[English] 日本語
Yorodumi
- PDB-2mjm: The solution NMR structure of the NLRC5 caspase recruitment domai... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2mjm
TitleThe solution NMR structure of the NLRC5 caspase recruitment domain (CARD)
ComponentsProtein NLRC5
KeywordsSIGNALING PROTEIN / PROTEIN BINDING / NLRC5 / CARD / RIG-I / DEATH FOLD / PROTEIN-PROTEIN INTERACTION / INFLAMMATION / INNATE IMMUNE SYSTEM
Function / homology
Function and homology information


positive regulation of MHC class I biosynthetic process / regulation of kinase activity / positive regulation of type II interferon-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / negative regulation of type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / response to bacterium / defense response to virus / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...positive regulation of MHC class I biosynthetic process / regulation of kinase activity / positive regulation of type II interferon-mediated signaling pathway / positive regulation of type I interferon-mediated signaling pathway / negative regulation of type I interferon-mediated signaling pathway / negative regulation of NF-kappaB transcription factor activity / response to bacterium / defense response to virus / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / innate immune response / centrosome / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Death Domain, Fas - #20 / NLRC5, atypical caspase recruitment domain / Atypical caspase recruitment domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. ...Death Domain, Fas - #20 / NLRC5, atypical caspase recruitment domain / Atypical caspase recruitment domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / Death Domain, Fas / Leucine Rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / molecular dynamics
AuthorsGutte, P.G.M. / Zerbe, O.
CitationJournal: Biochemistry / Year: 2014
Title: Unusual structural features revealed by the solution NMR structure of the NLRC5 caspase recruitment domain.
Authors: Gutte, P.G. / Jurt, S. / Grutter, M.G. / Zerbe, O.
History
DepositionJan 12, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
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: Protein NLRC5


Theoretical massNumber of molelcules
Total (without water)11,6691
Polymers11,6691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein NLRC5


Mass: 11669.408 Da / Num. of mol.: 1
Fragment: NLRC5 caspase recruitment domain (UNP residues 1-96)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nlrc5 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C3VPR6

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D (H)CCH-TOCSY
1713D 1H-13C NOESY aliphatic
1813D 1H-13C NOESY aromatic
1913D HNCO
1101HB(CBCGCD)HD

-
Sample preparation

DetailsContents: 600 uM [U-100% 13C; U-100% 15N] protein, 20 mM MES, 100 mM sodium chloride, 50 mM potassium chloride, 2 mM TCEP, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
600 uMentity-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
50 mMpotassium chloride-41
2 mMTCEP-51
Sample conditionsIonic strength: 0 / pH: 6.2 / Pressure: ambient / Temperature: 310 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE7002

-
Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospinprocessing
CARA1.8.6Keller and Wuthrichdata analysis
UNIO'10Torsten Herrmannpeak picking
UNIO'10Torsten Herrmannstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CHARMMB. R. Brooks, C. L. Brooks III, D. M. York, and M. Karplusrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: RESTRAINED MOLECULAR DYNAMICS IN EXPLICIT SOLVENT
NMR constraintsNOE constraints total: 1278 / NOE intraresidue total count: 429 / NOE long range total count: 198 / NOE medium range total count: 304 / NOE sequential total count: 347
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://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