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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: 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
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

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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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