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- EMDB-22531: The Cryo-EM structure of the Glutamate decarboxylase from Escheri... -

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Basic information

Entry
Database: EMDB / ID: EMD-22531
TitleThe Cryo-EM structure of the Glutamate decarboxylase from Escherichia coli
Map data
Sample
  • Complex: Glutamate decarboxylase
    • Protein or peptide: Glutamate decarboxylase
KeywordsGlutamate decarboxylase beta / OXIDOREDUCTASE / LYASE
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / intracellular pH elevation / L-glutamate catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Glutamate decarboxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSu C-C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Methods / Year: 2021
Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.
Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu /
Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics.
History
DepositionSep 2, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jzh
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22531.png

Downloads & links

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Map

FileDownload / File: emd_22531.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 87 pix.
= 93.96 Å		1.08 Å/pix.
x 139 pix.
= 150.12 Å		1.08 Å/pix.
x 139 pix.
= 150.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.4763006 - 2.1033604
Average (Standard dev.)0.000000000002157 (±0.1655687)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin100106132
Dimensions13913987
Spacing13913987
CellA: 150.12001 Å / B: 150.12001 Å / C: 93.96001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z13913987
origin x/y/z0.0000.0000.000
length x/y/z150.120150.12093.960
α/β/γ90.00090.00090.000
start NX/NY/NZ107101134
NX/NY/NZ14113986
MAP C/R/S123
start NC/NR/NS106100132
NC/NR/NS13913987
D min/max/mean-1.4762.1030.000

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Supplemental data

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Sample components

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Entire : Glutamate decarboxylase

EntireName: Glutamate decarboxylase
Components
  • Complex: Glutamate decarboxylase
    • Protein or peptide: Glutamate decarboxylase

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Supramolecule #1: Glutamate decarboxylase

SupramoleculeName: Glutamate decarboxylase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Glutamate decarboxylase

MacromoleculeName: Glutamate decarboxylase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: glutamate decarboxylase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 52.727957 KDa
SequenceString: MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEE YPQSAAIDLR CVNMVADLWH APAPKNGQAV GTNTIGSSEA CMLGGMAMKW RWRKRMEAAG KPTDKPNLVC G PVQICWHK ...String:
MDKKQVTDLR SELLDSRFGA KSISTIAESK RFPLHEMRDD VAFQIINDEL YLDGNARQNL ATFCQTWDDE NVHKLMDLSI NKNWIDKEE YPQSAAIDLR CVNMVADLWH APAPKNGQAV GTNTIGSSEA CMLGGMAMKW RWRKRMEAAG KPTDKPNLVC G PVQICWHK FARYWDVELR EIPMRPGQLF MDPKRMIEAC DENTIGVVPT FGVTYTGNYE FPQPLHDALD KFQADTGIDI DM HIDAASG GFLAPFVAPD IVWDFRLPRV KSISASGHKF GLAPLGCGWV IWRDEEALPQ ELVFNVDYLG GQIGTFAINF SRP AGQVIA QYYEFLRLGR EGYTKVQNAS YQVAAYLADE IAKLGPYEFI CTGRPDEGIP AVCFKLKDGE DPGYTLYDLS ERLR LRGWQ VPAFTLGGEA TDIVVMRIMC RRGFEMDFAE LLLEDYKASL KYLSDHPKLQ GIAQQNSFKH T

UniProtKB: Glutamate decarboxylase

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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

Concentration0.5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 1.4) / Number images used: 32005
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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