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- PDB-9oyo: Structure of R15L D10-NT amyloid fibrils -

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Basic information

Entry
Database: PDB / ID: 9oyo
TitleStructure of R15L D10-NT amyloid fibrils
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 10, mitochondrial
KeywordsPROTEIN FIBRIL / CHCHD10 / R15L / 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: 3.15 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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Revision 1.1Aug 13, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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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)165,74918
Polymers165,74918
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 "M"
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 "K"
d_12ens_1chain "L"
d_13ens_1chain "A"
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_1MM
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ
d_11KK
d_12LL
d_13AA
d_14NN
d_15OO
d_16PP
d_17QQ
d_18RR

NCS oper:
IDCodeMatrixVector
1given(-0.997175498132, 0.0751066818147, -0.000110777746632), (-0.0751067059722, -0.997175475252, 0.000232967830197), (-9.29674114491E-5, 0.00024062996377, 0.999999966727)266.47173159, 287.223850885, -17.0328443416
2given(0.994234560352, -0.107226705918, -0.000269330101609), (0.107226614927, 0.994234551138, -0.000332226951414), (0.000303400894299, 0.000301432161883, 0.999999908543)15.6999319123, -14.0228120327, -24.3462620856
3given(-0.993008786535, 0.118039875867, -0.000370903468282), (-0.118039988717, -0.993008797481, 0.000298644369613), (-0.000333058462703, 0.000340337924286, 0.999999886621)259.977636302, 292.582954049, -26.6965085474
4given(0.996311558664, -0.0858095216553, -6.37686890443E-5), (0.0858093267631, 0.996310422978, -0.0015167419209), (0.000193684308261, 0.00150567555902, 0.999998847713)12.4154623667, -11.1421876172, -19.6751591557
5given(-0.995319286077, 0.0966410646125, -0.000152951601642), (-0.096640893119, -0.995318920841, -0.000885207762666), (-0.000237783043675, -0.00086628297898, 0.999999596506)263.234198011, 290.138740589, -21.7196491049
6given(0.991699255244, -0.128579108516, -1.07597264126E-6), (0.128579102669, 0.991699212606, -0.00029338242399), (3.8789891752E-5, 0.000290808783776, 0.999999956963)18.9752170734, -16.6359276345, -29.1664288124
7given(-0.99024163639, 0.139360996255, -0.000119507682184), (-0.139361029109, -0.990241582151, 0.000335476952788), (-7.15890739242E-5, 0.000348857960276, 0.999999936587)256.604400821, 295.150738294, -31.5921961091
8given(0.985232338593, -0.171222605523, -0.00024155406314), (0.171222548082, 0.985232348616, -0.000241390836159), (0.000279318444862, 0.000196466555834, 0.999999941691)25.8146108278, -21.665327572, -38.8697121949
9given(-0.983310919185, 0.181932646317, -0.000385247324634), (-0.181932791944, -0.983310892636, 0.000384238743247), (-0.000308912319295, 0.000447915273169, 0.999999851973)249.778332574, 300.077761892, -41.2561429096
10given(0.988688298084, -0.149984825361, 3.73266592587E-5), (0.149984728222, 0.988687306583, -0.00141106383599), (0.000174733768808, 0.00140070073134, 0.999999003752)22.351549994, -19.0022532967, -34.1993074472
11given(-0.986998505106, 0.160729408528, -9.02896881627E-5), (-0.160729290052, -0.986998217642, -0.000783383956616), (-0.000215028601285, -0.000758686596627, 0.999999689079)253.185610624, 297.849835935, -36.2791236008
12given(0.997933609955, -0.0642534762443, -3.02012597716E-5), (0.0642534591446, 0.997933531826, -0.000398804111721), (5.57634003481E-5, 0.000396039491464, 0.999999920022)9.19898048804, -8.56324404392, -14.6420549438
13given(-0.999940812163, 0.0108798168451, -4.19057297704E-5), (-0.0108798412676, -0.99994061119, 0.000634938512488), (-3.49952263152E-5, 0.000635356859539, 0.999999797548)275.746610689, 278.644361085, -2.51617753596
14given(0.999069897815, -0.0431194107686, -0.000235997415541), (0.04311943147, 0.999069921319, 8.33427982992E-5), (0.000232184227022, -9.34413553669E-5, 0.99999996868)6.13607904592, -5.86978869645, -9.70221223365
15given(-0.998541268183, 0.0539930372769, -0.000296074644806), (-0.0539932381626, -0.998541042615, 0.000718642495539), (-0.000256840993466, 0.000733580217677, 0.999999697946)269.609445792, 284.405699208, -12.1821314435
16given(0.999766390251, -0.0216137448144, -0.00010469102362), (0.0216136151782, 0.999765780098, -0.00111201761321), (0.00012870136782, 0.00110949508355, 0.999999376228)3.04344841567, -2.78228811183, -5.03189393514
17given(-0.999472151592, 0.0324868357814, -0.000153926262114), (-0.0324867589116, -0.999472051626, -0.000478031631118), (-0.000169374732093, -0.000472778737515, 0.999999873896)272.70272792, 281.759060277, -7.20430197917

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Components

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


Mass: 9208.280 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHCHD10, C22orf16 / Variant: R15L / Production host: Escherichia coli (E. coli) / Variant (production host): R15L / 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: R15L 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

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: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 51.21 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.3892 ° / Axial rise/subunit: 2.425 Å / Axial symmetry: C21
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 152213 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.37 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00083780
ELECTRON MICROSCOPYf_angle_d0.36775076
ELECTRON MICROSCOPYf_chiral_restr0.0448630
ELECTRON MICROSCOPYf_plane_restr0.0007648
ELECTRON MICROSCOPYf_dihedral_angle_d3.038594
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2MMELECTRON MICROSCOPYNCS constraints6.34649341469E-13
ens_1d_3MMELECTRON MICROSCOPYNCS constraints2.26003280829E-13
ens_1d_4MMELECTRON MICROSCOPYNCS constraints1.29640007962E-12
ens_1d_5MMELECTRON MICROSCOPYNCS constraints1.84439760412E-11
ens_1d_6MMELECTRON MICROSCOPYNCS constraints8.62913362952E-13
ens_1d_7MMELECTRON MICROSCOPYNCS constraints3.66542843498E-13
ens_1d_8MMELECTRON MICROSCOPYNCS constraints7.51472228503E-13
ens_1d_9MMELECTRON MICROSCOPYNCS constraints2.59599347004E-13
ens_1d_10MMELECTRON MICROSCOPYNCS constraints2.41912281401E-13
ens_1d_11MMELECTRON MICROSCOPYNCS constraints1.77121734666E-11
ens_1d_12MMELECTRON MICROSCOPYNCS constraints1.0258901801E-13
ens_1d_13MMELECTRON MICROSCOPYNCS constraints4.57123078189E-13
ens_1d_14MMELECTRON MICROSCOPYNCS constraints1.17052894255E-11
ens_1d_15MMELECTRON MICROSCOPYNCS constraints1.43852109687E-13
ens_1d_16MMELECTRON MICROSCOPYNCS constraints1.45052640711E-12
ens_1d_17MMELECTRON MICROSCOPYNCS constraints1.50670044231E-11
ens_1d_18MMELECTRON MICROSCOPYNCS constraints2.14665033993E-12

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