[English] 日本語
Yorodumi
- PDB-7a1d: Cryo-EM map of the large glutamate dehydrogenase composed of 180 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a1d
TitleCryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation)
ComponentsNAD-specific glutamate dehydrogenase
KeywordsOXIDOREDUCTASE / large glutamate dehydrogenase Mycobacterium metabolism
Function / homology
Function and homology information


glutamate dehydrogenase / L-glutamate dehydrogenase (NAD+) activity / L-glutamate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity
Similarity search - Function
NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain ...NAD-glutamate dehydrogenase, bacteria / Bacterial NAD-glutamate dehydrogenase, N-terminal / NAD-glutamate dehydrogenase / : / : / : / : / : / : / Bacterial NAD-glutamate dehydrogenase, catalytic domain / Glutamate dehydrogenase, helical motif 1 / Glutamate dehydrogenase, C-terminal / Glutamate dehydrogenase, ACT1 domain / Glutamate dehydrogenase, ACT2 domain / Glutamate dehydrogenase, ACT3 domain / Glutamate dehydrogenase, helical motif 3 / Glutamate dehydrogenase, helical motif 2 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NAD-specific glutamate dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsLazaro, M. / Melero, R. / Huet, C. / Lopez-Alonso, J.P. / Delgado, S. / Dodu, A. / Bruch, E.M. / Abriata, L.A. / Alzari, P.M. / Valle, M. / Lisa, M.N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPGC2018-098996-B-100 Spain
CitationJournal: Commun Biol / Year: 2021
Title: 3D architecture and structural flexibility revealed in the subfamily of large glutamate dehydrogenases by a mycobacterial enzyme.
Authors: Melisa Lázaro / Roberto Melero / Charlotte Huet / Jorge P López-Alonso / Sandra Delgado / Alexandra Dodu / Eduardo M Bruch / Luciano A Abriata / Pedro M Alzari / Mikel Valle / María-Natalia Lisa /
Abstract: Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs) contain long N- ...Glutamate dehydrogenases (GDHs) are widespread metabolic enzymes that play key roles in nitrogen homeostasis. Large glutamate dehydrogenases composed of 180 kDa subunits (L-GDHs) contain long N- and C-terminal segments flanking the catalytic core. Despite the relevance of L-GDHs in bacterial physiology, the lack of structural data for these enzymes has limited the progress of functional studies. Here we show that the mycobacterial L-GDH (mL-GDH) adopts a quaternary structure that is radically different from that of related low molecular weight enzymes. Intersubunit contacts in mL-GDH involve a C-terminal domain that we propose as a new fold and a flexible N-terminal segment comprising ACT-like and PAS-type domains that could act as metabolic sensors for allosteric regulation. These findings uncover unique aspects of the structure-function relationship in the subfamily of L-GDHs.
History
DepositionAug 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Mask / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 9, 2021Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / em_admin / pdbx_contact_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update
Revision 1.2Jul 10, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 2.0May 14, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / em_admin ...atom_site / em_admin / em_imaging / em_software / entity_src_gen / pdbx_entry_details / pdbx_poly_seq_scheme / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_ls_restr / software / struct_conf / struct_mon_prot_cis / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _em_admin.last_update / _em_imaging.microscope_model ..._em_admin.last_update / _em_imaging.microscope_model / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_oper_list.symmetry_operation / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_stereochemistry_target_values
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.0May 14, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Group: Data collection / Data processing ...Data collection / Data processing / Experimental summary / Source and taxonomy
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: em_admin / em_imaging ...em_admin / em_imaging / em_software / entity_src_gen
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _em_admin.last_update / _em_imaging.microscope_model ..._em_admin.last_update / _em_imaging.microscope_model / _em_imaging.nominal_defocus_max / _em_imaging.nominal_defocus_min / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 2.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Data updated
Revision 2.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Data updated
Revision 2.0May 14, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Data updated
Revision 2.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Data updated

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11606
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD-specific glutamate dehydrogenase
B: NAD-specific glutamate dehydrogenase
C: NAD-specific glutamate dehydrogenase
D: NAD-specific glutamate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)705,3674
Polymers705,3674
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-29 kcal/mol
Surface area191610 Å2
MethodPISA

-
Components

#1: Protein
NAD-specific glutamate dehydrogenase / NAD-GDH / NAD(+)-dependent glutamate dehydrogenase


Mass: 176341.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: gdh, MSMEG_4699, MSMEI_4582 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0R1C2, glutamate dehydrogenase
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.705 MDa / Experimental value: NO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21(DE3)
Buffer solutionpH: 6
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationCryogen name: ETHANE

-
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 / Calibrated magnification: 47170 X / Nominal defocus max: 3260 nm / Nominal defocus min: 670 nm / Calibrated defocus min: 670 nm / Calibrated defocus max: 3260 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20 / Used frames/image: 1-20

-
Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 63715 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
Details: Model fitting into the cryo-EM map was performed using the programs UCSF Chimera (Pettersen et al., 2004), Namdinator (Kidmose et al., 2019), phenix.real_space_refine (Afonine et al., 2018) ...Details: Model fitting into the cryo-EM map was performed using the programs UCSF Chimera (Pettersen et al., 2004), Namdinator (Kidmose et al., 2019), phenix.real_space_refine (Afonine et al., 2018) and Coot (Emsley, Lohkamp, Scott, & Cowtan, 2010). Residues 500-1588 from the crystal structure of Se-Met mL-GDH180 (PDB code 7JSR) were fitted into the cryo-EM map. Se-methionine residues were replaced by methionine residues using Coot (Emsley et al., 2010) and the model was finally refined employing phenix.real_space_refine (Afonine et al., 2018) with NCS and secondary structure restraints.
RefinementCross valid method: NONE

+
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