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- EMDB-71034: Structure of T61I D2-NT amyloid fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-71034
TitleStructure of T61I D2-NT amyloid fibrils
Map data
Sample
  • Complex: T61I of CHCHD2
    • Protein or peptide: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
KeywordsT61I CHCHD2 / Amyloid Fibril / PROTEIN FIBRIL
Function / homology
Function and homology information


regulation of generation of precursor metabolites and energy / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of cellular response to hypoxia / Mitochondrial protein import / Mitochondrial protein degradation / mitochondrion organization / mitochondrial intermembrane space / cellular response to oxidative stress / DNA-binding transcription factor binding / sequence-specific DNA binding ...regulation of generation of precursor metabolites and energy / positive regulation of mitochondrial ATP synthesis coupled electron transport / regulation of cellular response to hypoxia / Mitochondrial protein import / Mitochondrial protein degradation / mitochondrion organization / mitochondrial intermembrane space / cellular response to oxidative stress / DNA-binding transcription factor binding / sequence-specific DNA binding / positive regulation of transcription by RNA polymerase II / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 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: To Be Published
Title: Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration.
Authors: Lv G / Sayles NM / Huang Y / Mancinelli CD / McAvoy K / Shneider NA / Manfredi G / Kawamata H / Eliezer D
History
DepositionJun 4, 2025-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71034.png

Downloads & links

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Map

FileDownload / File: emd_71034.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.04961578 - 0.09489264
Average (Standard dev.)0.000039232622 (±0.0017083471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 296.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71034_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71034_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71034_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 : T61I of CHCHD2

EntireName: T61I of CHCHD2
Components
  • Complex: T61I of CHCHD2
    • Protein or peptide: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2

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Supramolecule #1: T61I of CHCHD2

SupramoleculeName: T61I of CHCHD2 / 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 2

MacromoleculeName: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.380803 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRGSRSRTS RMAPPASRAP QMRAAPRPAP VAQPPAAAPP SAVGSSAAAP RQPGLMAQMA ITAAGVAVGS AVGHTLGHAI TGGFSGGSN AEPARPDITY QEPQGTQPAQ QQQPM

UniProtKB: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.36 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.04 °
Applied symmetry - Helical parameters - Axial symmetry: C21 (21 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 315652
CTF correctionType: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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