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- EMDB-71032: Structure of D2-NT amyloid fibrils -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71032
TitleStructure of D2-NT amyloid fibrils
Map data
Sample
  • Complex: CHCHD2
    • Protein or peptide: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
KeywordsCHCHD2 / 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: 2.03 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_71032.png

Downloads & links

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Map

FileDownload / File: emd_71032.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.)
0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å		0.83 Å/pix.
x 256 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.04273427 - 0.09321416
Average (Standard dev.)0.00003416553 (±0.0016925297)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71032_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_71032_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_71032_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 : CHCHD2

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

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Supramolecule #1: CHCHD2

SupramoleculeName: 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.368748 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPRGSRSRTS RMAPPASRAP QMRAAPRPAP VAQPPAAAPP SAVGSSAAAP RQPGLMAQMA TTAAGVAVGS 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
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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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: 4.796 Å
Applied symmetry - Helical parameters - Δ&Phi: 1.34 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.0) / Number images used: 63528
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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