[English] 日本語
Yorodumi
- PDB-6h05: Cryo-electron microscopic structure of the dihydrolipoamide succi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h05
TitleCryo-electron microscopic structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate (2-oxoglutarate) dehydrogenase complex [residues 218-453]
ComponentsDihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
KeywordsTRANSFERASE / alpha-ketoglutarate dehydrogenase complex / 2-oxoglutarate dehydrogenase complex / dihydrolipoamide succinyltransferase / E2 component
Function / homology
Function and homology information


OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / L-lysine catabolic process to acetyl-CoA via saccharopine / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / Protein lipoylation / oxoglutarate dehydrogenase complex ...OGDH complex synthesizes succinyl-CoA from 2-OG / OADH complex synthesizes glutaryl-CoA from 2-OA / oxoadipate dehydrogenase complex / Glycine degradation / L-lysine catabolic process to acetyl-CoA via saccharopine / succinyl-CoA metabolic process / dihydrolipoyllysine-residue succinyltransferase / dihydrolipoyllysine-residue succinyltransferase activity / Protein lipoylation / oxoglutarate dehydrogenase complex / 2-oxoglutarate metabolic process / acyltransferase activity / tricarboxylic acid cycle / generation of precursor metabolites and energy / mitochondrial matrix / mitochondrion / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Dihydrolipoamide succinyltransferase / : / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 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. ...Dihydrolipoamide succinyltransferase / : / Chloramphenicol acetyltransferase-like domain / Chloramphenicol Acetyltransferase / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsNagy, B. / Zambo, Z. / Hubert, A. / Polak, M. / Nemeria, N.S. / Novacek, J. / Jordan, F. / Adam-Vizi, V. / Ambrus, A.
Funding support Hungary, United States, 6items
OrganizationGrant numberCountry
Hungarian Academy of SciencesMTA grant 02001 (to Vera Adam-Vizi) Hungary
Hungarian Academy of SciencesOTKA grant 112230 (to Vera Adam-Vizi) Hungary
Hungarian Academy of SciencesNAP grant KTIA_13_NAP-A-III/6 (to Vera Adam-Vizi) Hungary
Hungarian Academy of SciencesNAP 2 grant 2017-1.2.1-NKP- 2017-00002 (to Vera Adam-Vizi) Hungary
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-GM-050380 (to Frank Jordan) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH R15-GM116077 (to Frank Jordan) United States
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: ...Title: Structure of the dihydrolipoamide succinyltransferase (E2) component of the human alpha-ketoglutarate dehydrogenase complex (hKGDHc) revealed by cryo-EM and cross-linking mass spectrometry: Implications for the overall hKGDHc structure.
Authors: Balint Nagy / Martin Polak / Oliver Ozohanics / Zsofia Zambo / Eszter Szabo / Agnes Hubert / Frank Jordan / Jiří Novaček / Vera Adam-Vizi / Attila Ambrus /
Abstract: BACKGROUND: The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as ...BACKGROUND: The human mitochondrial alpha-ketoglutarate dehydrogenase complex (hKGDHc) converts KG to succinyl-CoA and NADH. Malfunction of and reactive oxygen species generation by the hKGDHc as well as its E1-E2 subcomplex are implicated in neurodegenerative disorders, ischemia-reperfusion injury, E3-deficiency and cancers.
METHODS: We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl ...METHODS: We performed cryo-EM, cross-linking mass spectrometry (CL-MS) and molecular modeling analyses to determine the structure of the E2 component of the hKGDHc (hE2k); hE2k transfers a succinyl group to CoA and forms the structural core of hKGDHc. We also assessed the overall structure of the hKGDHc by negative-stain EM and modeling.
RESULTS: We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few ...RESULTS: We report the 2.9 Å resolution cryo-EM structure of the hE2k component. The cryo-EM map comprises density for hE2k residues 151-386 - the entire (inner) core catalytic domain plus a few additional residues -, while residues 1-150 are not observed due to the inherent flexibility of the N-terminal region. The structure of the latter segment was also determined by CL-MS and homology modeling. Negative-stain EM on in vitro assembled hKGDHc and previous data were used to build a putative overall structural model of the hKGDHc.
CONCLUSIONS: The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in ...CONCLUSIONS: The E2 core of the hKGDHc is composed of 24 hE2k chains organized in octahedral (8 × 3 type) assembly. Each lipoyl domain is oriented towards the core domain of an adjacent chain in the hE2k homotrimer. hE1k and hE3 are most likely tethered at the edges and faces, respectively, of the cubic hE2k assembly.
GENERAL SIGNIFICANCE: The revealed structural information will support the future pharmacologically targeting of the hKGDHc.
History
DepositionJul 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 2, 2024Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: em_admin / em_imaging ...em_admin / em_imaging / em_software / entity_src_gen / pdbx_contact_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _em_admin.last_update / _em_imaging.nominal_defocus_max ..._em_admin.last_update / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity_src_gen.gene_src_common_name / _pdbx_contact_author.address_2 / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]

-
Structure visualization

Movie
  • Biological unit as author_defined_assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-0108
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0108
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial


Theoretical massNumber of molelcules
Total (without water)45,5431
Polymers45,5431
Non-polymers00
Water00
1
A: Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial
x 24


Theoretical massNumber of molelcules
Total (without water)1,093,03224
Polymers1,093,03224
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation23
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13670 Å2
MethodPISA

-
Components

#1: Protein Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial / 2-oxoglutarate dehydrogenase complex component E2 / OGDC-E2 / Dihydrolipoamide succinyltransferase ...2-oxoglutarate dehydrogenase complex component E2 / OGDC-E2 / Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex / E2K


Mass: 45543.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal Twin-Strep (affinity) tag with proteolytic cleavage site and linkers: MASWSHPQFEKGGGSGGGSGGSAWSHPQFEKLEVLFQGPG Density was found for 236 residues [218-453]
Source: (gene. exp.) Homo sapiens (human) / Gene: DLST, DLTS / Plasmid: pET52b+ / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36957, dihydrolipoyllysine-residue succinyltransferase

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Affinity purified human dihydrolipoamide succinyltransferase
Type: COMPLEX
Details: Protein in 100 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, pH 8.0.
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET52b+
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMTris-HClNH2C(CH2OH)3HCl1
2150 mMSodium clorideNaCl1
31 mMEthylenediaminetetraacetic acidC10H16N2O81
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was highly purified and monodisperse.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

-
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingAverage exposure time: 1 sec. / Electron dose: 48.8 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1

-
Processing

EM software
IDNameCategory
2cryoSPARCparticle selection
8UCSF Chimeramodel fitting
10PHENIXmodel refinement
13cryoSPARCclassification
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1533026
Details: Manual picking for the templates was performed by the EMAN2 E2boxer program. Automated selection was then applied by CryoSPARC.
SymmetryPoint symmetry: O (octahedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 740101 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Details: COOT was used for structure manipulations, while MOLPROBITY was applied for validation.

+
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