6WU6 | pdb_00006wu6

succinate-coenzyme Q reductase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6WU6

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: 362.22 kDa 
  • Atom Count: 21,969 
  • Modeled Residue Count: 2,781 
  • Deposited Residue Count: 3,210 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase iron-sulfur subunitA [auth B],
D [auth F],
G [auth J]
238Escherichia coliMutation(s): 0 
Gene Names: sdhB
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: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenaseB [auth C],
E [auth G],
H [auth K]
129Escherichia coliMutation(s): 0 
Gene Names: sdhCcybAdhsC
EC: 1.3.5.1
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase hydrophobic membrane anchor subunitC [auth D],
F [auth H],
I [auth L]
115Escherichia coli 908573Mutation(s): 0 
Gene Names: HMPREF1611_01928
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Succinate dehydrogenase flavoprotein subunitJ [auth A],
K [auth E],
L [auth I]
588Escherichia coli SE11Mutation(s): 0 
Gene Names: ECSE_0783
EC: 1.3.5.1

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD

Query on FAD



Download:Ideal Coordinates CCD File
AA [auth E],
CA [auth I],
Y [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
P [auth C],
T [auth G],
X [auth K]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4

Query on SF4



Download:Ideal Coordinates CCD File
N [auth B],
R [auth F],
V [auth J]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
(Subject of Investigation/LOI)

Query on F3S



Download:Ideal Coordinates CCD File
O [auth B],
S [auth F],
W [auth J]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
FES

Query on FES



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

Query on NA



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 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: 2021-02-03
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references