[English] 日本語
Yorodumi
- PDB-6e25: NMR solution structure of the CARD9 CARD bound to zinc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6.0E+25
TitleNMR solution structure of the CARD9 CARD bound to zinc
ComponentsCaspase recruitment domain-containing protein 9
KeywordsSIGNALING PROTEIN / CARD / innate immunity
Function / homology
Function and homology information


regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / response to peptidoglycan / antifungal innate immune response / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of innate immune response / neutrophil mediated immunity / positive regulation of T-helper 17 type immune response ...regulation of interleukin-2 production / host-mediated regulation of intestinal microbiota composition / CBM complex / response to peptidoglycan / antifungal innate immune response / positive regulation of stress-activated MAPK cascade / CARD domain binding / positive regulation of innate immune response / neutrophil mediated immunity / positive regulation of T-helper 17 type immune response / positive regulation of cytokine production involved in inflammatory response / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of macrophage cytokine production / response to aldosterone / response to exogenous dsRNA / : / positive regulation of interleukin-17 production / response to muramyl dipeptide / immunoglobulin mediated immune response / signaling adaptor activity / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / positive regulation of cytokine production / positive regulation of JNK cascade / NOD1/2 Signaling Pathway / protein homooligomerization / CLEC7A (Dectin-1) signaling / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / defense response to virus / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / response to xenobiotic stimulus / protein homodimerization activity / protein-containing complex / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CARD9, CARD domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Death-like domain superfamily
Similarity search - Domain/homology
Caspase recruitment domain-containing protein 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsHolliday, M.J. / Dueber, E.C. / Fairbrother, W.J.
CitationJournal: J Biol Chem / Year: 2018
Title: Picomolar zinc binding modulates formation of Bcl10-nucleating assemblies of the caspase recruitment domain (CARD) of CARD9.
Authors: Michael J Holliday / Ryan Ferrao / Gladys de Leon Boenig / Alberto Estevez / Elizabeth Helgason / Alexis Rohou / Erin C Dueber / Wayne J Fairbrother /
Abstract: The caspase recruitment domain-containing protein 9 (CARD9)-B-cell lymphoma/leukemia 10 (Bcl10) signaling axis is activated in myeloid cells during the innate immune response to a variety of diverse ...The caspase recruitment domain-containing protein 9 (CARD9)-B-cell lymphoma/leukemia 10 (Bcl10) signaling axis is activated in myeloid cells during the innate immune response to a variety of diverse pathogens. This signaling pathway requires a critical caspase recruitment domain (CARD)-CARD interaction between CARD9 and Bcl10 that promotes downstream activation of factors, including NF-κB and the mitogen-activated protein kinase (MAPK) p38. Despite these insights, CARD9 remains structurally uncharacterized, and little mechanistic understanding of its regulation exists. We unexpectedly found here that the CARD in CARD9 binds to Zn with picomolar affinity-a concentration comparable with the levels of readily accessible Zn in the cytosol. NMR solution structures of the CARD9-CARD in the apo and Zn-bound states revealed that Zn has little effect on the ground-state structure of the CARD; yet the stability of the domain increased considerably upon Zn binding, with a concomitant reduction in conformational flexibility. Moreover, Zn binding inhibited polymerization of the CARD9-CARD into helical assemblies. Here, we also present a 20-Å resolution negative-stain EM (NS-EM) structure of these filamentous assemblies and show that they adopt a similar helical symmetry as reported previously for filaments of the Bcl10 CARD. Using both bulk assays and direct NS-EM visualization, we further show that the CARD9-CARD assemblies can directly template and thereby nucleate Bcl10 polymerization, a capacity considered critical to propagation of the CARD9-Bcl10 signaling cascade. Our findings indicate that CARD9 is a potential target of Zn-mediated signaling that affects Bcl10 polymerization in innate immune responses.
History
DepositionJul 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model
Revision 1.3May 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: Caspase recruitment domain-containing protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3302
Polymers11,2651
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area100 Å2
ΔGint-35 kcal/mol
Surface area6210 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Caspase recruitment domain-containing protein 9 / hCARD9


Mass: 11264.877 Da / Num. of mol.: 1 / Fragment: CARD domain residues 1-97
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CARD9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H257
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D CBCA(CO)NH
141isotropic13D HNCA
1131isotropic13D HN(CA)CB
171isotropic13D H(CCO)NH
1121isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-15N NOESY
1101isotropic13D 1H-13C NOESY aliphatic
193isotropic13D 1H-13C NOESY aliphatic
183isotropic13D 1H-13C NOESY aromatic
162isotropic12D 1H-13C HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.40 mM [U-13C; U-15N] CARD9 CARD, 0.46 mM zinc, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution30.40 mM [U-13C; U-15N] CARD9 CARD, 0.46 mM zinc, 100% D2O13C15N_D2O_sample100% D2O
solution20.40 mM [U-10% 13C; U-100% 15N] CARD9 CARD, 0.46 mM zinc, 50% H2O/50% D2O[10%]13C[U]15N_sample50% H2O/50% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.40 mMCARD9 CARD[U-13C; U-15N]1
0.46 mMzincnone1
0.40 mMCARD9 CARD[U-13C; U-15N]3
0.46 mMzincnone3
0.40 mMCARD9 CARD[U-10% 13C; U-100% 15N]2
0.46 mMzincnone2
Sample conditionsDetails: 50 mM HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.0 / Ionic strength: 350 M / Label: Condition 1 / pH: 7 / Pressure: 1 atm / Temperature: 310 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger A. T. et.al.refinement
CYANA3.97Guntert, Mumenthaler and Wuthrichrefinement
Analysis2.4.2CCPNchemical shift assignment
Analysis2.4.2CCPNpeak picking
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
Refinement
MethodSoftware ordinal
simulated annealing2
simulated annealing1
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