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- EMDB-30595: Mycobacterium smegmatis Sdh1 complex in the apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-30595
TitleMycobacterium smegmatis Sdh1 complex in the apo form
Map data
Sample
  • Complex: Mycobacterium smegmatis Sdh1 complex in apo form
    • Protein or peptide: Succinate dehydrogenase subunit A
    • Protein or peptide: Fumarate reductase iron-sulfur subunit
    • Protein or peptide: Succinate dehydrogenase (Membrane anchor subunit)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
Keywordssuccinate dehydrogenase / electron transport chain / Mycobacterium smegmatis / Sdh1 / SQR / OXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors / membrane => GO:0016020 / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding
Similarity search - Function
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 ...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 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 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-type, iron-sulphur binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Succinate dehydrogenase subunit A / Fumarate reductase iron-sulfur subunit / Succinate dehydrogenase (Membrane anchor subunit)
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 51 (bacteria) / Mycolicibacterium smegmatis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsZhou X / Gao Y
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030201, XDB37020203 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Architecture of the mycobacterial succinate dehydrogenase with a membrane-embedded Rieske FeS cluster.
Authors: Xiaoting Zhou / Yan Gao / Weiwei Wang / Xiaolin Yang / Xiuna Yang / Fengjiang Liu / Yanting Tang / Sin Man Lam / Guanghou Shui / Lu Yu / Changlin Tian / Luke W Guddat / Quan Wang / Zihe Rao / Hongri Gong /
Abstract: Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been ...Complex II, also known as succinate dehydrogenase (SQR) or fumarate reductase (QFR), is an enzyme involved in both the Krebs cycle and oxidative phosphorylation. Mycobacterial Sdh1 has recently been identified as a new class of respiratory complex II (type F) but with an unknown electron transfer mechanism. Here, using cryoelectron microscopy, we have determined the structure of Sdh1 in the presence and absence of the substrate, ubiquinone-1, at 2.53-Å and 2.88-Å resolution, respectively. Sdh1 comprises three subunits, two that are water soluble, SdhA and SdhB, and one that is membrane spanning, SdhC. Within these subunits we identified a quinone-binding site and a rarely observed Rieske-type [2Fe-2S] cluster, the latter being embedded in the transmembrane region. A mutant, where two His ligands of the Rieske-type [2Fe-2S] were changed to alanine, abolished the quinone reduction activity of the Sdh1. Our structures allow the proposal of an electron transfer pathway that connects the substrate-binding and quinone-binding sites. Given the unique features of Sdh1 and its essential role in , these structures will facilitate antituberculosis drug discovery efforts that specifically target this complex.
History
DepositionOct 2, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d6x
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30595.png

Downloads & links

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Map

FileDownload / File: emd_30595.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.6
Minimum - Maximum-1.5003384 - 3.6520207
Average (Standard dev.)0.00029778882 (±0.05810524)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ160160160
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.5003.6520.000

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Supplemental data

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Sample components

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Entire : Mycobacterium smegmatis Sdh1 complex in apo form

EntireName: Mycobacterium smegmatis Sdh1 complex in apo form
Components
  • Complex: Mycobacterium smegmatis Sdh1 complex in apo form
    • Protein or peptide: Succinate dehydrogenase subunit A
    • Protein or peptide: Fumarate reductase iron-sulfur subunit
    • Protein or peptide: Succinate dehydrogenase (Membrane anchor subunit)
  • Ligand: FLAVIN-ADENINE DINUCLEOTIDE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
  • Ligand: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: Mycobacterium smegmatis Sdh1 complex in apo form

SupramoleculeName: Mycobacterium smegmatis Sdh1 complex in apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: succinate dehydrogenase
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria)

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Macromolecule #1: Succinate dehydrogenase subunit A

MacromoleculeName: Succinate dehydrogenase subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Oxidoreductases; Acting on the CH-CH group of donors
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 70.14718 KDa
SequenceString: MSELERHSYD VVVIGAGGAG LRAVIEARER GLRVAVVTKS LFGKAHTVMA EGGCAAAMRN VNTKDSWQVH FGDTMRGGKF LNNWRMAEL HAQEAPDRVW ELETYGALFD RTKDGKISQR NFGGHTYPRL AHVGDRTGLE IIRTLQQKIV SLQQEDKREL G DYEARIRV ...String:
MSELERHSYD VVVIGAGGAG LRAVIEARER GLRVAVVTKS LFGKAHTVMA EGGCAAAMRN VNTKDSWQVH FGDTMRGGKF LNNWRMAEL HAQEAPDRVW ELETYGALFD RTKDGKISQR NFGGHTYPRL AHVGDRTGLE IIRTLQQKIV SLQQEDKREL G DYEARIRV FHETSITELI LDDGKIAGAF GYYRETGNFV LFEAPAVVLA TGGIGKSFKV SSNSWEYTGD GHALALRAGS AL INMEFIQ FHPTGMVWPL SVKGILVTEG VRGDGGVLKN SEGKRFMFDY IPSVFKGQYA ETEEEADQWL KDNDSARRTP DLL PRDEVA RAINAEVKAG RGSPHGGVYL DIASRMPAEE IKRRLPSMYH QFIELAEVDI TKDAMEVGPT CHYVMGGIEV DPDT AAGAT PGLFAAGECS GGMHGSNRLG GNSLSDLLVF GRRAGLGAAD YVRALPDRPK VSEAAVEDAT RLVLAPFEPK AEPEN PYTL HAELQQSMND LVGIIRKEAE IQEALDRLQE LKRRYANVTV EGGRVFNPGW HLAIDMRNML LVSECVAKAA LQRTES RGG HTRDDYPEMD ANWRNTLLVC RVSGGDPVVP DVTVTPEQQV PMRPDLLGCF ELSELEKYYT PEELAEHPER KG

UniProtKB: Succinate dehydrogenase subunit A

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Macromolecule #2: Fumarate reductase iron-sulfur subunit

MacromoleculeName: Fumarate reductase iron-sulfur subunit / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 28.851988 KDa
SequenceString: MATYDAKLRV WRGDDTGGEL HDYTVEVNDG EVVLDIIHRL QATQTPDLAV RWNCKAGKCG SCSAEINGRP RLMCMTRMST FGEDEVVTV TPLRTFPVMR DLVTDVSFNY EKARQIPSFT PPKDLQPGEY RMQQEDVNRS QEFRKCIECF LCQNVCHVVR D HEENKENF ...String:
MATYDAKLRV WRGDDTGGEL HDYTVEVNDG EVVLDIIHRL QATQTPDLAV RWNCKAGKCG SCSAEINGRP RLMCMTRMST FGEDEVVTV TPLRTFPVMR DLVTDVSFNY EKARQIPSFT PPKDLQPGEY RMQQEDVNRS QEFRKCIECF LCQNVCHVVR D HEENKENF AGPRFHMRIA ELDMHPLDTV DRKEMAQDEF GLGYCNITKC CTEVCPEHIK ITDNALIPMK ERVADRKYDP IV WLGNKLF RR

UniProtKB: Fumarate reductase iron-sulfur subunit

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Macromolecule #3: Succinate dehydrogenase (Membrane anchor subunit)

MacromoleculeName: Succinate dehydrogenase (Membrane anchor subunit) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycolicibacterium smegmatis (bacteria)
Molecular weightTheoretical: 32.583545 KDa
SequenceString: MSAPTADRRA TGVFSPRRAQ IPERTLRTDR WWQAPLLTNL GLAAFVIYAT IRAFWGSAYW VADYHYLTPF YSPCVSTACA PGSSHFGQW VGDLPWFIPM AFISLPFLLA FRLTCYYYRK AYYRSVWQSP TACAVAEPHA KYTGETRFPL ILQNIHRYFF Y AAVLISLV ...String:
MSAPTADRRA TGVFSPRRAQ IPERTLRTDR WWQAPLLTNL GLAAFVIYAT IRAFWGSAYW VADYHYLTPF YSPCVSTACA PGSSHFGQW VGDLPWFIPM AFISLPFLLA FRLTCYYYRK AYYRSVWQSP TACAVAEPHA KYTGETRFPL ILQNIHRYFF Y AAVLISLV NTYDAITAFH SPSGFGFGLG NVILTGNVIL LWVYTLSCHS CRHVTGGRLK HFSKHPVRYW IWTQVSKLNT RH MLFAWIT LGTLVLTDFY IMLVASGTIS DLRFIGHHHH HHHHHH

UniProtKB: Succinate dehydrogenase (Membrane anchor subunit)

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Macromolecule #4: FLAVIN-ADENINE DINUCLEOTIDE

MacromoleculeName: FLAVIN-ADENINE DINUCLEOTIDE / type: ligand / ID: 4 / Number of copies: 1 / Formula: FAD
Molecular weightTheoretical: 785.55 Da
Chemical component information

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

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Macromolecule #5: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 5 / Number of copies: 2 / 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: 1 / 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: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #8: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY...

MacromoleculeName: (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 8 / Number of copies: 1 / Formula: PEV
Molecular weightTheoretical: 720.012 Da
Chemical component information

ChemComp-PEV:
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / POPE, phospholipid*YM

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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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-40 / Average exposure time: 5.0 sec. / Average electron dose: 60.0 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: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 254341
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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