4IRL

X-ray structure of the CARD domain of zebrafish GBP-NLRP1 like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structure of the caspase-recruitment domain from a zebrafish guanylate-binding protein.

Jin, T.Huang, M.Smith, P.Jiang, J.Xiao, T.S.

(2013) Acta Crystallogr.,Sect.F 69: 855-860

  • DOI: 10.1107/S1744309113015558

  • PubMed Abstract: 
  • The caspase-recruitment domain (CARD) mediates homotypic protein-protein interactions that assemble large oligomeric signaling complexes such as the inflammasomes during innate immune responses. Structural studies of the mammalian CARDs demonstrate t ...

    The caspase-recruitment domain (CARD) mediates homotypic protein-protein interactions that assemble large oligomeric signaling complexes such as the inflammasomes during innate immune responses. Structural studies of the mammalian CARDs demonstrate that their six-helix bundle folds belong to the death-domain superfamily, whereas such studies have not been reported for other organisms. Here, the zebrafish interferon-induced guanylate-binding protein 1 (zIGBP1) was identified that contains an N-terminal GTPase domain and a helical domain typical of the mammalian guanylate-binding proteins, followed by a FIIND domain and a C-terminal CARD similar to the mammalian inflammasome proteins NLRP1 and CARD8. The structure of the zIGBP1 CARD as a fusion with maltose-binding protein was determined at 1.47 Å resolution. This revealed a six-helix bundle fold similar to the NLRP1 CARD structure with the bent α1 helix typical of all known CARD structures. The zIGBP1 CARD surface contains a positively charged patch near its α1 and α4 helices and a negatively charged patch near its α2, α3 and α5 helices, which may mediate its interaction with partner domains. Further studies using binding assays and other analyses will be required in order to address the physiological function(s) of this zebrafish protein.


    Organizational Affiliation

    Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 4 Memorial Drive, Building 4, Room 228, Bethesda, MD 20892-0430, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein, Novel protein similar to vertebrate guanylate binding protein family
A, B, C
476Danio rerioEscherichia coli (strain K12)
This entity is chimeric
Mutation(s): 0 
Gene Names: gbp3, malE
Find proteins for B0V1H4 (Danio rerio)
Go to UniProtKB:  B0V1H4
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MLI
Query on MLI

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A, B, C
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
MTT
Query on MTT

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Download CCD File 
A, B, C
MALTOTETRAOSE
C24 H42 O21
LUEWUZLMQUOBSB-ZLBHSGTGSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.749α = 90.00
b = 124.750β = 90.00
c = 178.044γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Blu-Icedata collection
PHASERphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2014-11-26
    Type: Refinement description
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy
  • Version 1.4: 2017-11-15
    Type: Refinement description