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- EMDB-22528: Succinate: quinone oxidoreductase SQR from E.coli K12 -

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Basic information

Entry
Database: EMDB / ID: EMD-22528
TitleSuccinate: quinone oxidoreductase SQR from E.coli K12
Map data
SampleSuccinate: quinone oxidoreductase SQR from E.coli K12:
(Succinate dehydrogenase ...) x 4 / (ligand) x 8
Function / homology
Function and homology information


plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase / succinate dehydrogenase (ubiquinone) activity / cytochrome complex assembly / succinate dehydrogenase activity / anaerobic respiration / ubiquinone binding / iron-sulfur cluster binding / 3 iron, 4 sulfur cluster binding ...plasma membrane succinate dehydrogenase complex / succinate dehydrogenase complex / succinate dehydrogenase / succinate dehydrogenase (ubiquinone) activity / cytochrome complex assembly / succinate dehydrogenase activity / anaerobic respiration / ubiquinone binding / iron-sulfur cluster binding / 3 iron, 4 sulfur cluster binding / aerobic respiration / respiratory electron transport chain / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / flavin adenine dinucleotide binding / go:0055114: / electron transfer activity / oxidoreductase activity / heme binding / integral component of membrane / plasma membrane / metal ion binding
2Fe-2S ferredoxin-type iron-sulfur binding domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / FAD-dependent oxidoreductase 2, FAD binding domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Alpha-helical ferredoxin / Succinate dehydrogenase, flavoprotein subunit / Beta-grasp domain superfamily / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Succinate dehydrogenase, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b556 subunit ...2Fe-2S ferredoxin-type iron-sulfur binding domain / Succinate dehydrogenase/fumarate reductase type B, transmembrane subunit / FAD-dependent oxidoreductase 2, FAD binding domain / Succinate dehydrogenase/fumarate reductase iron-sulphur protein / Alpha-helical ferredoxin / Succinate dehydrogenase, flavoprotein subunit / Beta-grasp domain superfamily / Succinate dehydrogenase/fumarate reductase, flavoprotein subunit / Succinate dehydrogenase, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b556 subunit / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydogenase/fumarate reductase N-terminal / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / Fumarate reductase/succinate dehydrogenase, transmembrane subunit / 2Fe-2S ferredoxin-like superfamily / FAD/NAD(P)-binding domain superfamily / Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain superfamily / Fumarate reductase/succinate dehydrogenase, FAD-binding site
Succinate dehydrogenase hydrophobic membrane anchor subunit / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase cytochrome b556 subunit
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLyu M / Su C-C / Morgan CE / Bolla JR / Robinson CV / Yu EW
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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionSep 1, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateJan 20, 2021-
Current statusJan 20, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7jz2
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22528.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 140 pix.
= 151.2 Å
1.08 Å/pix.
x 140 pix.
= 151.2 Å
1.08 Å/pix.
x 137 pix.
= 147.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-1.543639 - 2.665797
Average (Standard dev.)-5.132398e-13 (±0.17199413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin109113104
Dimensions140137140
Spacing140140137
CellA: 151.20001 Å / B: 151.20001 Å / C: 147.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z140140137
origin x/y/z0.0000.0000.000
length x/y/z151.200151.200147.960
α/β/γ90.00090.00090.000
start NX/NY/NZ104109113
NX/NY/NZ140140137
MAP C/R/S321
start NC/NR/NS113109104
NC/NR/NS137140140
D min/max/mean-1.5442.666-0.000

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Supplemental data

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Additional map: #1

Fileemd_22528_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Succinate: quinone oxidoreductase SQR from E.coli K12

EntireName: Succinate: quinone oxidoreductase SQR from E.coli K12 / Number of components: 13

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Component #1: protein, Succinate: quinone oxidoreductase SQR from E.coli K12

ProteinName: Succinate: quinone oxidoreductase SQR from E.coli K12 / Recombinant expression: No
SourceSpecies: Escherichia coli (E. coli) / Strain: K-12

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Component #2: protein, Succinate dehydrogenase flavoprotein subunit

ProteinName: Succinate dehydrogenase flavoprotein subunit / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 64.502766 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K12

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Component #3: protein, Succinate dehydrogenase iron-sulfur subunit

ProteinName: Succinate dehydrogenase iron-sulfur subunit / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 26.800912 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K12

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Component #4: protein, Succinate dehydrogenase cytochrome b556 subunit

ProteinName: Succinate dehydrogenase cytochrome b556 subunit / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 14.3131 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K12

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Component #5: protein, Succinate dehydrogenase hydrophobic membrane anchor subunit

ProteinName: Succinate dehydrogenase hydrophobic membrane anchor subunit
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 12.874438 kDa
SourceSpecies: Escherichia coli (E. coli) / Strain: K-12

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Component #6: ligand, FLAVIN-ADENINE DINUCLEOTIDE

LigandName: FLAVIN-ADENINE DINUCLEOTIDEFlavin adenine dinucleotide
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.78555 kDa

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Component #7: ligand, SODIUM ION

LigandName: SODIUM IONSodium / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.29905 MDa

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Component #8: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Component #9: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Component #10: ligand, FE3-S4 CLUSTER

LigandName: FE3-S4 CLUSTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.295795 kDa

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Component #11: ligand, 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

LigandName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.748065 kDa

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Component #12: ligand, PROTOPORPHYRIN IX CONTAINING FE

LigandName: PROTOPORPHYRIN IX CONTAINING FE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.616487 kDa

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Component #13: ligand, UBIQUINONE-2

LigandName: UBIQUINONE-2Coenzyme Q10 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.318407 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 38471
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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