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- PDB-6lum: Structure of Mycobacterium smegmatis succinate dehydrogenase 2 -

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Entry
Database: PDB / ID: 6lum
TitleStructure of Mycobacterium smegmatis succinate dehydrogenase 2
Components(Succinate dehydrogenase subunit ...) x 5
KeywordsOXIDOREDUCTASE / electron transfer chain / trimer
Function / homology
Function and homology information


steroid dehydrogenase activity, acting on the CH-CH group of donors / : / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / steroid metabolic process / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding ...steroid dehydrogenase activity, acting on the CH-CH group of donors / : / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / steroid metabolic process / tricarboxylic acid cycle / electron transport chain / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / metal ion binding / membrane
Similarity search - Function
Succinate dehydrogenase membrane subunit SdhC, prokaryotes / 4Fe-4S dicluster domain / 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 / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 ...Succinate dehydrogenase membrane subunit SdhC, prokaryotes / 4Fe-4S dicluster domain / 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 / 4Fe-4S dicluster domain / Alpha-helical ferredoxin / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / 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. / FAD-dependent oxidoreductase SdhA/FrdA/AprA / 3 helical TM bundles of succinate and fumarate reductases / 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 / Beta-grasp domain superfamily / 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 / Ubiquitin-like (UB roll) / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LPP / MENAQUINONE-9 / Chem-PEV / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / IRON/SULFUR CLUSTER ...CARDIOLIPIN / FE3-S4 CLUSTER / FLAVIN-ADENINE DINUCLEOTIDE / FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LPP / MENAQUINONE-9 / Chem-PEV / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL / IRON/SULFUR CLUSTER / Succinate dehydrogenase iron-sulfur subunit / Succinate dehydrogenase flavoprotein subunit / Succinate dehydrogenase hydrophobic membrane anchor protein SdhD / Succinate dehydrogenase, cytochrome b556 subunit / Uncharacterized protein
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 51 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsGao, Y. / Gong, H. / Zhou, X. / Xiao, Y. / Wang, W. / Ji, W. / Wang, Q. / Rao, Z.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China (NSFC)81520108019, 813300237 China
Chinese Academy of Sciences2017YFC0840300 China
CitationJournal: Nat Commun / Year: 2020
Title: Cryo-EM structure of trimeric Mycobacterium smegmatis succinate dehydrogenase with a membrane-anchor SdhF.
Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / ...Authors: Hongri Gong / Yan Gao / Xiaoting Zhou / Yu Xiao / Weiwei Wang / Yanting Tang / Shan Zhou / Yuying Zhang / Wenxin Ji / Lu Yu / Changlin Tian / Sin Man Lam / Guanghou Shui / Luke W Guddat / Luet-Lok Wong / Quan Wang / Zihe Rao /
Abstract: Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by ...Diheme-containing succinate:menaquinone oxidoreductases (Sdh) are widespread in Gram-positive bacteria but little is known about the catalytic mechanisms they employ for succinate oxidation by menaquinone. Here, we present the 2.8 Å cryo-electron microscopy structure of a Mycobacterium smegmatis Sdh, which forms a trimer. We identified the membrane-anchored SdhF as a subunit of the complex. The 3 kDa SdhF forms a single transmembrane helix and this helix plays a role in blocking the canonically proximal quinone-binding site. We also identified two distal quinone-binding sites with bound quinones. One distal binding site is formed by neighboring subunits of the complex. Our structure further reveals the electron/proton transfer pathway for succinate oxidation by menaquinone. Moreover, this study provides further structural insights into the physiological significance of a trimeric respiratory complex II. The structure of the menaquinone binding site could provide a framework for the development of Sdh-selective anti-mycobacterial drugs.
History
DepositionJan 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.0Dec 2, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / em_software ...atom_site / em_software / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine_ls_restr / struct_asym / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _em_software.category / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _struct_asym.entity_id
Description: Ligand geometry / Details: The placement of molecule FAD head is opposite. / Provider: author / Type: Coordinate replacement
Revision 3.0Oct 20, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / database_2 ...atom_site / database_2 / em_software / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_struct_assembly_prop / pdbx_validate_close_contact / refine
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.pdbx_formal_charge / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_software.category / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _refine.ls_d_res_high
Description: Ligand geometry / Details: The molecule of FAD is corrected. / Provider: author / Type: Coordinate replacement
Revision 3.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
C: Succinate dehydrogenase subunit C
D: Succinate dehydrogenase subunit D
E: Succinate dehydrogenase subunit F
A: Succinate dehydrogenase subunit A
B: Succinate dehydrogenase subunit B
G: Succinate dehydrogenase subunit C
H: Succinate dehydrogenase subunit D
I: Succinate dehydrogenase subunit F
J: Succinate dehydrogenase subunit A
K: Succinate dehydrogenase subunit B
M: Succinate dehydrogenase subunit C
N: Succinate dehydrogenase subunit D
O: Succinate dehydrogenase subunit F
P: Succinate dehydrogenase subunit A
Q: Succinate dehydrogenase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,46954
Polymers397,06515
Non-polymers26,40439
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area88820 Å2
ΔGint-866 kcal/mol
Surface area112760 Å2

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Components

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Succinate dehydrogenase subunit ... , 5 types, 15 molecules CGMDHNEIOAJPBKQ

#1: Protein Succinate dehydrogenase subunit C


Mass: 15644.627 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria)
Strain: MC2 51 / References: UniProt: A0QT10*PLUS
#2: Protein Succinate dehydrogenase subunit D


Mass: 19280.400 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria)
Strain: MC2 51 / References: UniProt: A0QT09*PLUS
#3: Protein/peptide Succinate dehydrogenase subunit F


Mass: 3707.443 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria)
Strain: MC2 51 / References: UniProt: A0R4D1*PLUS
#4: Protein Succinate dehydrogenase subunit A


Mass: 64476.754 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria)
Strain: MC2 51 / References: UniProt: A0QT08*PLUS
#5: Protein Succinate dehydrogenase subunit B


Mass: 29245.760 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 51 (bacteria)
Strain: MC2 51 / References: UniProt: A0QT07*PLUS

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Non-polymers , 10 types, 39 molecules

#6: Chemical
ChemComp-PEV / (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLETHANOLAMINE / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 720.012 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C39H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: POPE, phospholipid*YM
#7: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-MQ9 / MENAQUINONE-9


Mass: 785.233 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C56H80O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


Mass: 1464.043 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#10: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#11: Chemical ChemComp-PIE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOINOSITOL


Mass: 836.061 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H80O13P / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#13: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


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


Mass: 295.795 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe3S4

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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: Mycobaterium smegmatis Succinate dehydrogenase 2 / Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Molecular weightValue: 0.4 MDa / Experimental value: YES
Source (natural)Organism: Mycolicibacterium smegmatis MC2 51 (bacteria) / Strain: mc2 51
Buffer solutionpH: 7.4 / Details: Solutions were made fresh
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
220 mMDVLFYONBTKHTER-UHFFFAOYSA-NMOPS1
30.1 %(v/w)digitonin1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was mono disperse.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEM3.6image acquisition
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 461385 / Algorithm: FOURIER SPACE
Details: cryoSPARC software was used for the reconstruction.
Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0126832
ELECTRON MICROSCOPYf_angle_d1.17636436
ELECTRON MICROSCOPYf_dihedral_angle_d11.06615537
ELECTRON MICROSCOPYf_chiral_restr0.0743945
ELECTRON MICROSCOPYf_plane_restr0.0064528

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