[English] 日本語
Yorodumi
- PDB-5i65: Porcine reproductive and respiratory syndrome virus nonstructural... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i65
TitlePorcine reproductive and respiratory syndrome virus nonstructural protein 7 alpha (nsp7 alpha)
ComponentsNonstructural proteins ORF1a
KeywordsUNKNOWN FUNCTION / nonstructural / complex / reproduction
Function / homology
Function and homology information


: / host cell membrane / host cell cytoplasm / membrane => GO:0016020 / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / ATP binding ...: / host cell membrane / host cell cytoplasm / membrane => GO:0016020 / RNA helicase activity / viral protein processing / cysteine-type endopeptidase activity / serine-type endopeptidase activity / host cell nucleus / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 ...Replicase polyprotein 1ab, peptidase C33-associated domain / Peptidase_C33-associated domain / Arterivirus polyprotein, nsp2, immunogenic region / Arterivirus papain-like cysteine protease beta (PCPbeta) domain superfamily / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain superfamily / Porcine arterivirus-type cysteine proteinase alpha / Equine arteritis virus putative proteinase / Immunogenic region of nsp2 protein of arterivirus polyprotein / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain / Arterivirus Nsp2, peptidase C33 / Equine arteritis virus peptidase S32 / Serine protease, chymotrypsin-like serine protease, C-terminal / Arterivirus NSP4 peptidase domain / Arterivirus papain-like cysteine protease beta (PCPbeta) domain / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp7 alpha superfamily / Equine arterivirus Nsp2-type cysteine proteinase / Equine arteritis virus serine endopeptidase S32 / Arterivirus nonstructural protein 7 alpha / Arterivirus nsp4 proteinase domain profile. / Arterivirus nsp2 cysteine protease (AV CP) domain profile. / Arterivirus papain-like cysteine protease alpha (PCPalpha) domain profile. / Arterivirus papain-like cysteine protease beta (PCPbeta) domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Non-structural protein 3
Similarity search - Component
Biological speciesPorcine reproductive and respiratory syndrome virus
MethodSOLUTION NMR
AuthorsChen, J. / Xu, X.
Funding support China, 1items
OrganizationGrant numberCountry
the Fundamental Research Funds for the Central UniversitiesQN2011065 China
CitationJournal: To Be Published
Title: Structure of porcine reproductive and respiratory syndrome virus nonstructural protein 7 alpha (nsp7 alpha)
Authors: Chen, J. / Xu, X.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Structure summary / Category: database_2 / entity / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nonstructural proteins ORF1a


Theoretical massNumber of molelcules
Total (without water)15,9311
Polymers15,9311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Nonstructural proteins ORF1a / nonstructural protein 7a


Mass: 15931.478 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 2200-2348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine reproductive and respiratory syndrome virus
Production host: Escherichia coli (E. coli) / References: UniProt: Q6QDR1

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
121isotropic23D CBCA(CO)NH
1122isotropic23D CBCA(CO)NH
131isotropic33D HNCA
1132isotropic33D HNCA
141isotropic43D HN(CA)CB
1142isotropic43D HN(CA)CB
151isotropic53D HNCO
1152isotropic53D HNCO
161isotropic63D HN(CO)CA
1162isotropic63D HN(CO)CA
171isotropic72D 1H-13C HSQC
181isotropic83D 1H-13C NOESY aliphatic
1172isotropic83D 1H-13C NOESY aliphatic
191isotropic93D HBHA(CO)NH
1182isotropic93D HBHA(CO)NH
1101isotropic103D (H)CCH-TOCSY
1192isotropic103D (H)CCH-TOCSY
1112isotropic113D 1H-15N NOESY

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solid10.002 w/v [U-13C] Glucose, 92% H2O/8% D2O13C_sample92% H2O/8% D2O
solid20.001 w/v [U-15N] NH4Cl, 92% H2O/8% D2O15N_sample92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.002 w/vGlucose[U-13C]1
0.001 w/vNH4Cl[U-15N]2
Sample conditionsIonic strength: 150 mM / Ionic strength err: 0.2 / Label: conditions_1 / pH: 7.5 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker 15N_HSQCBruker15N_HSQC6001
Bruker CBCACONHBrukerCBCACONH6002
Bruker HNCABrukerHNCA6003
Bruker HNCACBBrukerHNCACB6004
Bruker HNCOBrukerHNCO6005
Bruker HNCOCABrukerHNCOCA6006
Bruker 13C_HSQCBruker13C_HSQC6007
Bruker 13C_NOEBruker13C_NOE6008
Bruker HBHACONHBrukerHBHACONH6009
Beijing NMR Center HCCHTOCSYBeijing NMR CenterHCCHTOCSY60010
Beijing NMR Center 15N_NOEBeijing NMR Center15N_NOE60011

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARAKeller and Wuthrichchemical shift assignment
CARAKeller and Wuthrichdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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://pdbjlvh1.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