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- PDB-8k9f: Cryo-EM structure of the photosynthetic alternative complex III f... -

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Basic information

Entry
Database: PDB / ID: 8k9f
TitleCryo-EM structure of the photosynthetic alternative complex III from Chloroflexus aurantiacus at 2.9 angstrom
Components
  • (Quinol:cytochrome c oxidoreductase ...) x 2
  • Cytochrome c domain-containing protein
  • Cytochrome c7-like domain-containing protein
  • Fe-S-cluster-containing hydrogenase components 1-like protein
  • Polysulphide reductase NrfD
  • hypothetical protein
  • unknown
KeywordsMEMBRANE PROTEIN / Photosynthetic alternative complex III
Function / homology
Function and homology information


electron transfer 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 / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / 4Fe-4S dicluster domain ...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 / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome 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
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 ...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 / Uncharacterized protein
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsXu, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Plant Cell / Year: 2024
Title: Cryo-EM structure of HQNO-bound Alternative Complex III from the anoxygenic phototrophic bacterium Chloroflexus aurantiacus.
Authors: Jiyu Xin / Zhenzhen Min / Lu Yu / Xinyi Yuan / Aokun Liu / Wenping Wu / Xin Zhang / Huimin He / Jingyi Wu / Yueyong Xin / Robert E Blankenship / Changlin Tian / Xiaoling Xu /
Abstract: Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the ...Alternative complex III (ACIII) couples quinol oxidation and electron acceptor reduction with potential transmembrane proton translocation. It is compositionally and structurally different from the cytochrome bc1/b6f complexes, but functionally replaces these enzymes in the photosynthetic and/or respiratory electron transport chains (ETCs) of many bacteria. However, the true compositions and architectures of ACIIIs remain unclear, as do their structural and functional relevance in mediating the ETCs. We here determined cryogenic electron microscopy structures of photosynthetic ACIII isolated from Chloroflexus aurantiacus (CaACIIIp), in apo-form and in complexed form bound to a menadiol analog 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO). Besides six canonical subunits (ActABCDEF), the structures revealed conformations of two previously unresolved subunits, ActG and I, which contributed to the complex stability. We also elucidated the structural basis of menaquinol oxidation and subsequent electron transfer along the [3Fe-4S]-6 hemes wire to its periplasmic electron acceptors, using electron paramagnetic resonance (EPR), spectroelectrochemistry, enzymatic analyses and molecular dynamics (MD) simulations. A unique insertion loop in ActE was shown to function in determining the binding specificity of CaACIIIp for downstream electron acceptors. This study broadens our understanding of the structural diversity and molecular evolution of ACIIIs, enabling further investigation of the (mena)quinol oxidoreductases evolved coupling mechanism in bacterial energy conservation.
History
DepositionAug 1, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c7-like domain-containing protein
B: Fe-S-cluster-containing hydrogenase components 1-like protein
C: Polysulphide reductase NrfD
D: Quinol:cytochrome c oxidoreductase membrane protein
E: Cytochrome c domain-containing protein
F: Quinol:cytochrome c oxidoreductase quinone-binding subunit 2
G: hypothetical protein
I: unknown
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,96022
Polymers298,7818
Non-polymers7,17914
Water0
1


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

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Components

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Protein , 5 types, 5 molecules ABCEG

#1: Protein Cytochrome c7-like domain-containing protein


Mass: 25247.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV2
#2: Protein Fe-S-cluster-containing hydrogenase components 1-like protein


Mass: 113115.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV3
#3: Protein Polysulphide reductase NrfD


Mass: 55223.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV4
#5: Protein Cytochrome c domain-containing protein


Mass: 23017.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV6
#7: Protein hypothetical protein /


Mass: 12485.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV8

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Quinol:cytochrome c oxidoreductase ... , 2 types, 2 molecules DF

#4: Protein Quinol:cytochrome c oxidoreductase membrane protein


Mass: 19648.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV5
#6: Protein Quinol:cytochrome c oxidoreductase quinone-binding subunit 2


Mass: 45721.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
References: UniProt: A9WEV7

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Protein/peptide , 1 types, 1 molecules I

#8: Protein/peptide unknown


Mass: 4322.134 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)

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Non-polymers , 7 types, 14 molecules

#9: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


Mass: 295.795 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe3S4
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-JLQ / [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-tetradecanoyloxy-propyl] hexadecanoate / 1-hexadecanoyl-2-tetradecanoyl-sn-glycero-3-phosphoethanolamine / PE(16:0/14:0)


Mass: 663.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H70NO8P
#14: Chemical ChemComp-JL3 / [(2~{R})-3-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-2-pentadecanoyloxy-propyl] pentadecanoate / 1,2-Dipentadecanoyl-sn-glycero-3-phosphoethanolamine / PE(15:0/15:0)


Mass: 663.906 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H70NO8P
#15: Chemical ChemComp-JM9 / 1,3-bis(13-methyltetradecanoyloxy)propan-2-yl pentadecanoate


Mass: 765.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C48H92O6

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Details

Has ligand of interestN

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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: Alternative complex III / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Source (natural)Organism: Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (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 FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103633 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0120467
ELECTRON MICROSCOPYf_angle_d1.59928042
ELECTRON MICROSCOPYf_dihedral_angle_d11.9632862
ELECTRON MICROSCOPYf_chiral_restr0.1723044
ELECTRON MICROSCOPYf_plane_restr0.013536

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