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- PDB-6lod: Cryo-EM structure of the air-oxidized photosynthetic alternative ... -

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Basic information

Entry
Database: PDB / ID: 6lod
TitleCryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii
Components
  • (Uncharacterized protein ...) x 2
  • Cytochrome c domain-containing protein
  • Fe-S-cluster-containing hydrogenase components 1-like protein
  • MULTIHEME_CYTC domain-containing protein
  • Polysulphide reductase NrfD
KeywordsPHOTOSYNTHESIS / quinol:electron acceptor oxidoreductase
Function / homology
Function and homology information


molybdopterin cofactor binding / electron transfer activity / oxidoreductase activity / heme binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cytochrome C oxidase, cbb3-type, subunit III ...NrfD family / Alternative complex III, ActD subunit / MoCo/4Fe-4S cofactor protein extended Tat translocation domain / Polysulphide reductase, NrfD / Alternative complex III, ActD subunit / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / Aspartate decarboxylase-like domain superfamily / 4Fe-4S dicluster domain / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
[(2S)-2-octadecanoyloxypropyl] octadecanoate / FE3-S4 CLUSTER / HEME C / IRON/SULFUR CLUSTER / Cytochrome c7-like domain-containing protein / Fe-S-cluster-containing hydrogenase components 1-like protein / Polysulphide reductase NrfD / Quinol:cytochrome c oxidoreductase membrane protein / Cytochrome c domain-containing protein / Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShi, Y. / Xin, Y.Y. / Wang, C. / Blankenship, R.E. / Sun, F. / Xu, X.L.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570738 China
National Natural Science Foundation of China (NSFC)31870740 China
National Natural Science Foundation of China (NSFC)31400630 China
Chinese Academy of SciencesXDB08030202 China
Ministry of Science and Technology (MoST, China)2017YFA0504700 China
CitationJournal: Sci Adv / Year: 2020
Title: Cryo-EM structures of the air-oxidized and dithionite-reduced photosynthetic alternative complex III from .
Authors: Yang Shi / Yueyong Xin / Chao Wang / Robert E Blankenship / Fei Sun / Xiaoling Xu /
Abstract: Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and ...Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation in both the respiratory and photosynthetic electron transport chains of bacteria. The coupling mechanism, however, is poorly understood. Here, we report the cryo-EM structures of air-oxidized and dithionite-reduced ACIII from the photosynthetic bacterium at 3.3- and 3.5-Å resolution, respectively. We identified a menaquinol binding pocket and an electron transfer wire comprising six hemes and four iron-sulfur clusters that is capable of transferring electrons to periplasmic acceptors. We detected a proton translocation passage in which three strictly conserved, mid-passage residues are likely essential for coupling the redox-driven proton translocation across the membrane. These results allow us to propose a previously unrecognized coupling mechanism that links the respiratory and photosynthetic functions of ACIII. This study provides a structural basis for further investigation of the energy transformation mechanisms in bacterial photosynthesis and respiration.
History
DepositionJan 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: MULTIHEME_CYTC domain-containing protein
B: Fe-S-cluster-containing hydrogenase components 1-like protein
C: Polysulphide reductase NrfD
D: Uncharacterized protein ActD
E: Cytochrome c domain-containing protein
F: Uncharacterized protein ActF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,68018
Polymers268,4006
Non-polymers6,28012
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area40270 Å2
ΔGint-414 kcal/mol
Surface area75170 Å2

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Components

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Protein , 4 types, 4 molecules ABCE

#1: Protein MULTIHEME_CYTC domain-containing protein / ActA


Mass: 26076.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ87
#2: Protein Fe-S-cluster-containing hydrogenase components 1-like protein / ActB


Mass: 102515.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ88
#3: Protein Polysulphide reductase NrfD / ActC


Mass: 53938.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ89
#5: Protein Cytochrome c domain-containing protein


Mass: 18252.623 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ91

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Uncharacterized protein ... , 2 types, 2 molecules DF

#4: Protein Uncharacterized protein ActD


Mass: 21070.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ90
#6: Protein Uncharacterized protein ActF


Mass: 46545.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
References: UniProt: A7NJ92

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Non-polymers , 4 types, 12 molecules

#7: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-EL6 / [(2S)-2-octadecanoyloxypropyl] octadecanoate


Mass: 609.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C39H76O4
#9: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-F3S / FE3-S4 CLUSTER


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4 / Feature type: SUBJECT OF INVESTIGATION

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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: Air-oxidized alternative complex III / Type: COMPLEX / Entity ID: #1-#4, #6 / Source: NATURAL
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Buffer solutionpH: 8
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: 59 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 257815
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 177489 / Symmetry type: POINT

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