7JZ2 | pdb_00007jz2

Succinate: quinone oxidoreductase SQR from E.coli K12


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7JZ2

This is version 1.1 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: https://doi.org/10.1038/s41592-020-01021-2
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 365.42 kDa 
  • Atom Count: 22,866 
  • Modeled Residue Count: 2,871 
  • Deposited Residue Count: 3,210 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoprotein subunit
A, E, I
588Escherichia coli K-12Mutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P0AC41 (Escherichia coli (strain K12))
Explore P0AC41 
Go to UniProtKB:  P0AC41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AC41
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase iron-sulfur subunit
B, F, J
238Escherichia coli K-12Mutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for P07014 (Escherichia coli (strain K12))
Explore P07014 
Go to UniProtKB:  P07014
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07014
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase cytochrome b556 subunit
C, G, K
129Escherichia coli K-12Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P69054 (Escherichia coli (strain K12))
Explore P69054 
Go to UniProtKB:  P69054
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69054
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase hydrophobic membrane anchor subunit
D, H, L
115Escherichia coli K-12Mutation(s): 0 

Small Molecules

Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
CA [auth I],
M [auth A],
U [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
3PE

Query on 3PE



Download:Ideal Coordinates CCD File
AA [auth G],
IA [auth K],
R [auth C]
1,2-Distearoyl-sn-glycerophosphoethanolamine
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
HA [auth K],
S [auth D],
Z [auth G]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4

Query on SF4



Download:Ideal Coordinates CCD File
FA [auth J],
P [auth B],
X [auth F]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UQ2

Query on UQ2



Download:Ideal Coordinates CCD File
BA [auth H],
JA [auth L],
T [auth D]
UBIQUINONE-2
C19 H26 O4
SQQWBSBBCSFQGC-JLHYYAGUSA-N
F3S
(Subject of Investigation/LOI)

Query on F3S



Download:Ideal Coordinates CCD File
GA [auth J],
Q [auth B],
Y [auth F]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES

Query on FES



Download:Ideal Coordinates CCD File
EA [auth J],
O [auth B],
W [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
DA [auth I],
N [auth A],
V [auth E]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


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
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Structure summary