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- EMDB-21906: succinate-coenzyme Q reductase -

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Basic information

Entry
Database: EMDB / ID: EMD-21906
Titlesuccinate-coenzyme Q reductase
Map datasuccinate-coenzyme Q reductase
Sample
  • Complex: succinate-coenzyme Q reductase complex
    • Protein or peptide: Succinate dehydrogenase flavoprotein subunit
  • Protein or peptide: Succinate dehydrogenase iron-sulfur subunit
  • Protein or peptide: Succinate dehydrogenase
  • Protein or peptide: Succinate dehydrogenase hydrophobic membrane anchor subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: SODIUM ION
KeywordsComplex / succinate-coenzyme Q reductase / ELECTRON TRANSPORT
Function / homology
Function and homology information


succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / membrane => GO:0016020 / tricarboxylic acid cycle ...succinate dehydrogenase activity / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / cytochrome complex assembly / aerobic electron transport chain / 3 iron, 4 sulfur cluster binding / ubiquinone binding / iron-sulfur cluster binding / membrane => GO:0016020 / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Succinate dehydrogenase, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / 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, hydrophobic membrane anchor / Succinate dehydrogenase, cytochrome b subunit, conserved site / Succinate dehydrogenase cytochrome b subunit signature 1. / Succinate dehydrogenase cytochrome b subunit signature 2. / Succinate dehydrogenase, cytochrome b556 subunit / 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 / FAD binding domain / Alpha-helical ferredoxin / 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
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) / Escherichia coli (strain SE11) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLyu M / Su C-C
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.
History
DepositionMay 4, 2020-
Header (metadata) releaseFeb 3, 2021-
Map releaseFeb 3, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wu6
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21906.png

Downloads & links

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Map

FileDownload / File: emd_21906.map.gz / Format: CCP4 / Size: 11.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsuccinate-coenzyme Q reductase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 144 pix.
= 155.52 Å		1.08 Å/pix.
x 147 pix.
= 158.76 Å		1.08 Å/pix.
x 139 pix.
= 150.12 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.2
Minimum - Maximum-2.0588317 - 1.922677
Average (Standard dev.)0.000000000000616 (±0.09907924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin767580
Dimensions147139144
Spacing139147144
CellA: 150.12001 Å / B: 158.76001 Å / C: 155.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z139147144
origin x/y/z0.0000.0000.000
length x/y/z150.120158.760155.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS757680
NC/NR/NS139147144
D min/max/mean-2.0591.9230.000

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Supplemental data

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Additional map: succinate-coenzyme Q reductase

Fileemd_21906_additional_1.map
Annotationsuccinate-coenzyme Q reductase
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : succinate-coenzyme Q reductase complex

EntireName: succinate-coenzyme Q reductase complex
Components
  • Complex: succinate-coenzyme Q reductase complex
    • Protein or peptide: Succinate dehydrogenase flavoprotein subunit
  • Protein or peptide: Succinate dehydrogenase iron-sulfur subunit
  • Protein or peptide: Succinate dehydrogenase
  • Protein or peptide: Succinate dehydrogenase hydrophobic membrane anchor subunit
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: SODIUM ION

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Supramolecule #1: succinate-coenzyme Q reductase complex

SupramoleculeName: succinate-coenzyme Q reductase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Succinate dehydrogenase iron-sulfur subunit

MacromoleculeName: Succinate dehydrogenase iron-sulfur subunit / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 26.800912 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLEFSIYRY NPDVDDAPRM QDYTLEADEG RDMMLLDALI QLKEKDPSLS FRRSCREGVC GSDGLNMNGK NGLACITPIS ALNQPGKKI VIRPLPGLPV IRDLVVDMGQ FYAQYEKIKP YLLNNGQNPP AREHLQMPEQ REKLDGLYEC ILCACCSTSC P SFWWNPDK ...String:
MRLEFSIYRY NPDVDDAPRM QDYTLEADEG RDMMLLDALI QLKEKDPSLS FRRSCREGVC GSDGLNMNGK NGLACITPIS ALNQPGKKI VIRPLPGLPV IRDLVVDMGQ FYAQYEKIKP YLLNNGQNPP AREHLQMPEQ REKLDGLYEC ILCACCSTSC P SFWWNPDK FIGPAGLLAA YRFLIDSRDT ETDSRLDGLS DAFSVFRCHS IMNCVSVCPK GLNPTRAIGH IKSMLLQRNA

UniProtKB: Succinate dehydrogenase iron-sulfur subunit

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Macromolecule #2: Succinate dehydrogenase

MacromoleculeName: Succinate dehydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 14.3131 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIRNVKKQRP VNLDLQTIRF PITAIASILH RVSGVITFVA VGILLWLLGT SLSSPEGFEQ ASAIMGSFFV KFIMWGILTA LAYHVVVGI RHMMMDFGYL EETFEAGKRS AKISFVITVV LSLLAGVLVW

UniProtKB: Succinate dehydrogenase cytochrome b556 subunit

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Macromolecule #3: Succinate dehydrogenase hydrophobic membrane anchor subunit

MacromoleculeName: Succinate dehydrogenase hydrophobic membrane anchor subunit
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli 908573 (bacteria)
Molecular weightTheoretical: 12.874438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVSNASALGR NGVHDFILVR ATAIVLTLYI IYMVGFFATS GELTYEVWIG FFASAFTKVF TLLALFSILI HAWIGMWQVL TDYVKPLAL RLMLQLVIVV ALVVYVIYGF VVVWGV

UniProtKB: Succinate dehydrogenase hydrophobic membrane anchor subunit

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Macromolecule #4: Succinate dehydrogenase flavoprotein subunit

MacromoleculeName: Succinate dehydrogenase flavoprotein subunit / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO / EC number: succinate dehydrogenase
Source (natural)Organism: Escherichia coli (strain SE11) (bacteria) / Strain: SE11
Molecular weightTheoretical: 64.502766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLPVREFDA VVIGAGGAGM RAALQISQSG QTCALLSKVF PTRSHTVSAQ GGITVALGNT HEDNWEWHMY DTVKGSDYIG DQDAIEYMC KTGPEAILEL EHMGLPFSRL DDGRIYQRPF GGQSKNFGGE QAARTAAAAD RTGHALLHTL YQQNLKNHTT I FSEWYALD ...String:
MKLPVREFDA VVIGAGGAGM RAALQISQSG QTCALLSKVF PTRSHTVSAQ GGITVALGNT HEDNWEWHMY DTVKGSDYIG DQDAIEYMC KTGPEAILEL EHMGLPFSRL DDGRIYQRPF GGQSKNFGGE QAARTAAAAD RTGHALLHTL YQQNLKNHTT I FSEWYALD LVKNQDGAVV GCTALCIETG EVVYFKARAT VLATGGAGRI YQSTTNAHIN TGDGVGMAIR AGVPVQDMEM WQ FHPTGIA GAGVLVTEGC RGEGGYLLNK HGERFMERYA PNAKDLAGRD VVARSIMIEI REGRGCDGPW GPHAKLKLDH LGK EVLESR LPGILELSRT FAHVDPVKEP IPVIPTCHYM MGGIPTKVTG QALTVNEKGE DVVVPGLFAV GEIACVSVHG ANRL GGNSL LDLVVFGRAA GLHLQESIAE QGALRDASES DVEASLDRLN RWNNNRNGED PVAIRKALQE CMQHNFSVFR EGDAM AKGL EQLKVIRERL KNARLDDTSS EFNTQRVECL ELDNLMETAY ATAVSANFRT ESRGAHSRFD FPDRDDENWL CHSLYL PES ESMTRRSVNM EPKLRPAFPP KIRTY

UniProtKB: Succinate dehydrogenase flavoprotein subunit

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Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 3 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #7: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #8: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 8 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #9: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 9 / Number of copies: 3 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

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Macromolecule #10: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 10 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12706
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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