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- PDB-9oyq: Structure of D10-NT amyloid fibrils -

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Basic information

Entry
Database: PDB / ID: 9oyq
TitleStructure of D10-NT amyloid fibrils
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
KeywordsPROTEIN FIBRIL / CHCHD10 / Amyloid 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
B: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
C: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
D: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
E: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
F: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
G: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
H: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
I: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
J: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
K: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
L: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
M: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
N: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
O: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
P: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
Q: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
R: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial


Theoretical massNumber of molelcules
Total (without water)166,54218
Polymers166,54218
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 "G"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "H"
d_8ens_1chain "A"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_15ens_1chain "O"
d_16ens_1chain "P"
d_17ens_1chain "Q"
d_18ens_1chain "R"

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: 43 - 76 / Label seq-ID: 43 - 76

Dom-IDAuth asym-IDLabel asym-ID
d_1GG
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7HH
d_8AA
d_9II
d_10JJ
d_11KK
d_12LL
d_13MM
d_14NN
d_15OO
d_16PP
d_17QQ
d_18RR

NCS oper:
IDCodeMatrixVector
1given(-0.997176905338, 0.0750878925663, -0.000166881841255), (-0.0750879344892, -0.997176881986, 0.000261010973279), (-0.000146811950202, 0.000272804927358, 0.999999952012)285.452298345, 307.672180421, -16.662996653
2given(0.996374255898, -0.0850773263388, -0.000436723633286), (0.0850772855043, 0.996374348881, -0.000111276944272), (0.000444607370658, 7.37182213117E-5, 0.999999898445)13.2121684426, -12.0826861773, -19.0871087359
3given(-0.995364885929, 0.0961624912118, -0.00123253526921), (-0.0961627707046, -0.99536560762, 0.00016940515555), (-0.00121053279537, 0.000287143949809, 0.999999226079)282.210336009, 310.53666975, -21.2544950084
4given(0.994340073905, -0.106244139284, -1.71323005221E-5), (0.106244120829, 0.994339973867, -0.000450730921235), (6.4922850029E-5, 0.000446359611325, 0.999999898274)16.5916930423, -14.8934930133, -23.839431921
5given(-0.993069752938, 0.11752516991, -0.000547938746981), (-0.117525032479, -0.993069881815, -0.000276718277831), (-0.000576662829326, -0.000210404032763, 0.999999811595)278.58369312, 313.420407206, -26.0298684956
6given(-0.999941201103, 0.0108437919356, 8.07063477035E-5), (-0.0108437835943, -0.999941199137, 0.000103083322907), (8.18194162063E-5, 0.000102202099552, 0.99999999143)295.366299664, 298.561863497, -2.40939290189
7given(0.997932430158, -0.0642713463785, -0.000242639797725), (0.0642713856515, 0.997932444669, 0.000157678911766), (0.000232003890563, -0.000172947695618, 0.999999958132)9.88522809945, -9.25623906782, -14.2709536322
8given(0.99978230995, -0.020863552752, -0.000211843539019), (0.0208634982071, 0.999782300628, -0.000256502930424), (0.000217148983233, 0.000252027294992, 0.999999944664)3.13750789925, -3.03351925285, -4.81761305035
9given(-0.999487642339, 0.0319918055118, -0.000988529714118), (-0.031991899414, -0.999488125032, 7.93217361012E-5), (-0.000985486064948, 0.000110906038184, 0.999999508258)292.313964767, 301.62978562, -6.99956348458
10given(0.999112719268, -0.0421157936838, 0.000184713611961), (0.0421159008061, 0.999112539152, -0.000620489962222), (-0.000158417258631, 0.000627718793594, 0.999999790437)6.3281346303, -6.05499520596, -9.57096781156
11given(-0.998570065817, 0.0534575786573, -0.000333074106503), (-0.0534574404631, -0.998570044244, -0.00041084960881), (-0.000354560850546, -0.000392456831693, 0.999999860132)288.878932199, 304.741582539, -11.7735681821
12given(0.991709689662, -0.128498573651, 8.94410843988E-5), (0.128498587152, 0.991709677968, -0.000166505474704), (-6.73038730018E-5, 0.000176618145625, 0.999999982138)20.2972655939, -17.817610234, -28.5139898106
13given(-0.990258019663, 0.139244495102, 0.000158355713205), (-0.139244505506, -0.990258029242, -5.66329024456E-5), (0.000148927196571, -7.81313488027E-5, 0.999999985858)274.849657667, 316.224018689, -30.8903336464
14given(0.988812718034, -0.149162332163, -8.55415217903E-5), (0.149162280446, 0.988812629839, -0.000444031046883), (0.000150817243628, 0.000426303977897, 0.99999989776)23.7980259511, -20.4228976237, -33.3314052056
15given(-0.987090497357, 0.160160989676, -0.000898561817412), (-0.16016086003, -0.987090903987, -0.000214897051699), (-0.000921380321116, -6.82084041746E-5, 0.999999573203)271.427572264, 318.874849093, -35.4802794118
16given(0.985417176894, -0.170155403794, 0.000355024698339), (0.170155629161, 0.985416916132, -0.000750510658352), (-0.000222143899264, 0.000799975545095, 0.999999655346)27.3504685335, -23.0094911215, -38.0847936289
17given(-0.983422123598, 0.1813308892, -0.000188255022517), (-0.18133074483, -0.983421977128, -0.00061309101253), (-0.000296306464911, -0.00056879084205, 0.99999979434)267.621112279, 321.519683157, -40.2538868561

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Components

#1: Protein
Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial / Protein N27C7-4


Mass: 9252.316 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD10, C22orf16 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WYQ3
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: CHCHD10 / 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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 100000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.418 ° / Axial rise/subunit: 2.38 Å / Axial symmetry: C21
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 351565 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 65.4 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00213780
ELECTRON MICROSCOPYf_angle_d0.38355076
ELECTRON MICROSCOPYf_chiral_restr0.0463630
ELECTRON MICROSCOPYf_plane_restr0.001648
ELECTRON MICROSCOPYf_dihedral_angle_d3.4287594
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2GGELECTRON MICROSCOPYNCS constraints3.41026944601E-11
ens_1d_3GGELECTRON MICROSCOPYNCS constraints3.58003759414E-13
ens_1d_4GGELECTRON MICROSCOPYNCS constraints1.14527245962E-12
ens_1d_5GGELECTRON MICROSCOPYNCS constraints2.06728625228E-13
ens_1d_6GGELECTRON MICROSCOPYNCS constraints2.01773162908E-13
ens_1d_7GGELECTRON MICROSCOPYNCS constraints3.52159761618E-12
ens_1d_8GGELECTRON MICROSCOPYNCS constraints1.9844378647E-13
ens_1d_9GGELECTRON MICROSCOPYNCS constraints2.57724068873E-13
ens_1d_10GGELECTRON MICROSCOPYNCS constraints4.26654426834E-12
ens_1d_11GGELECTRON MICROSCOPYNCS constraints1.03484599451E-13
ens_1d_12GGELECTRON MICROSCOPYNCS constraints7.73330906657E-13
ens_1d_13GGELECTRON MICROSCOPYNCS constraints5.20286943961E-12
ens_1d_14GGELECTRON MICROSCOPYNCS constraints6.25874592529E-13
ens_1d_15GGELECTRON MICROSCOPYNCS constraints3.01906159511E-13
ens_1d_16GGELECTRON MICROSCOPYNCS constraints1.479744014E-13
ens_1d_17GGELECTRON MICROSCOPYNCS constraints4.87220551158E-11
ens_1d_18GGELECTRON MICROSCOPYNCS constraints5.8162506193E-14

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