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- PDB-9s6e: Cryo-EM structure of human caspase-9 CARD (H38R) mutant filament -

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Basic information

Entry
Database: PDB / ID: 9s6e
TitleCryo-EM structure of human caspase-9 CARD (H38R) mutant filament
ComponentsCaspase-9
KeywordsPROTEIN FIBRIL / Cell death / caspase-9 / Cryo-EM / filament / oligomerization
Function / homology
Function and homology information


response to indole-3-methanol / caspase-9 / apoptosome / Formation of apoptosome / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / platelet formation / response to anesthetic / Caspase activation via Dependence Receptors in the absence of ligand ...response to indole-3-methanol / caspase-9 / apoptosome / Formation of apoptosome / leukocyte apoptotic process / glial cell apoptotic process / response to cobalt ion / platelet formation / response to anesthetic / Caspase activation via Dependence Receptors in the absence of ligand / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / Regulation of the apoptosome activity / AKT phosphorylates targets in the cytosol / cellular response to dexamethasone stimulus / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of execution phase of apoptosis / response to ischemia / kidney development / intrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / protein processing / intrinsic apoptotic signaling pathway in response to DNA damage / protein maturation / NOD1/2 Signaling Pathway / enzyme activator activity / positive regulation of neuron apoptotic process / cellular response to UV / response to estradiol / peptidase activity / response to lipopolysaccharide / response to hypoxia / response to ethanol / positive regulation of apoptotic process / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / protein kinase binding / protein-containing complex / mitochondrion / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site ...CASP9, CARD domain / Caspase recruitment domain / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Peptidase C14 family / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Death-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRawal, S. / Bohn, S. / Alderson, T.R. / Madl, T. / Pavkov-Keller, T. / Desfosses, A.
Funding support Austria, Germany, France, 5items
OrganizationGrant numberCountry
Austrian Science Fund10.55776/DOC130 Austria
Helmholtz Association Germany
Grenoble Alliance for Integrated Structural Cell Biology (GRAL) France
Grenoble Instruct-ERIC Center (ISBG) France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INBS-0005-02 France
CitationJournal: To Be Published
Title: Cryo-EM structure of Caspase-9 CARD (H38R) mutant filament
Authors: Rawal, S. / Bohn, S. / Alderson, T.R. / Madl, T. / Pavkov-Keller, T. / Desfosses, A.
History
DepositionJul 31, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Caspase-9
A: Caspase-9
C: Caspase-9
D: Caspase-9
E: Caspase-9
F: Caspase-9
G: Caspase-9
H: Caspase-9
I: Caspase-9
J: Caspase-9
K: Caspase-9
L: Caspase-9
M: Caspase-9
N: Caspase-9
O: Caspase-9
P: Caspase-9


Theoretical massNumber of molelcules
Total (without water)180,86216
Polymers180,86216
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Caspase-9 / CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like ...CASP-9 / Apoptotic protease Mch-6 / Apoptotic protease-activating factor 3 / APAF-3 / ICE-like apoptotic protease 6 / ICE-LAP6


Mass: 11303.899 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP9, MCH6 / Production host: Escherichia coli (E. coli) / References: UniProt: P55211, caspase-9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Caspase-9 CARD (H38R) helical filament (16 repeats) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
7Cootmodel fitting
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -67.2 ° / Axial rise/subunit: 9.13 Å / Axial symmetry: C2
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 291659 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13ygs

3ygs

13ygs1PDBexperimental model
29R44

9r44

19R442PDBexperimental model
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212704
ELECTRON MICROSCOPYf_angle_d0.37617008
ELECTRON MICROSCOPYf_dihedral_angle_d2.5511792
ELECTRON MICROSCOPYf_chiral_restr0.0311888
ELECTRON MICROSCOPYf_plane_restr0.0032288

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