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- PDB-9oyt: Structure of T61I D2-NT amyloid fibrils -

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Basic information

Entry
Database: PDB / ID: 9oyt
TitleStructure of T61I D2-NT amyloid fibrils
ComponentsCoiled-coil-helix-coiled-coil-helix domain-containing protein 2
KeywordsPROTEIN FIBRIL / T61I 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: 3.1 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

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Assembly

Deposited unit
A: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
B: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
C: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
D: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
E: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
I: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
J: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
K: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
L: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
M: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
N: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
R: 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
H: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
O: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
P: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2
Q: Coiled-coil-helix-coiled-coil-helix domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)204,85418
Polymers204,85418
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"
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 "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: 54 - 87 / Label seq-ID: 54 - 87

Dom-IDAuth asym-IDLabel asym-ID
d_1CC
d_2BB
d_3AA
d_4DD
d_5EE
d_6FM
d_7GN
d_8HO
d_9IF
d_10JG
d_11KH
d_12LI
d_13MJ
d_14NK
d_15OP
d_16PQ
d_17QR
d_18RL

NCS oper:
IDCodeMatrixVector
1given(0.999417779781, -0.0340992086985, 0.00115992418652), (0.034104155972, 0.999407914423, -0.00455270616258), (-0.00100399373456, 0.00458961372038, 0.99998896366)4.90377058006, -4.12680488527, -5.46510471389
2given(0.997223913411, -0.0744342363293, 0.00200274373482), (0.0744391257728, 0.997222453718, -0.00248884622068), (-0.00181192565363, 0.00263101946083, 0.999994897318)11.1481730971, -10.1034051951, -9.75706175219
3given(-0.998131343463, 0.0610931166428, -0.00120511236488), (-0.0610973835569, -0.998124206703, 0.00389585886525), (-0.000964841663108, 0.0039622080555, 0.999991684959)287.798876985, 304.97728059, -7.67619106613
4given(-0.999798460149, 0.0196546344027, 0.00409077374413), (-0.019630440497, -0.9997900566, 0.00587269363784), (0.00420534055959, 0.00579120636546, 0.999974388192)293.332804633, 298.735787589, -4.0293705205
5given(0.985113003033, -0.171880505148, -0.00307623238759), (0.17187078915, 0.985114347647, -0.00318651787664), (0.00357814096401, 0.00261036570661, 0.999990191401)28.2124233859, -22.6152563039, -24.6493714105
6given(0.990449162237, -0.137874406405, -0.00105122871777), (0.137871709583, 0.990447401734, -0.00230999882812), (0.00135967646937, 0.0021430017036, 0.999996779407)22.0309963845, -18.6196474102, -19.5398727003
7given(0.993813269055, -0.111045792259, -0.00200456250137), (0.111035592683, 0.993805628957, -0.00463346634658), (0.00250667243882, 0.00438222255154, 0.999987256278)17.7499790842, -14.6475432589, -15.3086188471
8given(-0.999887668538, -0.0142947144636, 0.00450682195999), (0.0142893676353, -0.999897161929, -0.00121636331915), (0.00452374605344, -0.00115182704743, 0.999989104449)298.308180256, 294.974148105, 1.96433395029
9given(0.963076235475, -0.269201857796, -0.00381109195642), (0.269197358328, 0.963083607061, -0.00165773346969), (0.004116665118, 0.000570587822398, 0.999991363712)46.0134217931, -34.0482370617, -38.7108025582
10given(0.970655548828, -0.240467747995, -0.00175148597586), (0.240470325734, 0.970655411221, 0.00144744928994), (0.00135202446906, -0.00182615508806, 0.99999741859)40.3837871543, -31.4647629113, -33.0490806659
11given(0.978360048515, -0.206897175584, 0.0022746880169), (0.2068940409, 0.978362145329, 0.00153896922917), (-0.002543877035, -0.00103504661411, 0.999996228677)33.5815204768, -27.5971655457, -27.9103672031
12given(-0.966908629082, 0.254949773115, 0.00939766963797), (-0.25494743301, -0.966953802626, 0.00146628396805), (0.00946094115724, -0.000978149129085, 0.999954765885)252.68533635, 329.403972097, -36.8825255985
13given(-0.973919946116, 0.226884712739, 0.00180712012101), (-0.226883401124, -0.973921509469, 0.000903154963453), (0.00196490521049, 0.000469595074047, 0.999997959312)259.064393895, 326.458776158, -31.1246414434
14given(-0.987011325866, 0.160643887182, 0.00147787821883), (-0.160631678113, -0.986994295577, 0.00630273636895), (0.00247115344173, 0.00598347812177, 0.999979045476)270.875321431, 317.619034755, -22.5700589803
15given(-0.991688692339, 0.128650780655, 0.00158559876555), (-0.128636910438, -0.991667415366, 0.00694856634442), (0.00246632511428, 0.00668684814534, 0.999974601329)276.373941053, 313.48124647, -18.0089453688
16given(-0.996044177854, 0.0888594028618, 4.78093479985E-5), (-0.0888561668726, -0.996012217432, 0.00801525642444), (0.000759849594374, 0.00797930134017, 0.999967876173)283.229910107, 308.151290112, -13.3106184034
17given(-0.979818533088, 0.199849450294, 0.00397987878756), (-0.199839256902, -0.979824646806, 0.00281654262774), (0.00446246782323, 0.00196436464643, 0.999988113756)263.520883298, 322.895578125, -27.0252567709

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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: 11380.803 Da / Num. of mol.: 18
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: T61I of 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
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 179.04 ° / Axial rise/subunit: 2.36 Å / Axial symmetry: C21
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 315652 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 62.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00123870
ELECTRON MICROSCOPYf_angle_d0.37865202
ELECTRON MICROSCOPYf_chiral_restr0.0484630
ELECTRON MICROSCOPYf_plane_restr0.001666
ELECTRON MICROSCOPYf_dihedral_angle_d3.6858594
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CCELECTRON MICROSCOPYNCS constraints1.92667017154E-13
ens_1d_3CCELECTRON MICROSCOPYNCS constraints1.70152772993E-12
ens_1d_4CCELECTRON MICROSCOPYNCS constraints7.63193454675E-11
ens_1d_5CCELECTRON MICROSCOPYNCS constraints6.5853844243E-11
ens_1d_6CCELECTRON MICROSCOPYNCS constraints1.55988496108E-13
ens_1d_7CCELECTRON MICROSCOPYNCS constraints3.32073444104E-11
ens_1d_8CCELECTRON MICROSCOPYNCS constraints1.29920293696E-13
ens_1d_9CCELECTRON MICROSCOPYNCS constraints3.73933042929E-11
ens_1d_10CCELECTRON MICROSCOPYNCS constraints3.73600038627E-11
ens_1d_11CCELECTRON MICROSCOPYNCS constraints1.48665723903E-13
ens_1d_12CCELECTRON MICROSCOPYNCS constraints4.33750396606E-11
ens_1d_13CCELECTRON MICROSCOPYNCS constraints5.98740837235E-11
ens_1d_14CCELECTRON MICROSCOPYNCS constraints1.40004712375E-13
ens_1d_15CCELECTRON MICROSCOPYNCS constraints3.32914016651E-13
ens_1d_16CCELECTRON MICROSCOPYNCS constraints1.17017018874E-12
ens_1d_17CCELECTRON MICROSCOPYNCS constraints1.28008840187E-13
ens_1d_18CCELECTRON MICROSCOPYNCS constraints2.00976552305E-13

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