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- PDB-9oyr: Structure of D2-NT amyloid fibrils -

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Basic information

Entry
Database: PDB / ID: 9oyr
TitleStructure of D2-NT amyloid fibrils
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 2
KeywordsPROTEIN FIBRIL / CHCHD2 / Amyloid 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.03 Å
AuthorsLv, G. / Eliezer, D.
Funding support United States, 1items
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
DepositionJun 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
C: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
B: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
E: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
F: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
G: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)68,2126
Polymers68,2126
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "E"
d_5ens_1chain "F"
d_6ens_1chain "G"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 54 - 86 / Label seq-ID: 54 - 86

Dom-IDAuth asym-IDLabel asym-ID
d_1BC
d_2AA
d_3CB
d_4ED
d_5FE
d_6GF

NCS oper:
IDCodeMatrixVector
1given(0.999678911727, -0.0253383597127, 0.000202422231263), (0.0253385333764, 0.999678516217, -0.000907160605569), (-0.000179371194057, 0.0009119984094, 0.999999568042)2.65323697407, -2.54928048957, -4.84711313024
2given(0.998726599816, -0.0504494690725, 0.000172887236289), (0.050449626632, 0.998726025187, -0.00107786230426), (-0.000118289401321, 0.00108521185073, 0.999999404161)5.42672370487, -5.05701674767, -9.63147902432
3given(-0.999842477229, 0.011030313319, -0.0139051399619), (-0.0110817027792, -0.99993202858, 0.00362409770094), (-0.0138642198766, 0.00377761945119, 0.999896751169)211.527031282, 209.058841166, -1.26789275449
4given(-0.999851602734, -0.00980693984278, -0.0141632073246), (0.00975100345898, -0.999944404985, 0.00401308741647), (-0.0142017760278, 0.00387438640166, 0.999891643473)213.677340881, 206.804352482, 3.51325820406
5given(-0.999228791079, 0.0367353630138, -0.0138685320992), (-0.0368063360704, -0.999310416779, 0.00489740164317), (-0.013679060765, 0.00540407457658, 0.999891833787)208.818191241, 211.586365284, -6.23594330293

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Components

#1: Protein
Coiled-coil-helix-coiled-coil-helix domain-containing protein 2 / Aging-associated gene 10 protein / HCV NS2 trans-regulated protein / NS2TP


Mass: 11368.748 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD2, C7orf17, AAG10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6H1
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: CHCHD2 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K

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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 magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 48.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1CTF correction
9RELION4.0.0initial Euler assignment
10RELION4.0.0final Euler assignment
12RELION4.0.03D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 1.34 ° / Axial rise/subunit: 4.796 Å / Axial symmetry: C1
3D reconstructionResolution: 2.03 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63528 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 25.58 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00531260
ELECTRON MICROSCOPYf_angle_d0.67461698
ELECTRON MICROSCOPYf_chiral_restr0.0507210
ELECTRON MICROSCOPYf_plane_restr0.0022216
ELECTRON MICROSCOPYf_dihedral_angle_d4.8311192
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CBELECTRON MICROSCOPYNCS constraints9.87401669946E-11
ens_1d_3CBELECTRON MICROSCOPYNCS constraints1.35566786597E-10
ens_1d_4CBELECTRON MICROSCOPYNCS constraints1.70973769052E-13
ens_1d_5CBELECTRON MICROSCOPYNCS constraints6.002525437E-14
ens_1d_6CBELECTRON MICROSCOPYNCS constraints6.77097988087E-14

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