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- EMDB-54625: Cryo-EM structure of human caspase-9 CARD (H38R) mutant filament -

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Basic information

Entry
Database: EMDB / ID: EMD-54625
TitleCryo-EM structure of human caspase-9 CARD (H38R) mutant filament
Map data
Sample
  • Complex: Caspase-9 CARD (H38R) helical filament (16 repeats)
    • Protein or peptide: Caspase-9
KeywordsCell death / caspase-9 / Cryo-EM / filament / oligomerization / PROTEIN FIBRIL
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)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsRawal S / Bohn S / Alderson TR / Madl T / Pavkov-Keller T / Desfosses A
Funding support Austria, Germany, France, 5 items
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 TR / Madl T / Pavkov-Keller T / Desfosses A
History
DepositionJul 31, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54625.png

Downloads & links

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Map

FileDownload / File: emd_54625.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å		0.95 Å/pix.
x 360 pix.
= 342. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.41860154 - 0.7553337
Average (Standard dev.)0.0015875971 (±0.02517322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 342.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54625_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54625_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Caspase-9 CARD (H38R) helical filament (16 repeats)

EntireName: Caspase-9 CARD (H38R) helical filament (16 repeats)
Components
  • Complex: Caspase-9 CARD (H38R) helical filament (16 repeats)
    • Protein or peptide: Caspase-9

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Supramolecule #1: Caspase-9 CARD (H38R) helical filament (16 repeats)

SupramoleculeName: Caspase-9 CARD (H38R) helical filament (16 repeats) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Caspase-9

MacromoleculeName: Caspase-9 / type: protein_or_peptide / ID: 1 / Number of copies: 16 / Enantiomer: LEVO / EC number: caspase-9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.303899 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGMDEADRRL LRRCRLRLVE ELQVDQLWDA LLSRELFRPR MIEDIQRAGS GSRRDQARQL IIDLETRGSQ ALPLFISCLE DTGQDMLAS FLRTNRQA

UniProtKB: Caspase-9

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.13 Å
Applied symmetry - Helical parameters - Δ&Phi: -67.2 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 291659
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

3ygs

source_name: PDB, initial_model_type: experimental model

9r44

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

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

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