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- EMDB-45976: Structure of D10-NT amyloid fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-45976
TitleStructure of D10-NT amyloid fibrils
Map data
Sample
  • Complex: CHCHD10
    • Protein or peptide: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
KeywordsCHCHD10 / Amyloid Fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


: / MICOS complex / mitochondria-nucleus signaling pathway / positive regulation of cristae formation / positive regulation of mitochondrial transcription / stabilization of membrane potential / maintenance of synapse structure / Mitochondrial protein import / maintenance of protein location in nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...: / MICOS complex / mitochondria-nucleus signaling pathway / positive regulation of cristae formation / positive regulation of mitochondrial transcription / stabilization of membrane potential / maintenance of synapse structure / Mitochondrial protein import / maintenance of protein location in nucleus / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / oxidative phosphorylation / mitochondrion organization / mitochondrial intermembrane space / protein-containing complex assembly / mitochondrion / nucleus
Similarity search - Function
: / CHCH / CHCH domain / Coiled coil-helix-coiled coil-helix (CHCH) domain profile.
Similarity search - Domain/homology
Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsLv G / Eliezer D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)RF1AG066493 United States
CitationJournal: Nat Commun / Year: 2025
Title: Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration.
Authors: Guohua Lv / Nicole M Sayles / Yun Huang / Chiara Mancinelli / Kevin McAvoy / Neil A Shneider / Giovanni Manfredi / Hibiki Kawamata / David Eliezer /
Abstract: Mitochondrial proteins CHCHD10 and CHCHD2 are mutated in rare cases of heritable FTD, ALS and PD and aggregate in tissues affected by these diseases. Here, we show that both proteins form amyloid ...Mitochondrial proteins CHCHD10 and CHCHD2 are mutated in rare cases of heritable FTD, ALS and PD and aggregate in tissues affected by these diseases. Here, we show that both proteins form amyloid fibrils and report cryo-EM structures of fibrils formed from their disordered N-terminal domains. The ordered cores of these fibrils are comprised of a region highly conserved between the two proteins, and a subset of the CHCHD10 and CHCHD2 fibril structures share structural similarities and appear compatible with sequence variations in this region. In contrast, disease-associated mutations p.S59L in CHCHD10 and p.T61I in CHCHD2, situated within the ordered cores of these fibrils, cannot be accommodated by the wildtype structures and promote different protofilament folds and fibril structures. These results link CHCHD10 and CHCHD2 amyloid fibrils to neurodegeneration and further suggest that fibril formation by the WT proteins could also be involved in disease etiology.
History
DepositionJul 30, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateAug 13, 2025-
Current statusAug 13, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45976.png

Downloads & links

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Map

FileDownload / File: emd_45976.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 275.456 Å		1.08 Å/pix.
x 256 pix.
= 275.456 Å		1.08 Å/pix.
x 256 pix.
= 275.456 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.076 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.052064348 - 0.10351467
Average (Standard dev.)0.00003588102 (±0.0017432278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 275.456 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45976_msk_1.map
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Half map: #2

Fileemd_45976_half_map_1.map
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Half map: #1

Fileemd_45976_half_map_2.map
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Sample components

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Entire : CHCHD10

EntireName: CHCHD10
Components
  • Complex: CHCHD10
    • Protein or peptide: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial

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Supramolecule #1: CHCHD10

SupramoleculeName: CHCHD10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10,...

MacromoleculeName: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.252316 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRGSRSAAS RPASRPAAPS AHPPAHPPPS AAAPAPAPSG QPGLMAQMAT TAAGVAVGSA VGHVMGSALT GAFSGGSSEP SQPAVQQAP TPAAPQPLQ

UniProtKB: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.03 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.82 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 64000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.365 Å
Applied symmetry - Helical parameters - Δ&Phi: 178.845 °
Applied symmetry - Helical parameters - Axial symmetry: C21 (21 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 667405
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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