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 9R44 | pdb_00009r44

Crystal structure of human caspase-9 CARD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9R44

This is version 1.1 of the entry. See complete history. 

Literature

Structural insights into human caspase-9 CARD assembly modes driven by conserved arginine hotspots.

Rawal, S., Grininger, C., Peijnenborgh, S., Fischer, P.D., Madl, T., Pavkov-Keller, T.

(2026) J Struct Biol X 14: 100163-100163

  • DOI: https://doi.org/10.1016/j.yjsbx.2026.100163
  • Primary Citation Related Structures: 
    9R44

  • PubMed Abstract: 

    Caspase-9 (C9) is a key initiator of the intrinsic apoptotic pathway and contains an N-terminal caspase activation and recruitment domain (CARD) that mediates homotypic and heterotypic interactions. While previous studies have shown that C9 CARD can form filamentous assemblies under specific conditions, its intrinsic structural properties and interaction modes below saturation concentration remain incompletely understood. Here, we present a 2.4 Å resolution crystal structure of the isolated human C9 CARD , revealing a sulfate-mediated dimer-of-dimers assembly involving a conserved arginine-rich surface. Notably, these residues overlap with those previously shown in filament formation and in interactions with APAF-1 CARD , indicating reuse of a common interaction hotspot across distinct assembly states. Complementary biophysical analyses show that C9 CARD remains predominantly monomeric under physiological conditions, while sulfate induces changes in its hydrodynamic properties. Compared to WT C9 CARD , a triple-arginine mutant (R10E/R52E/R56E) shows different sulfate-dependent behavior and abolishes formation of higher-order assemblies. Additionally, WT C9 CARD exhibits reversible temperature-dependent transitions between filamentous and droplet-like assemblies. Finally, AlphaFold3 predictions suggest that filament-forming propensity and electrostatically regulated higher-order assemblies may extend to other human CARDs. Together, our findings suggest a model in which a conserved electrostatic interaction motif enables multiple structurally distinct assembly modes of C9 CARD . This work highlights conserved electrostatic interaction modes in CARD-CARD association and suggests that environmental conditions can modulate their assembly behavior.


  • Organizational Affiliation: 
    • Research Unit Integrative Structural Biology, Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, 8010 Graz, Austria.

Macromolecule Content 

  • Total Structure Weight: 48.54 kDa 
  • Atom Count: 3,430 
  • Modeled Residue Count: 396 
  • Deposited Residue Count: 404 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-9A,
B [auth E],
C [auth H],
D [auth L]
101Homo sapiensMutation(s): 0 
Gene Names: CASP9, MCH6
EC: 3.4.22.62
UniProt & NIH Common Fund Data Resources
Find proteins for P55211 (Homo sapiens)
Explore P55211 
Go to UniProtKB:  P55211
PHAROS:  P55211
GTEx:  ENSG00000132906 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55211
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth E],
L [auth E],
M [auth E],
N [auth E],
O [auth E],
P [auth H],
Q [auth H],
R [auth H],
T [auth L],
U [auth L],
V [auth L],
W [auth L],
X [auth L]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A],
S [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.265 (Depositor), 0.263 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.915α = 90
b = 86.394β = 90
c = 129.961γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaDOC130

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-20
    Type: Initial release
  • Version 1.1: 2026-10-21
    Changes: Database references