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- PDB-6wu6: succinate-coenzyme Q reductase -

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Basic information

Entry
Database: PDB / ID: 6wu6
Titlesuccinate-coenzyme Q reductase
Components
  • (Succinate dehydrogenase ...) x 3
  • Succinate dehydrogenase
KeywordsELECTRON TRANSPORT / Complex / succinate-coenzyme Q reductase
Function / homology
Function and homology information


succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding ...succinate dehydrogenase complex / succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / : / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / ubiquinone binding / 3 iron, 4 sulfur cluster binding / iron-sulfur cluster binding / electron transport chain / aerobic respiration / tricarboxylic acid cycle / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Succinate dehydrogenase, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit ...Succinate dehydrogenase, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b556 subunit / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, flavoprotein subunit / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / Succinate dehydrogenase/Fumarate reductase transmembrane subunit / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Fumarate reductase/succinate dehydrogenase, FAD-binding site / Fumarate reductase / succinate dehydrogenase FAD-binding site. / 4Fe-4S dicluster domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Succinate dehydogenase/fumarate reductase N-terminal / 2Fe-2S iron-sulfur cluster binding domain / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / Fumarate reductase flavoprotein C-term / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / Alpha-helical ferredoxin / FAD binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / IRON/SULFUR CLUSTER / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase cytochrome b556 subunit / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase cytochrome b556 subunit / Succinate dehydrogenase hydrophobic membrane anchor subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Escherichia coli 908573 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLyu, M. / Su, C.-C. / Morgan, C.E. / Yu, E.W.
Funding support United States, 1items
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
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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  • EMDB-21906
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Assembly

Deposited unit
B: Succinate dehydrogenase iron-sulfur subunit
C: Succinate dehydrogenase
D: Succinate dehydrogenase hydrophobic membrane anchor subunit
F: Succinate dehydrogenase iron-sulfur subunit
G: Succinate dehydrogenase
H: Succinate dehydrogenase hydrophobic membrane anchor subunit
J: Succinate dehydrogenase iron-sulfur subunit
K: Succinate dehydrogenase
L: Succinate dehydrogenase hydrophobic membrane anchor subunit
A: Succinate dehydrogenase flavoprotein subunit
E: Succinate dehydrogenase flavoprotein subunit
I: Succinate dehydrogenase flavoprotein subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,21830
Polymers355,47412
Non-polymers6,74518
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Succinate dehydrogenase ... , 3 types, 9 molecules BFJDHLAEI

#1: Protein Succinate dehydrogenase iron-sulfur subunit


Mass: 26800.912 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sdhB / Production host: Escherichia coli (E. coli)
References: UniProt: A0A037Y3E8, UniProt: P07014*PLUS, succinate dehydrogenase
#3: Protein Succinate dehydrogenase hydrophobic membrane anchor subunit


Mass: 12874.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli 908573 (bacteria) / Gene: HMPREF1611_01928 / Production host: Escherichia coli (E. coli) / References: UniProt: V0YWY6
#4: Protein Succinate dehydrogenase flavoprotein subunit


Mass: 64502.766 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain SE11) (bacteria)
Strain: SE11 / Gene: ECSE_0783 / Production host: Escherichia coli (E. coli) / References: UniProt: B6I7Z5, succinate dehydrogenase

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Protein , 1 types, 3 molecules CGK

#2: Protein Succinate dehydrogenase / / Succinate dehydrogenase cytochrome b556 large membrane subunit / Succinate dehydrogenase cytochrome ...Succinate dehydrogenase cytochrome b556 large membrane subunit / Succinate dehydrogenase cytochrome b556 subunit / Succinate dehydrogenase / cytochrome b556 / cytochrome b556 subunit


Mass: 14313.100 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sdhC, cybA, dhsC / Production host: Escherichia coli (E. coli)
References: UniProt: C3TIP7, UniProt: P69054*PLUS, succinate dehydrogenase

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Non-polymers , 6 types, 18 molecules

#5: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe2S2
#6: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#7: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#9: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: succinate-coenzyme Q reductase complex / Type: COMPLEX / Entity ID: #4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12706 / Symmetry type: POINT

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