[English] 日本語
Yorodumi
- PDB-4cbh: Pestivirus NS3 helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cbh
TitlePestivirus NS3 helicase
ComponentsSERINE PROTEASE NS3
KeywordsHYDROLASE / SF2 HELICASES / FLAVIVIRIDAE NS3 / SAXS
Function / homology
Function and homology information


pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...pestivirus NS3 polyprotein peptidase / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell surface / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / RNA helicase activity / viral protein processing / RNA helicase / induction by virus of host autophagy / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / GTP binding / host cell plasma membrane / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 ...Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / : / Flavivirus NS3 helicase, C-terminal helical domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal 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. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesCLASSICAL SWINE FEVER VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsTortorici, M.A. / Duquerroy, S. / Kwok, J. / Vonrhein, C. / Perez, J. / Lamp, B. / Bricogne, G. / Rumenapf, T. / Vachette, P. / Rey, F.A.
CitationJournal: J.Virol. / Year: 2015
Title: X-Ray Structure of the Pestivirus Ns3 Helicase and its Conformation in Solution.
Authors: Tortorici, M.A. / Duquerroy, S. / Kwok, J. / Vonrhein, C. / Perez, J. / Lamp, B. / Bricogne, G. / Rumenapf, T. / Vachette, P. / Rey, F.A.
History
DepositionOct 14, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Oct 14, 2015Group: Refinement description
Revision 1.4Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SERINE PROTEASE NS3
B: SERINE PROTEASE NS3
C: SERINE PROTEASE NS3
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)232,0924
Polymers232,0924
Non-polymers00
Water13,836768
1
A: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: SERINE PROTEASE NS3


Theoretical massNumber of molelcules
Total (without water)58,0231
Polymers58,0231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.070, 144.440, 118.690
Angle α, β, γ (deg.)90.00, 92.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.8159, -0.5781, -0.008363), (-0.578, -0.8154, -0.03218), (0.01179, 0.03109, -0.9994)16, 49.25, 54.59
3given(-0.9998, -0.004143, 0.01775), (0.005176, -0.9983, 0.05858), (0.01747, 0.05866, 0.9981)29.15, 42.24, -1.335
4given(-0.7941, 0.6078, -0.003618), (0.6076, 0.7937, -0.02796), (-0.01412, -0.0244, -0.9996)13.34, -3.866, 56.72

-
Components

#1: Protein
SERINE PROTEASE NS3 / NON-STRUCTURAL PROTEIN 3


Mass: 58023.031 Da / Num. of mol.: 4 / Fragment: HELICASE DOMAIN, 1782-2280
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLASSICAL SWINE FEVER VIRUS / Strain: ALFORT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P19712, pestivirus NS3 polyprotein peptidase, nucleoside-triphosphate phosphatase, RNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHISTAG N-TERMINAL PLUS TEV CLEAVAGE SITE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.04 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M NA-CACODYLATE, 0.2 M MAGNESIUM ACETATE, 12% PEG 8000, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→44.34 Å / Num. obs: 71319 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 63.93 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.8
Reflection shellResolution: 2.51→2.58 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / % possible all: 49.6

-
Processing

Software
NameVersionClassification
BUSTER2.13.0refinement
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CBG

4cbg


Resolution: 2.51→72.22 Å / Cor.coef. Fo:Fc: 0.9197 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.394 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.248
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3572 5.01 %RANDOM
Rwork0.2034 ---
obs0.2048 71319 88.63 %-
Displacement parametersBiso mean: 60.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.7644 Å20 Å2-0.367 Å2
2--2.287 Å20 Å2
3----1.5227 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.51→72.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11023 0 0 768 11791
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0111239HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2815196HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4015SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes295HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1598HARMONIC5
X-RAY DIFFRACTIONt_it11239HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.56
X-RAY DIFFRACTIONt_other_torsion21.19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1482SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13421SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2759 118 5.26 %
Rwork0.2432 2125 -
all0.245 2243 -
obs--88.63 %
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)
12.6191-0.1274-0.2721.8936-0.58373.1520.0655-0.518-0.19210.26730.12030.1752-0.2652-0.2927-0.1858-0.163-0.04060.0123-0.03730.0662-0.0511-2.8678-0.69146.6993
22.0786-0.25140.40871.8334-0.70162.80720.0338-0.3689-0.04190.2141-0.0137-0.2564-0.00420.5364-0.0201-0.2698-0.0367-0.0489-0.0376-0.0107-0.096828.0079-4.034540.7464
33.98420.0862-0.82251.4096-0.35114.58390.28490.93010.3302-0.3603-0.14430.1989-0.3984-0.9336-0.1406-0.16510.157-0.0203-0.00280.0799-0.173513.390551.64549.8015
42.87780.1254-0.44461.6179-0.04581.49930.02930.2757-0.2022-0.0919-0.0338-0.21240.04760.06690.0045-0.1230.0133-0.0093-0.1842-0.0192-0.068240.346235.663515.7121
51.5946-0.30670.17031.63920.99493.42430.0737-0.41430.21990.29550.0358-0.12020.30060.2866-0.1095-0.1351-0.0769-0.0202-0.0674-0.0618-0.092231.814444.776247.0159
62.2958-0.5681-0.58282.04240.69492.28920.0328-0.33610.12260.1798-0.11840.2058-0.0066-0.6310.0856-0.2775-0.04910.02430.0114-0.0759-0.1240.956148.271241.0165
71.6505-0.3824-1.63191.30530.24324.08940.05410.2904-0.2008-0.3075-0.0159-0.050.14960.2279-0.0382-0.1020.0133-0.0073-0.1475-0.0822-0.038616.2987-6.70879.2617
86.921.8603-8.82330.8734-6.95392.32130.03020.1734-0.0586-0.25070.33810.12220.17550.1972-0.3684-0.0727-0.30320.01470.7218-0.1353-0.34035.311117.6218-9.0749
91.4614-0.68020.21181.5314-0.23211.83040.15310.1484-0.0248-0.12420.02640.2550.0907-0.2699-0.1795-0.2380.0022-0.023-0.20320.0387-0.0972-11.93187.90616.4174
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|202 - A|351}
2X-RAY DIFFRACTION2{A|471 - A|496,A|526 - A|682}
3X-RAY DIFFRACTION3{B|206 - B|351}
4X-RAY DIFFRACTION4{B|471 - B|496,B|526 - B|687}
5X-RAY DIFFRACTION5{C|205 - C|351}
6X-RAY DIFFRACTION6{C|471 - C|496,C|526 - C|681}
7X-RAY DIFFRACTION7{D|202 - D|351}
8X-RAY DIFFRACTION8{D|366 - D|474,D|491 - D|525}
9X-RAY DIFFRACTION9{D|475 - D|490,D|526 - D|688}

+
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