[English] 日本語
Yorodumi
- PDB-7q5q: Protein community member oxoglutarate dehydrogenase complex E2 co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q5q
TitleProtein community member oxoglutarate dehydrogenase complex E2 core from C. thermophilum
ComponentsDihydrolipoyllysine-residue succinyltransferase
KeywordsTRANSFERASE / Dihydrolipoyl Succinyltransferase / E2 / Oxoglutarate / a-Ketoglutarate
Function / homology
Function and homology information


L-lysine catabolic process to acetyl-CoA via saccharopine / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / oxoglutarate dehydrogenase complex / tricarboxylic acid cycle
Similarity search - Function
Dihydrolipoamide succinyltransferase / : / 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 succinyltransferase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.38 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

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-13844
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13844
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Dihydrolipoyllysine-residue succinyltransferase
A: Dihydrolipoyllysine-residue succinyltransferase
C: Dihydrolipoyllysine-residue succinyltransferase
D: Dihydrolipoyllysine-residue succinyltransferase
E: Dihydrolipoyllysine-residue succinyltransferase
F: Dihydrolipoyllysine-residue succinyltransferase
G: Dihydrolipoyllysine-residue succinyltransferase
H: Dihydrolipoyllysine-residue succinyltransferase
I: Dihydrolipoyllysine-residue succinyltransferase
J: Dihydrolipoyllysine-residue succinyltransferase
K: Dihydrolipoyllysine-residue succinyltransferase
L: Dihydrolipoyllysine-residue succinyltransferase
M: Dihydrolipoyllysine-residue succinyltransferase
N: Dihydrolipoyllysine-residue succinyltransferase
O: Dihydrolipoyllysine-residue succinyltransferase
P: Dihydrolipoyllysine-residue succinyltransferase
Q: Dihydrolipoyllysine-residue succinyltransferase
R: Dihydrolipoyllysine-residue succinyltransferase
S: Dihydrolipoyllysine-residue succinyltransferase
T: Dihydrolipoyllysine-residue succinyltransferase
V: Dihydrolipoyllysine-residue succinyltransferase
W: Dihydrolipoyllysine-residue succinyltransferase
X: Dihydrolipoyllysine-residue succinyltransferase
Y: Dihydrolipoyllysine-residue succinyltransferase


Theoretical massNumber of molelcules
Total (without water)1,103,68824
Polymers1,103,68824
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 "C"
d_2ens_1chain "B"
d_3ens_1chain "H"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "A"
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"
d_19ens_1chain "S"
d_20ens_1chain "T"
d_21ens_1chain "V"
d_22ens_1chain "W"
d_23ens_1chain "X"
d_24ens_1chain "Y"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSLEUC1 - 228
d_21ens_1LYSLEUA1 - 228
d_31ens_1LYSLEUH1 - 228
d_41ens_1LYSLEUD1 - 228
d_51ens_1LYSLEUE1 - 228
d_61ens_1LYSLEUF1 - 228
d_71ens_1LYSLEUG1 - 228
d_81ens_1LYSLEUB1 - 228
d_91ens_1LYSLEUI1 - 228
d_101ens_1LYSLEUJ1 - 228
d_111ens_1LYSLEUK1 - 228
d_121ens_1LYSLEUL1 - 228
d_131ens_1LYSLEUM1 - 228
d_141ens_1LYSLEUN1 - 228
d_151ens_1LYSLEUO1 - 228
d_161ens_1LYSLEUP1 - 228
d_171ens_1LYSLEUQ1 - 228
d_181ens_1LYSLEUR1 - 228
d_191ens_1LYSLEUS1 - 228
d_201ens_1LYSLEUT1 - 228
d_211ens_1LYSLEUU1 - 228
d_221ens_1LYSLEUV1 - 228
d_231ens_1LYSLEUW1 - 228
d_241ens_1LYSLEUX1 - 228

NCS oper:
IDCodeMatrixVector
1given(-0.999984214916, -0.00442558384691, -0.0034618095935), (0.0044265146535, -0.999990168807, -0.000261262912188), (-0.00346061931886, -0.000276582539024, 0.99999397379)151.184857124, 150.12877201, 0.456304200117
2given(0.000503802330591, 0.999975835402, -0.00693359904983), (-0.999986082321, 0.00046736942478, -0.00525516223025), (-0.00525179468917, 0.00693615011321, 0.999962153521)0.922021083341, 151.166448158, -0.0726079214872
3given(0.00696212911552, -0.00838071549933, -0.999940644421), (-0.999975324263, -0.000996220921271, -0.00695402103568), (-0.000937882118126, 0.999964384942, -0.00838744451768)150.534824162, 151.438879476, 1.13796293525
4given(0.000249430035319, -0.00313467133793, -0.999995055798), (0.0011678984792, -0.999994404002, 0.00313496060516), (-0.999999286899, -0.0011686746582, -0.000245767661621)150.245992701, 149.950618413, 150.531600457
5given(0.999953175984, -0.00918410604381, 0.00304926808695), (0.00297350701714, -0.00825153903702, -0.99996153444), (0.00920891392668, 0.999923779245, -0.00822384366305)0.106919219547, 150.729431574, 0.703949963576
6given(-0.00103244801254, -0.999997916748, 0.00176083832968), (-0.000521510218097, -0.00176030059707, -0.999998314683), (0.999999331039, -0.00103336456772, -0.000519691712807)150.195257213, 150.193479305, 0.188722557447
7given(0.00173226987871, -0.999989101265, 0.00433550361591), (0.999997636228, 0.0017379492736, 0.00130654904888), (-0.00131406969451, 0.0043332300722, 0.999989748116)149.73482455, -0.280538515751, 0.105244089969
8given(-0.00154239511825, 0.00899406523382, 0.999958363037), (0.999998496999, 0.000805685588898, 0.00153521033278), (-0.000791844260715, 0.999959227999, -0.00899529440125)-0.343170448868, -0.323367621381, 1.28008622419
9given(-0.999968180976, -0.00557539974978, -0.00570543193285), (-0.00571760395439, 0.00216967064147, 0.999981300592), (-0.00556291658494, 0.999982103563, -0.00220147953232)151.547413163, 0.418538854943, 0.724353652348
10given(-0.00607455441887, 0.00737804328723, 0.99995433109), (-0.000427349628291, 0.999972670395, -0.00738077467873), (-0.999981458409, -0.000472165029139, -0.00607123539964)-0.0835127493382, 1.03473379556, 151.310767936
11given(0.00600645946936, -0.999965841594, 0.00567785965398), (-0.00452331147773, 0.00565073485027, 0.999973804081), (-0.999971730649, -0.00603198485238, -0.00448921605877)149.598562797, -0.144298054132, 151.38625926
12given(0.00402316584576, -0.00413844918675, -0.999983343549), (0.000900474339883, 0.999991046007, -0.00413485824556), (0.999991501605, -0.000883824120705, 0.00402685638965)150.586683957, 0.45808775337, -0.42871497937
13given(0.00246554318654, -0.00946400219584, -0.999952175736), (0.999996296686, -0.00112888101802, 0.00247633621725), (-0.00115226308152, -0.999954578113, 0.00946118384277)150.760847343, -0.199080223137, 149.294668835
14given(-0.00368839088881, 0.00573945172482, 0.999976726962), (-0.999986203267, -0.00376132685233, -0.00366683738562), (0.00374019367867, -0.99997645528, 0.00575324578283)0.142408916521, 151.158374474, 149.425532571
15given(0.00268706495943, 0.999974416483, -0.00662918249285), (-0.00577378185539, 0.00664461016822, 0.999961255549), (0.999979721357, -0.00264868539698, 0.00579148864089)0.834018533274, -0.0376688795401, -0.623340912487
16given(0.999994585769, 0.000250592985007, -0.00328110288691), (0.00328095221987, 0.000599305029209, 0.999994438078), (0.00025255797269, -0.999999789018, 0.000598479600822)0.328046364213, 0.309042312531, 150.139008594
17given(-0.999989091383, -0.00156856085122, -0.0043996286965), (-0.00156444781205, 0.999998336191, -0.00093814629299), (0.00440109291591, -0.000931253069623, -0.999989881523)151.090380891, 0.328973472249, 149.93216105
18given(0.00519659495525, -0.999970056015, 0.00573432417028), (-0.999985223906, -0.0052056553998, -0.00156624417946), (0.00159604819545, -0.00572610030277, -0.999982332047)149.400985204, 150.944036896, 150.386555388
19given(0.99999415772, 2.67757513798E-5, -0.00341815867043), (2.59440080724E-5, -0.999999970048, -0.000243374915493), (-0.0034181650846, 0.000243284812892, -0.999994128463)0.412698451194, 150.319935269, 150.056472448
20given(0.00421562621356, 0.999980573934, -0.00459132339988), (0.999984021909, -0.00419825963404, 0.00378557030581), (0.00376622119937, -0.00460720858871, -0.999982294447)0.515941651513, -0.279664672413, 150.424201671
21given(-0.9999858741, -0.00289725412347, -0.00445617772355), (0.00446098786028, -0.00165590268539, -0.999988678723), (0.0028898423262, -0.999994431937, 0.00166880390975)151.135743086, 149.991403027, 150.056415183
22given(-0.00252875934068, 0.00626903370508, 0.999977152035), (0.00296615732158, -0.999975903271, 0.00627652674577), (0.999992403615, 0.00298196137656, 0.00251010346562)0.0565976933484, 149.413840961, -0.509176853341
23given(0.00177843752252, 0.999990936607, -0.00386831539326), (0.00411940836553, -0.00387561475585, -0.999984004915), (-0.999989933767, 0.00176247390547, -0.00412626356842)0.510538984609, 150.387078532, 150.954450741

-
Components

#1: Protein ...
Dihydrolipoyllysine-residue succinyltransferase


Mass: 45987.004 Da / Num. of mol.: 24 / 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: G0SAX9, dihydrolipoyllysine-residue succinyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Native 24-mer core of Oxoglutarate Dehydrogenase Complex
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 4 MDa / 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.

-
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

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.1particle selectionBlob Picker
2EPU2.6image acquisitionImage Collection
3cryoSPARC3.1image acquisitionComplete Image Analysis Pipeline
5cryoSPARC3.1CTF correctionPatch CTF
8Coot0.9.2-premodel fitting
12cryoSPARC3.1classification2D Classification
13cryoSPARC3.13D reconstructionHomogeneous Refinement (NEW)
14Coot0.9.2-premodel refinement
15PHENIX1.18.2model refinementphenix.real_space_refine
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 276399
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1819 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial models were predicted using AlphaFold v.2.0.1, 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: 199.2 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.009142864
ELECTRON MICROSCOPYf_angle_d1.433157768
ELECTRON MICROSCOPYf_chiral_restr0.06656888
ELECTRON MICROSCOPYf_plane_restr0.01097344
ELECTRON MICROSCOPYf_dihedral_angle_d26.494916464
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CELECTRON MICROSCOPYNCS constraints0.0745406088144
ens_1d_3CELECTRON MICROSCOPYNCS constraints0.000703254381658
ens_1d_4CELECTRON MICROSCOPYNCS constraints0.000701594851739
ens_1d_5CELECTRON MICROSCOPYNCS constraints0.000706851776884
ens_1d_6CELECTRON MICROSCOPYNCS constraints0.000706333526491
ens_1d_7CELECTRON MICROSCOPYNCS constraints0.0745318362808
ens_1d_8CELECTRON MICROSCOPYNCS constraints0.0745419572555
ens_1d_9CELECTRON MICROSCOPYNCS constraints0.000712929843831
ens_1d_10CELECTRON MICROSCOPYNCS constraints0.000709742479185
ens_1d_11CELECTRON MICROSCOPYNCS constraints0.00070540535618
ens_1d_12CELECTRON MICROSCOPYNCS constraints0.000708825463666
ens_1d_13CELECTRON MICROSCOPYNCS constraints0.000705526409312
ens_1d_14CELECTRON MICROSCOPYNCS constraints0.000703380683359
ens_1d_15CELECTRON MICROSCOPYNCS constraints0.000698223036465
ens_1d_16CELECTRON MICROSCOPYNCS constraints0.0745383763961
ens_1d_17CELECTRON MICROSCOPYNCS constraints0.0745219700567
ens_1d_18CELECTRON MICROSCOPYNCS constraints0.000710763633752
ens_1d_19CELECTRON MICROSCOPYNCS constraints0.000702182139235
ens_1d_20CELECTRON MICROSCOPYNCS constraints0.000703336703291
ens_1d_21CELECTRON MICROSCOPYNCS constraints0.000708274387001
ens_1d_22CELECTRON MICROSCOPYNCS constraints0.000706943344046
ens_1d_23CELECTRON MICROSCOPYNCS constraints0.000707259659069
ens_1d_24CELECTRON MICROSCOPYNCS constraints0.000705419959836

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more