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- PDB-6u8y: Structure of the membrane-bound sulfane sulfur reductase (MBS), a... -

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Basic information

Entry
Database: PDB / ID: 6u8y
TitleStructure of the membrane-bound sulfane sulfur reductase (MBS), an archaeal respiratory membrane complex
Components
  • (Monovalent cation/H+ antiporter subunit ...) x 5
  • (NADH dehydrogenase subunit ...) x 6
  • DUF4040 domain-containing protein
  • NADH dehydrogenase subunit
KeywordsMEMBRANE PROTEIN / cryoEM / respiratory system
Function / homology
Function and homology information


NADH dehydrogenase (quinone) / sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / NAD binding ...NADH dehydrogenase (quinone) / sodium:proton antiporter activity / monoatomic cation transmembrane transporter activity / oxidoreductase activity, acting on NAD(P)H / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
: / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD ...: / MrpA C-terminal/MbhE / : / : / MBH, subunit E / Na+/H+ antiporter subunit E / Na+/H+ antiporter subunit G / Na+/H+ antiporter MnhB subunit-related protein / Na(+)/H(+) antiporter subunit F-like / MrpA C-terminal/MbhD / : / Na+/H+ ion antiporter subunit / Na+/H+ antiporter subunit / Domain related to MnhB subunit of Na+/H+ antiporter / Multiple resistance and pH regulation protein F (MrpF / PhaF) / MBH, subunit D / NADH:ubiquinone oxidoreductase Nqo5 subunit / Rossmann fold - #12280 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Beta Polymerase; domain 2 / 4Fe-4S dicluster domain / 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 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / NADH dehydrogenase subunit C / NADH dehydrogenase subunit M / Monovalent cation/H+ antiporter subunit G / NADH dehydrogenase subunit I / Monovalent cation/H+ antiporter subunit B / Monovalent cation/H+ antiporter subunit C / Monovalent cation/H+ antiporter subunit E / NADH dehydrogenase subunit B / NADH dehydrogenase subunit N ...IRON/SULFUR CLUSTER / NADH dehydrogenase subunit C / NADH dehydrogenase subunit M / Monovalent cation/H+ antiporter subunit G / NADH dehydrogenase subunit I / Monovalent cation/H+ antiporter subunit B / Monovalent cation/H+ antiporter subunit C / Monovalent cation/H+ antiporter subunit E / NADH dehydrogenase subunit B / NADH dehydrogenase subunit N / Monovalent cation/H+ antiporter subunit F / NADH dehydrogenase subunit D / NADH dehydrogenase subunit / MrpA C-terminal/MbhD domain-containing protein
Similarity search - Component
Biological speciesPyrococcus furiosus COM1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsYu, H.J. / Li, H.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020085 United States
Department of Energy (DOE, United States)DE-FG02-95ER20175 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the respiratory MBS complex reveals iron-sulfur cluster catalyzed sulfane sulfur reduction in ancient life.
Authors: Hongjun Yu / Dominik K Haja / Gerrit J Schut / Chang-Hao Wu / Xing Meng / Gongpu Zhao / Huilin Li / Michael W W Adams /
Abstract: Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas- ...Modern day aerobic respiration in mitochondria involving complex I converts redox energy into chemical energy and likely evolved from a simple anaerobic system now represented by hydrogen gas-evolving hydrogenase (MBH) where protons are the terminal electron acceptor. Here we present the cryo-EM structure of an early ancestor in the evolution of complex I, the elemental sulfur (S)-reducing reductase MBS. Three highly conserved protein loops linking cytoplasmic and membrane domains enable scalable energy conversion in all three complexes. MBS contains two proton pumps compared to one in MBH and likely conserves twice the energy. The structure also reveals evolutionary adaptations of MBH that enabled S reduction by MBS catalyzed by a site-differentiated iron-sulfur cluster without participation of protons or amino acid residues. This is the simplest mechanism proposed for reduction of inorganic or organic disulfides. It is of fundamental significance in the iron and sulfur-rich volcanic environments of early earth and possibly the origin of life. MBS provides a new perspective on the evolution of modern-day respiratory complexes and of catalysis by biological iron-sulfur clusters.
History
DepositionSep 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2020Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.0Sep 9, 2020Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Revision 1.1Dec 16, 2020Group: Author supporting evidence / Structure summary / Category: pdbx_audit_support / struct / Item: _struct.title
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
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
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 28, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
A: Monovalent cation/H+ antiporter subunit E
B: Monovalent cation/H+ antiporter subunit F
C: Monovalent cation/H+ antiporter subunit G
D: DUF4040 domain-containing protein
E: Monovalent cation/H+ antiporter subunit B
G: Monovalent cation/H+ antiporter subunit C
H: NADH dehydrogenase subunit N
X: NADH dehydrogenase subunit M
J: NADH dehydrogenase subunit B
K: NADH dehydrogenase subunit C
L: NADH dehydrogenase subunit D
M: NADH dehydrogenase subunit
N: NADH dehydrogenase subunit I
a: Monovalent cation/H+ antiporter subunit E
b: Monovalent cation/H+ antiporter subunit F
c: Monovalent cation/H+ antiporter subunit G
d: DUF4040 domain-containing protein
e: Monovalent cation/H+ antiporter subunit B
g: Monovalent cation/H+ antiporter subunit C
h: NADH dehydrogenase subunit N
x: NADH dehydrogenase subunit M
j: NADH dehydrogenase subunit B
k: NADH dehydrogenase subunit C
l: NADH dehydrogenase subunit D
m: NADH dehydrogenase subunit
n: NADH dehydrogenase subunit I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)717,70732
Polymers715,59726
Non-polymers2,1106
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Monovalent cation/H+ antiporter subunit ... , 5 types, 10 molecules AaBbCcEeGg

#1: Protein Monovalent cation/H+ antiporter subunit E


Mass: 19134.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6UQN5
#2: Protein Monovalent cation/H+ antiporter subunit F


Mass: 9328.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6UZW2
#3: Protein Monovalent cation/H+ antiporter subunit G


Mass: 13550.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6TXQ5
#5: Protein Monovalent cation/H+ antiporter subunit B


Mass: 25691.111 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6U860
#6: Protein Monovalent cation/H+ antiporter subunit C


Mass: 12073.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6UQN0

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Protein , 2 types, 4 molecules DdMm

#4: Protein DUF4040 domain-containing protein


Mass: 10560.460 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6V2A4
#12: Protein NADH dehydrogenase subunit


Mass: 33677.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6V2A1

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NADH dehydrogenase subunit ... , 6 types, 12 molecules HhXxJjKkLlNn

#7: Protein NADH dehydrogenase subunit N


Mass: 53019.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6UZV7
#8: Protein NADH dehydrogenase subunit M


Mass: 67561.906 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6TXQ1
#9: Protein NADH dehydrogenase subunit B


Mass: 22731.473 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6UZV3, NADH dehydrogenase (quinone)
#10: Protein NADH dehydrogenase subunit C


Mass: 20966.279 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6TXP7, NADH dehydrogenase (quinone)
#11: Protein NADH dehydrogenase subunit D


Mass: 44756.504 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6V297, NADH dehydrogenase (quinone)
#13: Protein NADH dehydrogenase subunit I


Mass: 24746.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus COM1 (archaea) / References: UniProt: I6U853, NADH dehydrogenase (quinone)

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Non-polymers , 1 types, 6 molecules

#14: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN
Has protein modificationN

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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: respiratory membrane complex / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Source (natural)Organism: Pyrococcus furiosus (archaea)
Buffer solutionpH: 8.2
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 FIELD
Image recordingElectron dose: 1.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
8PHENIXmodel refinement
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 203673 / Symmetry type: POINT
RefinementHighest resolution: 4 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00849638
ELECTRON MICROSCOPYf_angle_d1.15167486
ELECTRON MICROSCOPYf_dihedral_angle_d13.7328962
ELECTRON MICROSCOPYf_chiral_restr0.0647768
ELECTRON MICROSCOPYf_plane_restr0.0098264

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