7JZH

The Cryo-EM structure of the Glutamate decarboxylase from Escherichia coli

  • Classification: LYASE
  • Organism(s): Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-09-02 Released: 2021-01-20 
  • Deposition Author(s): Su, C.-C.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins.

Su, C.C.Lyu, M.Morgan, C.E.Bolla, J.R.Robinson, C.V.Yu, E.W.

(2021) Nat Methods 18: 69-75

  • DOI: 10.1038/s41592-020-01021-2
  • Primary Citation of Related Structures:  
    6WTI, 6WTZ, 6WU0, 6WU6, 7JZ2, 7JZ3, 7JZ6, 7JZH

  • PubMed 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 samples hampers the progress of their structural determination ...

    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.


    Organizational Affiliation

    Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA. edward.w.yu@case.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate decarboxylase
A, B, C, D, E, F
A, B, C, D, E, F
466Escherichia coliMutation(s): 0 
Gene Names: 
gadBgadAgadA_1gadA_2gadB_1gadB_2gadB_3ACN68_15540AM464_25360APX88_23675AT335_003128B6R31_000508B6R48_000508B6R87_000508BANRA_02466BF481_002380BG944_004013BJI68_04220BJJ90_12745BK292_08440BMT50_24220BON86_15850BvCmsF30A_01595BvCmsHHP019_03224BvCmsHHP056_00275BvCmsKSNP073_02715BVL39_20730C2U48_00750C3F40_04095C9E67_14475CA593_20435CDL37_12790CO706_03805CV83915_04915DAH17_18555DAH18_18795DAH20_08605DAH21_21495DAH23_14430DAH24_13935DAH25_19580DAH26_18580DAH27_19440DAH28_18680DAH29_01840DAH32_16110DAH33_21325DAH36_21800DAH37_11520DAH42_08070DAH43_18235DAH45_17795DAH46_10185DAH47_20425DAH48_19690DAH49_10850DKP82_05005E2113_17230E2114_19630E2115_18900E2120_19385E2121_11685E2123_17110E2124_18695E2128_24245E2130_19255E2136_18420E5P30_00190E5P34_15555E5P47_20065E5P52_02745EAN77_18960EC1094V2_2298EC95NR1_00130EKI52_00300EL79_2281EL80_2290ELT16_01655ELT25_00130ELT28_01760ELT30_21185ELT51_14480ELT58_10080ELT72_02965ELU91_19590ELU94_13290ELV03_04665ELV10_14970ELV12_24870ELV13_25775ELV22_06585ELV40_09380ELX48_00220ExPECSC038_01442F0L67_13050F3N40_21555F9S83_18415FFF58_00575FGG80_15195FOI11_005655FOI11_12625FQF29_18090G3565_17260G5603_21985G9448_03330GIB53_06175GQW68_22320HHH44_002894HIE29_001126HJU54_000595HLV18_05115HMJ82_23025HNC66_05265HV109_12450HVW04_03365HVW19_02455HVW43_03690HVX16_12750HX136_12370I6H00_06570I6H01_00240I6H02_01005IT029_000387JFD_02620JNP96_13165NCTC10082_00090NCTC10090_01069NCTC10764_02206NCTC10865_03132NCTC10974_02926NCTC11112_05623NCTC11181_04997NCTC12950_02812NCTC13127_03426NCTC13148_00808NCTC13216_04132NCTC4450_07807NCTC8008_02035NCTC8009_04286NCTC8179_03545NCTC8333_02996NCTC8450_02959NCTC8500_02852NCTC8960_05369NCTC8985_01238NCTC9037_02824NCTC9073_01178NCTC9111_02603NCTC9117_03305NCTC9775_00696NCTC9962_05357SAMEA3472044_02196SAMEA3472147_00647SAMEA3751407_04007SAMEA3753106_01821

EC: 4.1.1.15
UniProt
Find proteins for A5YKJ2 (Escherichia coli)
Explore A5YKJ2 
Go to UniProtKB:  A5YKJ2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5YKJ2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2021-01-20 
  • Deposition Author(s): Su, C.-C.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release