[English] 日本語
Yorodumi
- EMDB-11613: Cryo-EM map of the large glutamate dehydrogenase composed of 180 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11613
TitleCryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (monomer)
Map data
Sample
  • Complex: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (monomer)
    • Protein or peptide: Large Glutamate Dehydrogenase
Function / homologyNAD-glutamate dehydrogenase, bacteria / NAD-glutamate dehydrogenase / Bacterial NAD-glutamate dehydrogenase, catalytic domain / glutamate dehydrogenase / glutamate catabolic process to 2-oxoglutarate / glutamate dehydrogenase (NAD+) activity / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding domain superfamily / NAD-specific glutamate dehydrogenase
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsLazaro M / Melero R / Huet C / Lopez-Alonso JP / Delgado S / Dodu A / Bruch EM / Abriata LA / Alzari PM / Valle M / Lisa MN
Funding support Spain, 1 items
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 14, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0257
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0257
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11613.png

Downloads & links

-
Map

FileDownload / File: emd_11613.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0257 / Movie #1: 0.0257
Minimum - Maximum-0.04459886 - 0.079281114
Average (Standard dev.)3.721138e-05 (±0.0010836804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 402.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z402.800402.800402.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0450.0790.000

-
Supplemental data

-
Mask #1

Fileemd_11613_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11613_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11613_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM map of the large glutamate dehydrogenase composed of 180 ...

EntireName: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (monomer)
Components
  • Complex: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (monomer)
    • Protein or peptide: Large Glutamate Dehydrogenase

-
Supramolecule #1: Cryo-EM map of the large glutamate dehydrogenase composed of 180 ...

SupramoleculeName: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (monomer)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3)
Molecular weightTheoretical: 705 KDa

-
Macromolecule #1: Large Glutamate Dehydrogenase

MacromoleculeName: Large Glutamate Dehydrogenase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HMHHHHHENL YFQGAASMIR RLSVAFLSTY RGPQADAPGV TSTGPLAVAA HDDLVSDDLV AAHYRLASMR APGETKAAVY PGDAGSGAAL QIVTDQAPML VDSVTVLLHR HGIAYTAIMN PVFRVRRGLD GELLDVRPAA EAAPGDGADE CWILVPITAA ADGEALTEAT ...String:
HMHHHHHENL YFQGAASMIR RLSVAFLSTY RGPQADAPGV TSTGPLAVAA HDDLVSDDLV AAHYRLASMR APGETKAAVY PGDAGSGAAL QIVTDQAPML VDSVTVLLHR HGIAYTAIMN PVFRVRRGLD GELLDVRPAA EAAPGDGADE CWILVPITAA ADGEALTEAT RLVPGILAEA RQIGLDSGAM IAALHGLAND LATDLEGHFP NAERKEVAAL LRWLADGHFV LLGYQQCVVG DGNAEVDPAS RLGVLRLRND VLPPLTDSDD LLVLAQATMP SYLRYGAYPY IVVVRESPGA SRVIEHRFVG LFTVAAMNAN ALEIPLISRR VEEALAMAHR DPSHPGQLLR DIIQTIPRPE LFALSSKQLL EMALAVVDLG SRRRTLLFLR ADHLAHFVSC LVYLPRDRYT TAVRLEMQDI LVRELGGAGI DYSARVSESP WAVVHFTVRL PEGTAADSVD TSLENESRIQ DLLTEATRNW GDRMISAAAA ASISPAALEH YAHAFPEDYK QAFAPQDAIA DISLIEALQD DSVKLVLADT AEDRVWKLTW YLGGHSASLS ELLPMLQSMG VVVLEERPFT LRRTDGLPVW IYQFKISPHP SIPHAPDAEA QRDTAQRFAD AVTAIWHGRV EIDRFNELVM RAGLTWQQVV VLRAYAKYLR QAGFPYSQSH IESVLNENPH TTRSLIDLFE ALFDPSQETD GRRDAQGAAA AVAADIDALV SLDTDRVLRA FANLIEATLR TNYFVARPDS ARARNVLAFK LNPLVIKELP LPRPKFEIFV YSPRVEGVHL RFGFVARGGL RWSDRREDFR TEILGLVKAQ AVKNAVIVPV GAKGGFVVKR PPTLTGDAAA DREATRAEGV ECYRLFISGL LDVTDNVDKA TGAVVTPPEV VRRDGEDAYL VVAADKGTAT FSDIANEVAK SYGFWLGDAF ASGGSIGYDH KAMGITAKGA WESVKRHFRE MGVDTQTQDF TVVGIGDMSG DVFGNGMLLS KHIRLVAAFD HRDIFLDPNP DAGRSWDERK RLFDLPRSSW ADYDKSLISE GGGVYSRQQK SIPISPQVRT ALGLDADVEE LTPPALIKAI LKAPVDLLWN GGIGTYIKAE TEADADVGDR ANDQIRVCGN QVRAKVIGEG GNLGVTALGR IEFDLAGGRI NTDALDNSAG VDCSDHEVNI KILIDSAVTA GKVTPEERTE LLLSMTDEVG ELVLADNRDQ NDLMGTSRAN AASLLSVHAR MIKDLVDNRG LNRELEALPS EKEIRRRADA GIGLTSPELA TLMAHVKLAL KDDVLASDLP DQEVFASRLP YYFPTRLREE LHGEIRSHQL RREIITTMLV NDLVDTAGIS YAYRITEDVG VGPVDAVRSY VAINAIFGIG DVWRRIRAAG DAGVPTSVTD RMTLDLRRLV DRAGRWLLNY RPQPLAVGAE INRFGAKVAA LTPRMSEWLR GDDKAIVSKE AGDFASHGVP EDLAYHIATG LYQYSLLDVI DIADIVDREP DEVADTYFAL MDHLGADALL TAVSRLSRDD RWHSLARLAI RDDIYGSLRA LCFDVLAVGE PDENGEEKIA EWETTNSSRV TRARRTLTEI YKDGEQDLAT LSVAARQIRS MTRTSGTGTT G

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.2600000000000002 µm / Calibrated defocus min: 0.67 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: MotionCorr2 (ver. 2_1.4.0_Cuda110)
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN
Final 3D classificationNumber classes: 1 / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 254860

-
Atomic model buiding 1

RefinementProtocol: OTHER

+
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