4IKM | pdb_00004ikm

X-ray structure of CARD8 CARD domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.2 of the entry. See complete history

Literature

The structure of the CARD8 caspase-recruitment domain suggests its association with the FIIND domain and procaspases through adjacent surfaces.

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

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 482-487

  • DOI: https://doi.org/10.1107/S1744309113010075
  • Primary Citation Related Structures: 
    4IKM

  • PubMed Abstract: 

    CARD8 plays crucial roles in regulating apoptotic and inflammatory signaling pathways through the association of its caspase-recruitment domain (CARD) with those of procaspase-9 and procaspase-1. The CARD8 CARD has also been predicted to form an intramolecular complex with its FIIND domain. Here, the first crystal structure of the CARD8 CARD is reported; it adopts a six-helix bundle fold with a unique conformation of the α6 helix that is described here for the first time. The surface of the CARD8 CARD displays a prominent acidic patch at its α2, α3 and α5 helices that may interact with the procaspase-9 CARD, whereas an adjacent charged surface at its α3 and α4 helices may associate with the CARD8 FIIND domain without interfering with the CARD-CARD interaction. This suggests that the function of CARD8 may be regulated by both intramolecular and intermolecular interactions involving electrostatic attractions.


  • Organizational Affiliation
    • Structural Immunobiology Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892-0430, USA.

Macromolecule Content 

  • Total Structure Weight: 54.09 kDa 
  • Atom Count: 3,703 
  • Modeled Residue Count: 463 
  • Deposited Residue Count: 469 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein, Caspase recruitment domain-containing protein 8469Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: b4034CARD8TUCANCARDINALJW3994malEKIAA0955NDPP1
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q9Y2G2 (Homo sapiens)
Explore Q9Y2G2 
Go to UniProtKB:  Q9Y2G2
PHAROS:  Q9Y2G2
GTEx:  ENSG00000105483 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ9Y2G2P0AEX9
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
B
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.253 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.877α = 90
b = 94.877β = 90
c = 219.39γ = 120
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-08
    Type: Initial release
  • Version 1.1: 2013-06-05
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Advisory, Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-30
    Changes: Structure summary