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- EMDB-52426: CryoEM map of the large glutamate dehydrogenase composed of 180 k... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52426
TitleCryoEM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis obtained in the presence of NAD+ and L-glutamate. cofactor/ligand-monomer in Closed1 tetramer.
Map data
Sample
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
    • Protein or peptide: NAD-specific glutamate dehydrogenase|Mycolicibacterium smegmatis
KeywordsLarge glutamate dehydrogenase / Tetramer / OXIDOREDUCTASE
Biological speciesMycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsLazaro M / Chamorro N / Lopez-Alonso JP / Charro D / Rasia RM / Jimenez-Oses G / Valle M / Lisa MN
Funding support Spain, 1 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2021-124074NB-I00 Spain
CitationJournal: To Be Published
Title: Tertiary and quaternary structure remodeling by occupancy of the substrate binding pocket in a large glutamate dehydrogenase
Authors: Lazaro M / Chamorro N / Lopez-Alonso JP / Charro D / Rasia RM / Jimenez-Oses G / Valle M / Lisa MN
History
DepositionDec 24, 2024-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52426.png

Downloads & links

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Map

FileDownload / File: emd_52426.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 680 pix.
= 439.416 Å		0.65 Å/pix.
x 680 pix.
= 439.416 Å		0.65 Å/pix.
x 680 pix.
= 439.416 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6462 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.45
Minimum - Maximum-0.4365407 - 18.393303
Average (Standard dev.)0.00525127 (±0.19993134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions680680680
Spacing680680680
CellA=B=C: 439.41602 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52426_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52426_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52426_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

EntireName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
Components
  • Complex: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
    • Protein or peptide: NAD-specific glutamate dehydrogenase|Mycolicibacterium smegmatis

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Supramolecule #1: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis...

SupramoleculeName: NAD-specific glutamate dehydrogenase from Mycobacterium smegmatis, MsLGDH180, in the presence of NAD+ and L-glutamate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: MsLGDH180 cofactor/ligand-monomer in Closed1 tetramer
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria) / Strain: strain ATCC 700084 / mc(2)155
Molecular weightTheoretical: 174 KDa

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Macromolecule #1: NAD-specific glutamate dehydrogenase

MacromoleculeName: NAD-specific glutamate dehydrogenase|Mycolicibacterium smegmatis
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: MHHHHHHENL YFQGAASMIR RLSVAFLSTY RGPQADAPGV TSTGPLAVAA HDDLVSDDLV AAHYRLASMR APGETKAAVY PGDAGSGAAL QIVTDQAPML VDSVTVLLHR HGIAYTAIMN PVFRVRRGLD GELLDVRPAA EAAPGDGADE CWILVPITAA ADGEALTEAT ...String:
MHHHHHHENL 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 I YQFKISPH PSIPHAPDAE AQRDTAQRFA DAVTAIWHGR VEIDRFNELV MRAGLTWQQV VVLRAYAKYL RQAGFPYSQS HIESVLNENP HTTRSLIDLF EALFDPSQET DGRRDAQGAA AAVAADIDAL VSLDTDRVLR AFANLIEATL RTNYFVARPD SARARNVLAF KLNPLVIKEL PLPRPKFEIF VYSPRVEGVH LRFGFVARGG LRWSDRREDF RTEILGLVKA QAVKNAVIVP VGAKGGFVVK RPPTLTGDAA ADREATRAEG VECYRLFISG LLDVTDNVDK ATGAVVTPPE VVRRDGEDAY LVVAADKGTA TFSDIANEVA KSYGFWLGDA FASGGSIGYD HKAMGITAKG AWESVKRHFR EMGVDTQTQD FTVVGIGDMS GDVFGNGMLL SKHIRLVAAF DHRDIFLDPN PDAGRSWDER KRLFDLPRSS WADYDKSLIS EGGGVYSRQQ KSIPISPQVR TALGLDADVE ELTPPALIKA ILKAPVDLLW NGGIGTYIKA ETEADADVGD RANDQIRVCG NQVRAKVIGE GGNLGVTALG RIEFDLAGGR INTDALDNSA GVDCSDHEVN IKILIDSAVT AGKVTPEERT ELLLSMTDEV GELVLADNRD QNDLMGTSRA NAASLLSVHA RMIKDLVDNR GLNRELEALP SEKEIRRRAD AGIGLTSPEL ATLMAHVKLA LKDDVLASDL PDQEVFASRL PYYFPTRLRE ELHGEIRSHQ LRREIITTML VNDLVDTAGI SYAYRITEDV GVGPVDAVRS YVAINAIFGI GDVWRRIRAA GDAGVPTSVT DRMTLDLRRL VDRAGRWLLN YRPQPLAVGA EINRFGAKVA ALTPRMSEWL RGDDKAIVSK EAGDFASHGV PEDLAYHIAT GLYQYSLLDV IDIADIVDRE PDEVADTYFA LMDHLGADAL LTAVSRLSRD DRWHSLARLA IRDDIYGSLR ALCFDVLAVG EPDENGEEKI AEWETTNSSR VTRARRTLTE IYKDGEQDLA TLSVAARQIR SMTRTSGTGT TG

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.125 mg/mL
BufferpH: 6.5
Component:
ConcentrationName
20.0 mMMES
300.0 mMNaCl
42.0 mMGlutamate
4.0 mMNAD
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

11606


Details: Cryo-EM map of the large glutamate dehydrogenase composed of 180 kDa subunits from Mycobacterium smegmatis (open conformation) at 4.19 A resolution
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 46380
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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