444-0.04790.15980.0366-0.00140.08690.02350.082314.7338-15.247449.3469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A190 - 276
2X-RAY DIFFRACTION2A277 - 330
3X-RAY DIFFRACTION3A331 - 405
4X-RAY DIFFRACTION4A406 - 487
5X-RAY DIFFRACTION5A488 - 627
6X-RAY DIFFRACTION6B186 - 246
7X-RAY DIFFRACTION7B249 - 328
8X-RAY DIFFRACTION8B329 - 480
9X-RAY DIFFRACTION9B481 - 601
10X-RAY DIFFRACTION10B602 - 629

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more