[English] 日本語
Yorodumi
- EMDB-22531: The Cryo-EM structure of the Glutamate decarboxylase from Escheri... -

+
Open data


ID or keywords:

Loading...

-
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 / glutamate metabolic process / pyridoxal phosphate binding
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-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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

emd_22531.png

Downloads & links

-
Map

FileDownload / File: emd_22531.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
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

-
Supplemental data

-
Sample components

-
Entire : Glutamate decarboxylase

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

-
Supramolecule #1: Glutamate decarboxylase

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
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

+
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