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

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Basic information

Entry
Database: PDB / ID: 9cww
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: 2.3 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: To Be Published
Title: Amyloid fibril structures link CHCHD10 and CHCHD2 to neurodegeneration.
Authors: Lv, G. / Sayles, N.M. / Huang, Y. / Mancinelli, C.D. / McAvoy, K. / Shneider, N.A. / Manfredi, G. / Kawamata, H. / Eliezer, D.
History
DepositionJul 30, 2024Deposition 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

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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


Theoretical massNumber of molelcules
Total (without water)55,5146
Polymers55,5146
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 "C"
d_2ens_1chain "B"
d_3ens_1chain "A"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 42 - 75 / Label seq-ID: 42 - 75

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD
d_5EE
d_6FF

NCS oper:
IDCodeMatrixVector
1given(0.999400193289, 0.0346300971691, 0.000100122656201), (-0.0346288744777, 0.999382246438, -0.00599721237369), (-0.000307744852319, 0.00599014807056, 0.999982011548)-4.73322579679, 5.68793591438, 4.05760243701
2given(0.996996721697, 0.077249546024, 0.00548129215492), (-0.0772359151423, 0.997009305602, -0.00265668109122), (-0.00567012669341, 0.0022253497228, 0.999981448569)-10.9389310915, 11.3840386812, 9.8926077546
3given(-0.995418004369, -0.0952490463768, -0.00840331730742), (0.0952640348076, -0.995451054191, -0.00140085033519), (-0.00823166141383, -0.00219496555755, 0.99996371028)289.065919266, 261.938072506, 13.20362531
4given(-0.998443868045, -0.0551236049515, -0.00843981872704), (0.0551298740945, -0.998479060898, -0.000511791857896), (-0.00839877046453, -0.000976281586034, 0.999964253126)284.01630431, 267.735504711, 8.36260544027
5given(-0.999904796028, -0.0125175009572, 0.00580612182474), (0.0125645126265, -0.999887992517, 0.00813237010657), (0.00570367454505, 0.00820454696361, 0.999950075507)276.392471656, 272.697503041, 0.416307276052

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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.: 6
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: FEI TITAN 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 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4.1CTF correction
10RELION4.0.0initial Euler assignment
11RELION4.0.0final Euler assignment
13RELION4.0.03D reconstruction
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 178.845 ° / Axial rise/subunit: 2.365 Å / Axial symmetry: C21
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 667405 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 33.04 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00151284
ELECTRON MICROSCOPYf_angle_d0.46821728
ELECTRON MICROSCOPYf_chiral_restr0.0443216
ELECTRON MICROSCOPYf_plane_restr0.001216
ELECTRON MICROSCOPYf_dihedral_angle_d4.9466198
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.61437152943E-12
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.71380008665E-13
ens_1d_4CCELECTRON MICROSCOPYNCS constraints1.47399452758E-13
ens_1d_5CCELECTRON MICROSCOPYNCS constraints7.90684947565E-14
ens_1d_6CCELECTRON MICROSCOPYNCS constraints1.16953807946E-13

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