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- PDB-7q5r: Protein community member pyruvate dehydrogenase complex E2 core f... -

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Basic information

Entry
Database: PDB / ID: 7q5r
TitleProtein community member pyruvate dehydrogenase complex E2 core from C. thermophilum
ComponentsAcetyltransferase component of pyruvate dehydrogenase complex
KeywordsTRANSFERASE / Dihydrolipoyl / transacetylase / E2 / Pyruvate
Function / homology
Function and homology information


dihydrolipoyllysine-residue acetyltransferase / dihydrolipoyllysine-residue acetyltransferase activity / pyruvate decarboxylation to acetyl-CoA / pyruvate dehydrogenase complex / mitochondrion
Similarity search - Function
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) ...Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex / Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component / Peripheral subunit-binding domain / e3 binding domain / Peripheral subunit-binding (PSBD) domain profile. / E3-binding domain superfamily / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / 2-oxoacid dehydrogenase acyltransferase, catalytic domain / 2-oxoacid dehydrogenases acyltransferase (catalytic domain) / Biotin-requiring enzyme / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / Chloramphenicol acetyltransferase-like domain superfamily
Similarity search - Domain/homology
Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.84 Å
AuthorsChojnowski, G. / Skalidis, I. / Kyrilis, F.L. / Tueting, C. / Hamdi, F. / Kastritis, P.L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Cryo-EM and artificial intelligence visualize endogenous protein community members.
Authors: Ioannis Skalidis / Fotis L Kyrilis / Christian Tüting / Farzad Hamdi / Grzegorz Chojnowski / Panagiotis L Kastritis /
Abstract: Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and ...Cellular function is underlined by megadalton assemblies organizing in proximity, forming communities. Metabolons are protein communities involving metabolic pathways such as protein, fatty acid, and thioesters of coenzyme-A synthesis. Metabolons are highly heterogeneous due to their function, making their analysis particularly challenging. Here, we simultaneously characterize metabolon-embedded architectures of a 60S pre-ribosome, fatty acid synthase, and pyruvate/oxoglutarate dehydrogenase complex E2 cores de novo. Cryo-electron microscopy (cryo-EM) 3D reconstructions are resolved at 3.84-4.52 Å resolution by collecting <3,000 micrographs of a single cellular fraction. After combining cryo-EM with artificial intelligence-based atomic modeling and de novo sequence identification methods, at this resolution range, polypeptide hydrogen bonding patterns are discernible. Residing molecular components resemble their purified counterparts from other eukaryotes but also exhibit substantial conformational variation with potential functional implications. Our results propose an integrated tool, boosted by machine learning, that opens doors for structural systems biology spearheaded by cryo-EM characterization of native cell extracts.
History
DepositionNov 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Acetyltransferase component of pyruvate dehydrogenase complex
B: Acetyltransferase component of pyruvate dehydrogenase complex
C: Acetyltransferase component of pyruvate dehydrogenase complex
D: Acetyltransferase component of pyruvate dehydrogenase complex
E: Acetyltransferase component of pyruvate dehydrogenase complex
F: Acetyltransferase component of pyruvate dehydrogenase complex
G: Acetyltransferase component of pyruvate dehydrogenase complex
H: Acetyltransferase component of pyruvate dehydrogenase complex
I: Acetyltransferase component of pyruvate dehydrogenase complex
J: Acetyltransferase component of pyruvate dehydrogenase complex
K: Acetyltransferase component of pyruvate dehydrogenase complex
L: Acetyltransferase component of pyruvate dehydrogenase complex
M: Acetyltransferase component of pyruvate dehydrogenase complex
N: Acetyltransferase component of pyruvate dehydrogenase complex
O: Acetyltransferase component of pyruvate dehydrogenase complex
P: Acetyltransferase component of pyruvate dehydrogenase complex
Q: Acetyltransferase component of pyruvate dehydrogenase complex
R: Acetyltransferase component of pyruvate dehydrogenase complex
S: Acetyltransferase component of pyruvate dehydrogenase complex
T: Acetyltransferase component of pyruvate dehydrogenase complex
V: Acetyltransferase component of pyruvate dehydrogenase complex
W: Acetyltransferase component of pyruvate dehydrogenase complex
X: Acetyltransferase component of pyruvate dehydrogenase complex
Y: Acetyltransferase component of pyruvate dehydrogenase complex
Z: Acetyltransferase component of pyruvate dehydrogenase complex
AA: Acetyltransferase component of pyruvate dehydrogenase complex
BA: Acetyltransferase component of pyruvate dehydrogenase complex
CA: Acetyltransferase component of pyruvate dehydrogenase complex
DA: Acetyltransferase component of pyruvate dehydrogenase complex
EA: Acetyltransferase component of pyruvate dehydrogenase complex
FA: Acetyltransferase component of pyruvate dehydrogenase complex
GA: Acetyltransferase component of pyruvate dehydrogenase complex
HA: Acetyltransferase component of pyruvate dehydrogenase complex
IA: Acetyltransferase component of pyruvate dehydrogenase complex
JA: Acetyltransferase component of pyruvate dehydrogenase complex
KA: Acetyltransferase component of pyruvate dehydrogenase complex
LA: Acetyltransferase component of pyruvate dehydrogenase complex
MA: Acetyltransferase component of pyruvate dehydrogenase complex
NA: Acetyltransferase component of pyruvate dehydrogenase complex
OA: Acetyltransferase component of pyruvate dehydrogenase complex
PA: Acetyltransferase component of pyruvate dehydrogenase complex
QA: Acetyltransferase component of pyruvate dehydrogenase complex
RA: Acetyltransferase component of pyruvate dehydrogenase complex
SA: Acetyltransferase component of pyruvate dehydrogenase complex
TA: Acetyltransferase component of pyruvate dehydrogenase complex
UA: Acetyltransferase component of pyruvate dehydrogenase complex
VA: Acetyltransferase component of pyruvate dehydrogenase complex
WA: Acetyltransferase component of pyruvate dehydrogenase complex
XA: Acetyltransferase component of pyruvate dehydrogenase complex
YA: Acetyltransferase component of pyruvate dehydrogenase complex
ZA: Acetyltransferase component of pyruvate dehydrogenase complex
AB: Acetyltransferase component of pyruvate dehydrogenase complex
BB: Acetyltransferase component of pyruvate dehydrogenase complex
CB: Acetyltransferase component of pyruvate dehydrogenase complex
DB: Acetyltransferase component of pyruvate dehydrogenase complex
EB: Acetyltransferase component of pyruvate dehydrogenase complex
FB: Acetyltransferase component of pyruvate dehydrogenase complex
GB: Acetyltransferase component of pyruvate dehydrogenase complex
HB: Acetyltransferase component of pyruvate dehydrogenase complex
IB: Acetyltransferase component of pyruvate dehydrogenase complex


Theoretical massNumber of molelcules
Total (without water)2,926,64960
Polymers2,926,64960
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "YA"
d_2ens_1chain "AA"
d_3ens_1chain "X"
d_4ens_1chain "B"
d_5ens_1chain "BA"
d_6ens_1chain "BB"
d_7ens_1chain "C"
d_8ens_1chain "CA"
d_9ens_1chain "CB"
d_10ens_1chain "D"
d_11ens_1chain "DA"
d_12ens_1chain "DB"
d_13ens_1chain "E"
d_14ens_1chain "EA"
d_15ens_1chain "EB"
d_16ens_1chain "F"
d_17ens_1chain "A"
d_18ens_1chain "FB"
d_19ens_1chain "G"
d_20ens_1chain "GA"
d_21ens_1chain "GB"
d_22ens_1chain "H"
d_23ens_1chain "HA"
d_24ens_1chain "HB"
d_25ens_1chain "I"
d_26ens_1chain "IA"
d_27ens_1chain "IB"
d_28ens_1chain "J"
d_29ens_1chain "JA"
d_30ens_1chain "K"
d_31ens_1chain "KA"
d_32ens_1chain "L"
d_33ens_1chain "LA"
d_34ens_1chain "M"
d_35ens_1chain "MA"
d_36ens_1chain "N"
d_37ens_1chain "NA"
d_38ens_1chain "O"
d_39ens_1chain "OA"
d_40ens_1chain "P"
d_41ens_1chain "PA"
d_42ens_1chain "Q"
d_43ens_1chain "QA"
d_44ens_1chain "R"
d_45ens_1chain "RA"
d_46ens_1chain "S"
d_47ens_1chain "SA"
d_48ens_1chain "T"
d_49ens_1chain "TA"
d_50ens_1chain "UA"
d_51ens_1chain "V"
d_52ens_1chain "VA"
d_53ens_1chain "W"
d_54ens_1chain "WA"
d_55ens_1chain "FA"
d_56ens_1chain "XA"
d_57ens_1chain "Y"
d_58ens_1chain "AB"
d_59ens_1chain "Z"
d_60ens_1chain "ZA"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULEUYA1 - 210
d_21ens_1GLULEUAA1 - 210
d_31ens_1GLULEUX1 - 210
d_41ens_1GLULEUB1 - 210
d_51ens_1GLULEUBA1 - 210
d_61ens_1GLULEUBB1 - 210
d_71ens_1GLULEUC1 - 210
d_81ens_1GLULEUCA1 - 210
d_91ens_1GLULEUCB1 - 210
d_101ens_1GLULEUD1 - 210
d_111ens_1GLULEUDA1 - 210
d_121ens_1GLULEUDB1 - 210
d_131ens_1GLULEUE1 - 210
d_141ens_1GLULEUEA1 - 210
d_151ens_1GLULEUEB1 - 210
d_161ens_1GLULEUF1 - 210
d_171ens_1GLULEUA1 - 210
d_181ens_1GLULEUFB1 - 210
d_191ens_1GLULEUG1 - 210
d_201ens_1GLULEUGA1 - 210
d_211ens_1GLULEUGB1 - 210
d_221ens_1GLULEUH1 - 210
d_231ens_1GLULEUHA1 - 210
d_241ens_1GLULEUHB1 - 210
d_251ens_1GLULEUI1 - 210
d_261ens_1GLULEUIA1 - 210
d_271ens_1GLULEUHB1 - 210
d_281ens_1GLULEUJ1 - 210
d_291ens_1GLULEUJA1 - 210
d_301ens_1GLULEUK1 - 210
d_311ens_1GLULEUKA1 - 210
d_321ens_1GLULEUL1 - 210
d_331ens_1GLULEULA1 - 210
d_341ens_1GLULEUM1 - 210
d_351ens_1GLULEUMA1 - 210
d_361ens_1GLULEUN1 - 210
d_371ens_1GLULEUNA1 - 210
d_381ens_1GLULEUO1 - 210
d_391ens_1GLULEUOA1 - 210
d_401ens_1GLULEUP1 - 210
d_411ens_1GLULEUPA1 - 210
d_421ens_1GLULEUQ1 - 210
d_431ens_1GLULEUQA1 - 210
d_441ens_1GLULEUR1 - 210
d_451ens_1GLULEURA1 - 210
d_461ens_1GLULEUS1 - 210
d_471ens_1GLULEUSA1 - 210
d_481ens_1GLULEUT1 - 210
d_491ens_1GLULEUTA1 - 210
d_501ens_1GLULEUUA1 - 210
d_511ens_1GLULEUV1 - 210
d_521ens_1GLULEUVA1 - 210
d_531ens_1GLULEUW1 - 210
d_541ens_1GLULEUWA1 - 210
d_551ens_1GLULEUFA1 - 210
d_561ens_1GLULEUXA1 - 210
d_571ens_1GLULEUY1 - 210
d_581ens_1GLULEUAB1 - 210
d_591ens_1GLULEUZ1 - 210
d_601ens_1GLULEUZA1 - 210

NCS oper:
IDCodeMatrixVector
1given(-0.309856389246, 0.805601601798, -0.50497037262), (-0.810401916574, -0.501532238663, -0.30284343677), (-0.497230079195, 0.31539098396, 0.808264050655)124.807855514, 323.638011004, 46.6481006432
2given(-0.808176075404, 0.503561513615, 0.305413217052), (-0.50028871704, -0.313376148338, -0.807159581034), (-0.310745282744, -0.805121848951, 0.505189249286)123.973489652, 324.36480872, 199.406909449
3given(0.49900539019, 0.307951829896, -0.810036598571), (0.308768742048, 0.810205235481, 0.498226193945), (0.809725561221, -0.498731537866, 0.309210880537)124.188224925, -76.3211188312, 47.1410381541
4given(-0.807129578424, 0.500559572959, -0.313020698281), (-0.502430608645, -0.303983927266, 0.809417849729), (0.310008592027, 0.810576267777, 0.496850869967)200.780623645, 123.414192743, -76.2965365799
5given(0.309859894489, 0.805917562365, -0.504463802922), (0.808007728025, -0.502848404063, -0.307029304764), (-0.501109127077, -0.31247458329, -0.807000171969)48.0619942652, 123.812762322, 324.303899159
6given(-0.500747660854, -0.310910825597, -0.807828099707), (0.31088717343, 0.806394120981, -0.503068272746), (0.807837202378, -0.503053655363, -0.307141782049)324.241246833, 47.8242344896, 123.869589935
7given(-0.807846840129, 0.503843588474, 0.3058187719), (0.500142389002, 0.311492017522, 0.807979154275), (0.311835010247, 0.805676337851, -0.503631378104)123.865517966, -76.6164711563, 47.9558524348
8given(-0.503535838234, 0.308620109484, -0.806972916297), (0.305220934564, -0.810254751828, -0.500327311111), (-0.808264709559, -0.498237759671, 0.313794987403)247.546173321, 248.074544596, 246.928526217
9given(-0.809723486059, -0.494836064406, 0.315412659047), (-0.501506215647, 0.304456246765, -0.809813502896), (0.30469557232, -0.813906421629, -0.494688735509)246.47114971, 248.222520369, 247.599368377
10given(-0.306981564148, 0.811760457347, 0.49679702008), (0.809217343044, 0.49738570063, -0.312689552954), (-0.500928748417, 0.306026836563, -0.809578880847)0.0708154838954, 0.726824098766, 248.067964706
11given(-0.999998935984, -0.00085267738679, -0.00118362710703), (0.000848483085072, -0.999993375663, 0.0035395912037), (-0.00118663739566, 0.00353858314994, 0.999993035136)247.940603785, 247.197021385, -0.235027270929
12given(-0.001462512322, 0.00568824230563, 0.99998275233), (-0.999998306647, 0.00110869606606, -0.00146884171142), (-0.0011170320712, -0.999983207205, 0.00568661119177)-0.427691027501, 247.798738804, 246.961310705
13given(0.00177621749842, 0.999976103956, -0.00668106046179), (-0.00238337226011, -0.00667681872543, -0.999974869498), (-0.999995582284, 0.00179209631535, 0.00237145582469)0.653980006336, 248.349304685, 247.243548962
14given(0.499722283834, -0.309574478968, -0.808975451427), (0.307940006603, -0.809443066675, 0.499974873515), (-0.809599031233, -0.498964491506, -0.309166370815)200.439251797, 123.88272364, 324.257932862
15given(-0.809900125668, -0.501562595701, -0.304132781917), (0.498430137441, -0.315118329613, -0.807631002644), (0.309239687836, -0.805689394826, 0.505208288264)323.739349795, 200.774653624, 122.843280833
16given(0.810813156758, 0.497823318577, 0.3078213253), (-0.498854044993, 0.312682416443, 0.808315747862), (0.306148112231, -0.808950956442, 0.501868193302)-76.2794352577, 47.1431542892, 123.744865805
17given(-0.309222671431, -0.809445943394, -0.499177928394), (0.808872620081, -0.499902089041, 0.309552880547), (-0.500106412632, -0.308050590155, 0.809319720475)324.176898714, 47.2389798879, 123.842601243
18given(-0.501121682801, -0.303889304916, 0.810264370058), (-0.313318495249, -0.809075548324, -0.497220552309), (0.806665097523, -0.503038813076, 0.310231160551)123.338352026, 324.02138662, 47.5614571424
19given(0.807420634, -0.50191997772, 0.310077822096), (-0.501585906206, -0.307284906325, 0.808694976515), (-0.310617930079, -0.808487676041, -0.499864160751)47.3649830465, 123.939941344, 324.261926888
20given(-0.310123815676, -0.807102254639, 0.502403393209), (0.808343841212, -0.502016415865, -0.307505695192), (0.500403290681, 0.310749849169, 0.808103383186)199.97532525, 123.836842845, -76.4581232222
21given(0.501621095845, 0.308284304479, 0.808292684499), (-0.311682255441, -0.807192564894, 0.501292663844), (0.806988505399, -0.503389462338, -0.308818071623)-76.3783896035, 200.247216954, 124.181660289
22given(0.808759491862, -0.497354137596, -0.313921879039), (0.501433253913, 0.304150427803, 0.809973585457), (-0.307364240264, -0.812484694676, 0.495374449001)124.335973201, -76.3195413425, 201.158935648
23given(0.499849386598, -0.308020337813, 0.809490001304), (0.305317694713, -0.81196295479, -0.497490970113), (0.810513230005, 0.49582217734, -0.311815125426)-0.125247473339, 247.718229231, 0.680187977775
24given(0.809732695725, 0.497689651102, -0.310866486871), (0.499638499557, -0.306943872459, 0.810028906225), (0.307724440424, -0.811227754916, -0.497207399804)0.382829551162, -0.243910749959, 247.526442218
25given(0.312083414408, -0.807182109367, -0.501059861463), (0.808792546012, 0.50243278855, -0.305640165073), (0.498456176576, -0.309868254761, 0.809643813491)247.516929059, -0.698482462416, 0.0476456329307
26given(0.999996605323, 0.000933144026566, -0.00243281427741), (0.000944032278298, -0.999989526857, 0.0044782785512), (-0.00242860991932, -0.00448056000409, -0.999987013134)0.24058574007, 247.04767409, 248.084813789
27given(-0.00356410647924, -0.00707776464501, -0.999968600703), (0.999993378954, -0.000759510254216, -0.00355881899072), (-0.000734297922898, -0.999974663875, 0.00708042475822)248.309552739, 0.478698597679, 246.968167895
28given(0.000170171915684, -0.999968951757, 0.00787823352989), (-0.00131840710036, -0.0078784511459, -0.999968095396), (0.999999116422, 0.000159779767393, -0.00131970685726)246.603534398, 248.324828067, 0.142419883335
29given(-0.81012497878, -0.501561908747, -0.303534463365), (-0.497933029606, 0.315378650522, 0.807836001192), (-0.30945147727, 0.805587958257, -0.505240363319)323.701183328, 46.7476632649, 124.840473906
30given(0.306565799849, -0.808072956288, 0.503026348892), (0.810435163079, 0.498758306405, 0.307302779417), (-0.499211635289, 0.31346171873, 0.807792977243)123.482529496, -76.2557753495, 47.190691089
31given(-0.501648140913, -0.303572527846, 0.810057320846), (0.310411291608, 0.810876281611, 0.496109348796), (-0.807461437321, 0.500323271753, -0.312542238715)123.280274765, -76.2491042822, 200.763583548
32given(0.812801181743, -0.498666900949, 0.301140433777), (0.493644538628, 0.315123330974, -0.810562986916), (0.309304556127, 0.807482884136, 0.502296808059)48.1221274805, 123.913178825, -76.6854425816
33given(0.50035401321, 0.303399099735, 0.810922220527), (0.30727145288, 0.813404707366, -0.493920070741), (-0.809462856288, 0.496308138474, 0.313764427517)-76.437678533, 46.2497515186, 123.537856048
34given(0.807322950767, -0.503075183215, -0.308455852914), (-0.501970424733, -0.310639191516, -0.807173454338), (0.31025045666, 0.806485370436, -0.50331501211)124.086028742, 324.209707286, 47.8427861014
35given(0.807718304996, 0.499435782587, -0.313297045704), (-0.502534034301, 0.305340231819, -0.808842931107), (-0.308302909724, 0.810759669633, 0.49761237319)0.706409789431, 248.125190518, 0.14623488131
36given(0.305518387584, -0.812785457189, -0.496022494884), (-0.809329080144, -0.49610648815, 0.314427722138), (-0.501642257871, 0.305381978836, -0.80938056075)247.639957412, 246.716180499, 248.087281201
37given(-0.00324834454167, -0.00923018656633, -0.999952124811), (-0.999994439391, 0.000784570803555, 0.00324123991898), (0.000754615992921, 0.999957093132, -0.00923268379716)248.609647463, 247.180322149, 1.18775350069
38given(-0.000584428833994, -0.999974472169, 0.00712133788738), (0.00216950131959, 0.0071200544572, 0.999972298661), (-0.99999747585, 0.000599862396476, 0.00216528477181)246.737430206, -0.708062893891, 247.313892361
39given(0.811668263737, 0.497491653488, 0.306099141378), (0.497846294202, -0.315097007217, -0.807999346158), (-0.305522007378, 0.80821774959, -0.503428616842)-76.0630261544, 200.804387118, 124.221122883
40given(-0.4972693662, 0.31578524607, 0.808085921052), (-0.307454466362, 0.806822606796, -0.504488882214), (-0.811292135148, -0.499316492345, -0.304118582002)46.6856796788, 124.540851309, 323.64352648
41given(0.497651380166, 0.306165728158, -0.811545224076), (-0.310028834738, -0.811035798808, -0.496087748975), (-0.810077295972, 0.498481173118, -0.308692880704)124.594504423, 323.857566004, 200.534143887
42given(0.309734896908, 0.810064126362, 0.497855807256), (-0.808040071929, 0.500223266878, -0.311203993274), (-0.501134249272, -0.305896705532, 0.80950087693)-76.5308420273, 200.562586847, 123.599728228
43given(-0.501355605784, -0.314728495261, -0.80597055208), (-0.309182481508, -0.804830231082, 0.506610789724), (-0.808114317208, 0.503184134694, 0.306197610892)324.387805454, 199.081760247, 123.890952048
44given(0.312721588557, 0.80948123778, -0.496935945301), (-0.809016475777, 0.501124810354, 0.307190928202), (0.497692224143, 0.305964132097, 0.811596204955)46.7327588296, 124.032316342, -76.6295342126
45given(-0.810625175395, -0.495397873774, 0.312198289036), (0.499440521133, -0.306604429201, 0.810279513406), (-0.305689369896, 0.812757448846, 0.495963041444)246.989651823, -0.314671072399, 0.0284460333085
46given(-0.501553195693, 0.304804426815, -0.809653415533), (-0.306986970579, 0.812271240113, 0.495958095387), (0.808828406885, 0.497302416925, -0.313826248641)248.164684875, 0.148256516635, 0.927580237668
47given(0.00149375457947, 0.00423830325761, 0.99998990269), (0.999998813152, -0.000383675574244, -0.00149214173979), (0.000377347550956, 0.999990944748, -0.00423887134454)-0.363628636583, 0.267671605498, 0.508569582466
48given(-0.999996275734, 0.00204375117443, 0.00180875626864), (0.00202767368054, 0.999958814557, -0.00884633986772), (-0.00182676149171, -0.00884263935411, -0.999959234505)247.233336527, 1.06823819733, 248.572997093
49given(0.495624137453, -0.311129680824, -0.810897673005), (-0.309437391559, 0.809118037769, -0.499576322159), (0.811544955673, 0.498524144518, 0.304743272696)200.988932839, 123.790575334, -75.9967929174
50given(-0.30612390475, 0.808922883251, -0.501928205916), (0.811785954599, 0.497219460394, 0.306229280314), (0.497284344069, -0.313714164741, -0.80888299771)123.990236181, -76.0804744829, 200.829953854
51given(-0.310113012684, -0.811686163555, -0.494970192291), (-0.809887536113, 0.498224123156, -0.309604428191), (0.49790772058, 0.304857827517, -0.811880290922)323.853893873, 200.577281218, 124.762879292
52given(-0.809954771369, 0.49877311012, -0.308542789508), (0.497722671711, 0.306277364069, -0.811459375646), (-0.310234444254, -0.810814134608, -0.496321497337)200.412088142, 124.562596122, 324.00222222
53given(-0.310933546452, -0.80419806943, 0.506542984173), (-0.80621936315, 0.505413099804, 0.307519002712), (-0.503319648109, -0.312766787993, -0.805509942928)199.146902257, 123.434163468, 324.228384608
54given(0.309244202807, -0.804467519306, 0.507148926265), (-0.8099247493, -0.502281334506, -0.302878459912), (0.498387322774, -0.31708905908, -0.806885744768)122.505585384, 323.605535678, 200.844307406
55given(0.499605814232, -0.307488159767, 0.809842615567), (-0.305864148236, 0.812046957914, 0.497017968454), (-0.810457372852, -0.496014888633, 0.311653777524)-0.31521734345, 0.0316688139718, 247.072608574
56given(-0.304888342064, 0.812943284595, 0.496151503984), (-0.809794059159, -0.495479699432, 0.31421879193), (0.50127505486, -0.305978893852, 0.809382626384)-0.0291681253115, 246.66546264, -0.3132060579
57given(0.31075787372, 0.812060384352, 0.493950884285), (0.809042522365, -0.498751358911, 0.310961860989), (0.498878483126, 0.302993422617, -0.811982293479)-75.9620945859, 46.9305653271, 124.857496931
58given(-0.000522248531618, 0.999999089229, -0.00124450688779), (-0.00163680238305, 0.00124365057332, 0.999997887103), (0.999998524066, 0.00052428444, 0.00163615139761)0.21335268671, -0.0571702996732, -0.263499967411
59given(-0.499864735645, 0.314230756341, 0.807090006027), (0.305914466977, -0.807743651765, 0.503950922142), (0.810278708195, 0.49880780347, 0.307634832624)47.1649861644, 123.345665341, -76.2308972459

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Components

#1: Protein ...
Acetyltransferase component of pyruvate dehydrogenase complex


Mass: 48777.488 Da / Num. of mol.: 60 / Source method: isolated from a natural source
Source: (natural) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
References: UniProt: G0S4X6, dihydrolipoyllysine-residue acetyltransferase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native 60-mer core of Pyruvate Dehydrogenase Complex / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Buffer solutionpH: 7.4
Buffer componentConc.: 200 mM / Name: Ammonium acetate / Formula: NH4CH2COOH
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K
Details: For plunging, blot force 0 and blotting time of 4 sec were applied.

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 92000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER / Temperature (max): 103.15 K / Temperature (min): 77.15 K / Residual tilt: 14.7 mradians
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 2808

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.1particle selectionBlob Picker
2EPU2.9image acquisitionImage Collection
4cryoSPARC3.1CTF correctionPatch CTF
7Coot0.9.2-premodel fitting
11cryoSPARC3.1classification2D Classification
12cryoSPARC3.13D reconstructionHomogeneous Refinement (NEW)
13Coot0.9.2-premodel refinement
14PHENIX1.18.2model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 276399
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7825 / Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial models were predicted using AlphaFold v2.0.1, fitted into reconstructions using COOT and finally refined in real space using COOT and phenix.real_space_refine
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 116.68 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006197020
ELECTRON MICROSCOPYf_angle_d0.9184131820
ELECTRON MICROSCOPYf_chiral_restr0.067715960
ELECTRON MICROSCOPYf_plane_restr0.004716860
ELECTRON MICROSCOPYf_dihedral_angle_d27.235835880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000703918603866
ens_1d_3XELECTRON MICROSCOPYNCS constraints0.00071166023418
ens_1d_4BELECTRON MICROSCOPYNCS constraints0.000704595562037
ens_1d_5BAELECTRON MICROSCOPYNCS constraints0.000705762327078
ens_1d_6BBELECTRON MICROSCOPYNCS constraints0.000706574304355
ens_1d_7CELECTRON MICROSCOPYNCS constraints0.000716619456026
ens_1d_8CAELECTRON MICROSCOPYNCS constraints0.000715882041279
ens_1d_9CBELECTRON MICROSCOPYNCS constraints0.000710892119328
ens_1d_10DELECTRON MICROSCOPYNCS constraints0.000714090256894
ens_1d_11DAELECTRON MICROSCOPYNCS constraints0.00070510242282
ens_1d_12DBELECTRON MICROSCOPYNCS constraints0.000701288391771
ens_1d_13EELECTRON MICROSCOPYNCS constraints0.000715290930736
ens_1d_14EAELECTRON MICROSCOPYNCS constraints0.000704176477435
ens_1d_15EBELECTRON MICROSCOPYNCS constraints0.000706363051864
ens_1d_16FELECTRON MICROSCOPYNCS constraints0.000705359115161
ens_1d_17AELECTRON MICROSCOPYNCS constraints0.000704540479726
ens_1d_18FBELECTRON MICROSCOPYNCS constraints0.000698712011039
ens_1d_19GELECTRON MICROSCOPYNCS constraints0.000720913353966
ens_1d_20GAELECTRON MICROSCOPYNCS constraints0.00070318788731
ens_1d_21GBELECTRON MICROSCOPYNCS constraints0.000703962867622
ens_1d_22HELECTRON MICROSCOPYNCS constraints0.000707954922384
ens_1d_23HAELECTRON MICROSCOPYNCS constraints0.000712193418736
ens_1d_24HBELECTRON MICROSCOPYNCS constraints0.000706972392118
ens_1d_25IELECTRON MICROSCOPYNCS constraints0.00069422376741
ens_1d_26IAELECTRON MICROSCOPYNCS constraints0.000702216689961
ens_1d_27IBELECTRON MICROSCOPYNCS constraints0.000708496339058
ens_1d_28JELECTRON MICROSCOPYNCS constraints0.00069380947557
ens_1d_29JAELECTRON MICROSCOPYNCS constraints0.000704523163003
ens_1d_30KELECTRON MICROSCOPYNCS constraints0.000705144219844
ens_1d_31KAELECTRON MICROSCOPYNCS constraints0.000711722960838
ens_1d_32LELECTRON MICROSCOPYNCS constraints0.000711930015584
ens_1d_33LAELECTRON MICROSCOPYNCS constraints0.000697785316054
ens_1d_34MELECTRON MICROSCOPYNCS constraints0.000710908909477
ens_1d_35MAELECTRON MICROSCOPYNCS constraints0.000700966842197
ens_1d_36NELECTRON MICROSCOPYNCS constraints0.00070205759362
ens_1d_37NAELECTRON MICROSCOPYNCS constraints0.00070589509299
ens_1d_38OELECTRON MICROSCOPYNCS constraints0.000703290846864
ens_1d_39OAELECTRON MICROSCOPYNCS constraints0.000709674387682
ens_1d_40PELECTRON MICROSCOPYNCS constraints0.000696335320747
ens_1d_41PAELECTRON MICROSCOPYNCS constraints0.000717309083249
ens_1d_42QELECTRON MICROSCOPYNCS constraints0.000703698888636
ens_1d_43QAELECTRON MICROSCOPYNCS constraints0.000703374194052
ens_1d_44RELECTRON MICROSCOPYNCS constraints0.000708013112497
ens_1d_45RAELECTRON MICROSCOPYNCS constraints0.000703447733483
ens_1d_46SELECTRON MICROSCOPYNCS constraints0.000706919174436
ens_1d_47SAELECTRON MICROSCOPYNCS constraints0.000690812883105
ens_1d_48TELECTRON MICROSCOPYNCS constraints0.000703460103029
ens_1d_49TAELECTRON MICROSCOPYNCS constraints0.000706021078928
ens_1d_50UAELECTRON MICROSCOPYNCS constraints0.00071115082926
ens_1d_51VELECTRON MICROSCOPYNCS constraints0.000709836716486
ens_1d_52VAELECTRON MICROSCOPYNCS constraints0.000706749909247
ens_1d_53WELECTRON MICROSCOPYNCS constraints0.000712174281327
ens_1d_54WAELECTRON MICROSCOPYNCS constraints0.000708670357116
ens_1d_55FAELECTRON MICROSCOPYNCS constraints0.000698496063782
ens_1d_56XAELECTRON MICROSCOPYNCS constraints0.000705388646163
ens_1d_57YELECTRON MICROSCOPYNCS constraints0.000699340908364
ens_1d_58ABELECTRON MICROSCOPYNCS constraints0.000708725837454
ens_1d_59ZELECTRON MICROSCOPYNCS constraints0.000687611588812
ens_1d_60ZAELECTRON MICROSCOPYNCS constraints0.000706108457302

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