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

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Basic information

Entry
Database: PDB / ID: 9oyw
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: 2.63 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
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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
D: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
C: 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
S: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
T: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
U: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
V: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
W: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
X: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
Y: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
Z: Coiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
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


Theoretical massNumber of molelcules
Total (without water)333,08336
Polymers333,08336
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 "Q"
d_2ens_1chain "b"
d_3ens_1chain "c"
d_4ens_1chain "d"
d_5ens_1chain "e"
d_6ens_1chain "f"
d_7ens_1chain "g"
d_8ens_1chain "h"
d_9ens_1chain "i"
d_10ens_1chain "j"
d_11ens_1chain "A"
d_12ens_1chain "B"
d_13ens_1chain "C"
d_14ens_1chain "D"
d_15ens_1chain "E"
d_16ens_1chain "F"
d_17ens_1chain "G"
d_18ens_1chain "H"
d_19ens_1chain "I"
d_20ens_1chain "J"
d_21ens_1chain "K"
d_22ens_1chain "L"
d_23ens_1chain "M"
d_24ens_1chain "N"
d_25ens_1chain "O"
d_26ens_1chain "P"
d_27ens_1chain "a"
d_28ens_1chain "R"
d_29ens_1chain "S"
d_30ens_1chain "T"
d_31ens_1chain "U"
d_32ens_1chain "V"
d_33ens_1chain "W"
d_34ens_1chain "X"
d_35ens_1chain "Y"
d_36ens_1chain "Z"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 50 - 76 / Label seq-ID: 50 - 76

Dom-IDAuth asym-IDLabel asym-ID
d_1QQ
d_2bBA
d_3cCA
d_4dDA
d_5eEA
d_6fFA
d_7gGA
d_8hHA
d_9iIA
d_10jJA
d_11AA
d_12BB
d_13CD
d_14DC
d_15EE
d_16FF
d_17GG
d_18HH
d_19II
d_20JJ
d_21KK
d_22LL
d_23MM
d_24NN
d_25OO
d_26PP
d_27aAA
d_28RR
d_29SS
d_30TT
d_31UU
d_32VV
d_33WW
d_34XX
d_35YY
d_36ZZ

NCS oper:
IDCodeMatrixVector
1given(-0.989322524001, 0.144814013599, 0.0164269586161), (-0.143575478396, -0.987765766812, 0.0608676590459), (0.0250404773786, 0.0578592376354, 0.998010662825)193.854798544, 235.001652453, -40.1596875045
2given(0.99091442434, -0.134471490123, 0.00245397197213), (0.13447339053, 0.990917007405, -0.000625839410584), (-0.00234752500476, 0.000950147230626, 0.999996793168)15.7581851259, -13.9760618124, -28.1780160008
3given(-0.97596621458, 0.10442399229, 0.191273568046), (-0.112510830015, -0.99313870753, -0.0318876266742), (0.186631350872, -0.0526415941979, 0.981018654987)191.524438882, 280.78898835, -38.5404330629
4given(0.980558362813, -0.0979964754785, -0.170005846695), (0.11093036343, 0.991478094146, 0.0683055144079), (0.161863373207, -0.085836353738, 0.983072921401)17.8914259932, -56.3591530623, -27.990723071
5given(-0.993524032868, 0.11319627822, 0.0098284643025), (-0.112461505628, -0.992021532995, 0.0569709384375), (0.0161989464222, 0.0554966726192, 0.998327458033)199.143187886, 232.837390232, -33.85603432
6given(0.983537080172, -0.18057022771, 0.00701461266194), (0.180494413056, 0.983522538864, 0.0102558471683), (-0.00875093031296, -0.00882090758341, 0.999922803424)20.9725386447, -19.6334565194, -35.9122970263
7given(-0.968678003794, 0.154827832506, 0.194142389104), (-0.162166010706, -0.986509357695, -0.0223935738851), (0.18805613507, -0.0531754591987, 0.98071772728)182.454481884, 284.591055818, -48.3460353536
8given(0.974312615165, -0.139550024575, -0.1767504415), (0.152171576451, 0.98653582247, 0.0599239710267), (0.166008250548, -0.0852810742435, 0.982429844379)26.061404949, -60.2237060954, -38.1906184959
9given(-0.985968073407, 0.166421017053, 0.0130768232129), (-0.165459213668, -0.984644169397, 0.0556696352133), (0.0221406150419, 0.0527248020924, 0.998363605311)191.626958847, 237.652334753, -43.9220229626
10given(0.995541172007, -0.0940412816602, 0.00734929811372), (0.0940198925508, 0.995565162049, 0.00320435950462), (-0.00761804724225, -0.00249909159779, 0.999967859432)10.218777316, -10.2787997524, -17.9554962764
11given(-0.980041700337, 0.0709214751641, 0.185710554255), (-0.0761327425904, -0.996874991163, -0.0210726718678), (0.183635702157, -0.0347907509914, 0.982378507775)197.860944137, 275.494553525, -31.2368569803
12given(-0.996310352174, 0.0840057262915, 0.0175704325806), (-0.0828164891414, -0.994756622632, 0.0600057568533), (0.0225191313582, 0.058329235204, 0.998043380341)201.658113811, 229.769415854, -25.8516660069
13given(0.983576609621, -0.0643979525903, -0.168611852221), (0.0795027845144, 0.993253854597, 0.0844161571213), (0.162038144465, -0.0964348693723, 0.982061075345)12.5783936412, -54.4813445026, -17.4975635521
14given(0.997284439652, -0.0736459582454, -0.00013878624879), (0.0736458784264, 0.997284323746, -0.000512055493847), (0.000176120167789, 0.000500443941046, 0.999999859269)8.64331388231, -7.8525475001, -14.3006112227
15given(-0.981492159393, 0.0436469937747, 0.186462009495), (-0.0525855234351, -0.997678916552, -0.0432613244442), (0.184140988852, -0.052265853117, 0.981509234201)202.126980152, 275.613042397, -24.2442876016
16given(0.985090172429, -0.0369777680205, -0.168017846836), (0.050816342583, 0.995592500572, 0.0788243118077), (0.164362561155, -0.0861871073751, 0.982627462985)8.18017880574, -50.2854201925, -14.1041597855
17given(-0.998579175828, 0.0521937056511, 0.0107446122438), (-0.0515066702597, -0.997071542361, 0.0565278898613), (0.0136635471465, 0.0558941544691, 0.998343203)206.78818574, 227.286532817, -19.5351851803
18given(0.992750995216, -0.120081899716, 0.00507925759095), (0.120026552044, 0.99271956153, 0.010074669183), (-0.0062520637831, -0.00939199208236, 0.999936349066)13.5212642642, -13.8202906889, -22.020339832
19given(-0.977256696169, 0.0943613290166, 0.189908634293), (-0.102592888744, -0.994143270193, -0.0339684781571), (0.18559107999, -0.0526791981272, 0.981213969077)193.331382224, 279.960919359, -34.0726383868
20given(0.981366873126, -0.0787556913753, -0.175261522892), (0.0923624259205, 0.993199995033, 0.0708727884605), (0.168488108211, -0.0857397862261, 0.981967640225)16.1245103134, -54.6450627413, -24.2825553492
21given(-0.994292471396, 0.105778295892, 0.0139080352283), (-0.104867034685, -0.992962474637, 0.0550311638936), (0.0196312598152, 0.0532585775388, 0.998387769134)199.605814985, 232.549338924, -29.6211231283
22given(0.999760466168, -0.0204710586855, 0.00774248306184), (0.0204471491785, 0.999785957905, 0.00315475314308), (-0.00780540698128, -0.00299568576679, 0.999965050134)1.39224323468, -2.53801734114, -3.65377216516
23given(-0.982954758621, -0.00268942962012, 0.183827934418), (-0.00365880023306, -0.999408803001, -0.0341856353727), (0.183811195755, -0.0342755226553, 0.982363798631)209.567634878, 268.632228646, -17.1096832373
24given(0.98678942838, 0.00890703402461, -0.161763063714), (0.00693342887527, 0.995250857312, 0.0970961306308), (0.161859666382, -0.09693500794, 0.982041268295)0.489962116262, -46.7938137694, -3.17322917398
25given(-0.999699942441, 0.0105277542855, 0.0221176733061), (-0.00920541483484, -0.998211968835, 0.0590603556762), (0.0226998991295, 0.0588390318121, 0.998009360134)209.988590435, 222.754353895, -11.7008547399
26given(0.977288414977, -0.125245252736, -0.170941453775), (0.139467656684, 0.98746882321, 0.0738518512059), (0.159549762428, -0.0960153625963, 0.982509502984)22.5287187363, -60.2778507307, -31.3962366842
27given(-0.982666544122, -0.0299573811676, 0.182945397257), (0.0199351568872, -0.998210434587, -0.0563783451463), (0.184306952077, -0.0517540683921, 0.981505203155)213.832284959, 268.440468719, -10.1169946885
28given(0.986185407762, 0.0364266900527, -0.16159033934), (-0.0217835891229, 0.995568441298, 0.0914819869555), (0.16420662825, -0.0866981830502, 0.982608573286)-3.58550380307, -42.2846033258, 0.218624617404
29given(-0.999658296377, -0.0213683707275, 0.0150560026867), (0.0221815874891, -0.998179077308, 0.0560937322844), (0.0138299552028, 0.0564085308937, 0.998311980285)214.922677853, 219.903795639, -5.38384670141
30given(0.998893469297, -0.0466478432501, 0.00598462324922), (0.0465854389997, 0.998862491895, 0.0101744364946), (-0.00645243121053, -0.00988438186694, 0.999930330136)4.42368633508, -6.31477930222, -7.71714564288
31given(-0.982125553568, 0.0208848495965, 0.187064748377), (-0.0302521309148, -0.99841963006, -0.0473608581528), (0.185779992473, -0.0521734162883, 0.981205243071)205.378772871, 273.419326367, -19.9465305037
32given(0.985533815277, -0.00541551890334, -0.169392358448), (0.0199265640679, 0.996259483444, 0.0840831356054), (0.168303389717, -0.0862421811169, 0.981955322408)4.01348718462, -47.2224664795, -9.95805969618
33given(-0.999311942016, 0.0323731877297, 0.018100255789), (-0.0313469400789, -0.998029000977, 0.0543643500525), (0.0198245275125, 0.0537595565938, 0.998357099531)208.145645225, 225.676669426, -15.4710354043
34given(0.98790867745, -0.154733002963, 0.00970272197238), (0.154705370012, 0.987954304945, 0.00354116211575), (-0.0101337805904, -0.00199728158955, 0.999946657256)17.4696209803, -16.3012438923, -31.8373206987
35given(-0.973079879756, 0.131644366941, 0.189170051187), (-0.135926599189, -0.990670576829, -0.00978610434793), (0.186116918216, -0.0352359029684, 0.98189557688)187.255389389, 280.410764446, -45.5221725618

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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.: 36
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: 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: 64000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 51.82 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 1.27 ° / Axial rise/subunit: 4.73 Å / Axial symmetry: C1
3D reconstructionResolution: 2.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47048 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 35.32 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00155868
ELECTRON MICROSCOPYf_angle_d0.45727920
ELECTRON MICROSCOPYf_chiral_restr0.04671008
ELECTRON MICROSCOPYf_plane_restr0.00181008
ELECTRON MICROSCOPYf_dihedral_angle_d3.8337936
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2QQELECTRON MICROSCOPYNCS constraints9.98200076171E-14
ens_1d_3QQELECTRON MICROSCOPYNCS constraints9.81997214702E-13
ens_1d_4QQELECTRON MICROSCOPYNCS constraints5.67666108087E-14
ens_1d_5QQELECTRON MICROSCOPYNCS constraints1.28118762826E-11
ens_1d_6QQELECTRON MICROSCOPYNCS constraints1.31946754108E-13
ens_1d_7QQELECTRON MICROSCOPYNCS constraints5.00105502087E-11
ens_1d_8QQELECTRON MICROSCOPYNCS constraints4.34796454126E-11
ens_1d_9QQELECTRON MICROSCOPYNCS constraints6.16208438976E-14
ens_1d_10QQELECTRON MICROSCOPYNCS constraints8.59785346093E-14
ens_1d_11QQELECTRON MICROSCOPYNCS constraints8.3410111826E-14
ens_1d_12QQELECTRON MICROSCOPYNCS constraints1.07336066115E-13
ens_1d_13QQELECTRON MICROSCOPYNCS constraints9.83416701768E-14
ens_1d_14QQELECTRON MICROSCOPYNCS constraints1.41902005006E-11
ens_1d_15QQELECTRON MICROSCOPYNCS constraints1.18935835128E-10
ens_1d_16QQELECTRON MICROSCOPYNCS constraints9.483766658E-14
ens_1d_17QQELECTRON MICROSCOPYNCS constraints9.40655696102E-14
ens_1d_18QQELECTRON MICROSCOPYNCS constraints1.61670521709E-13
ens_1d_19QQELECTRON MICROSCOPYNCS constraints1.09526178552E-13
ens_1d_20QQELECTRON MICROSCOPYNCS constraints7.66905161058E-14
ens_1d_21QQELECTRON MICROSCOPYNCS constraints1.03763390016E-13
ens_1d_22QQELECTRON MICROSCOPYNCS constraints1.017373008E-13
ens_1d_23QQELECTRON MICROSCOPYNCS constraints1.08978487176E-13
ens_1d_24QQELECTRON MICROSCOPYNCS constraints2.85448286179E-11
ens_1d_25QQELECTRON MICROSCOPYNCS constraints9.51788103671E-14
ens_1d_26QQELECTRON MICROSCOPYNCS constraints1.22968278349E-13
ens_1d_27QQELECTRON MICROSCOPYNCS constraints1.05029135243E-13
ens_1d_28QQELECTRON MICROSCOPYNCS constraints9.52704480574E-14
ens_1d_29QQELECTRON MICROSCOPYNCS constraints6.93046216085E-14
ens_1d_30QQELECTRON MICROSCOPYNCS constraints7.79080939774E-14
ens_1d_31QQELECTRON MICROSCOPYNCS constraints8.05049530199E-14
ens_1d_32QQELECTRON MICROSCOPYNCS constraints9.46007694575E-14
ens_1d_33QQELECTRON MICROSCOPYNCS constraints7.07377718975E-14
ens_1d_34QQELECTRON MICROSCOPYNCS constraints8.10681743751E-14
ens_1d_35QQELECTRON MICROSCOPYNCS constraints9.73415054151E-14
ens_1d_36QQELECTRON MICROSCOPYNCS constraints3.57957764781E-13

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