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- EMDB-4165: Alternative complex III -

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Basic information

Entry
Database: EMDB / ID: EMD-4165
TitleAlternative complex III
Map data
Sample
  • Complex: Alternative complex III
    • Protein or peptide: Cytochrome c family protein
    • Protein or peptide: Fe-S-cluster-containing hydrogenase
    • Protein or peptide: Polysulphide reductase NrfD
    • Protein or peptide: ActD
    • Protein or peptide: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit
    • Protein or peptide: ActF
    • Protein or peptide: ActH
  • Ligand: HEME C
  • Ligand: FE3-S4 CLUSTER
  • Ligand: IRON/SULFUR CLUSTER
Keywordselectron transfer / quinol oxidation / respiratory chain / MEMBRANE PROTEIN
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / membrane / 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 / 4Fe-4S dicluster domain / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily ...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 / 4Fe-4S dicluster domain / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 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
Cytochrome c family protein / Fe-S-cluster-containing hydrogenase / Polysulphide reductase NrfD / DUF3341 domain-containing protein / Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit / Quinol:cytochrome c oxidoreductase quinone-binding subunit 2 / LemA family protein
Similarity search - Component
Biological speciesRhodothermus marinus (bacteria) / Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsSousa JS / Calisto F
Funding support Portugal, Germany, 2 items
OrganizationGrant numberCountry
Fundacao para a ciencia e tecnologiaIF/01507/2015 Portugal
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for energy transduction by respiratory alternative complex III.
Authors: Joana S Sousa / Filipa Calisto / Julian D Langer / Deryck J Mills / Patrícia N Refojo / Miguel Teixeira / Werner Kühlbrandt / Janet Vonck / Manuela M Pereira /
Abstract: Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may ...Electron transfer in respiratory chains generates the electrochemical potential that serves as energy source for the cell. Prokaryotes can use a wide range of electron donors and acceptors and may have alternative complexes performing the same catalytic reactions as the mitochondrial complexes. This is the case for the alternative complex III (ACIII), a quinol:cytochrome c/HiPIP oxidoreductase. In order to understand the catalytic mechanism of this respiratory enzyme, we determined the structure of ACIII from Rhodothermus marinus at 3.9 Å resolution by single-particle cryo-electron microscopy. ACIII presents a so-far unique structure, for which we establish the arrangement of the cofactors (four iron-sulfur clusters and six c-type hemes) and propose the location of the quinol-binding site and the presence of two putative proton pathways in the membrane. Altogether, this structure provides insights into a mechanism for energy transduction and introduces ACIII as a redox-driven proton pump.
History
DepositionNov 20, 2017-
Header (metadata) releaseMar 14, 2018-
Map releaseMay 9, 2018-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6f0k
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4165.png

Downloads & links

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Map

FileDownload / File: emd_4165.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 288 pix.
= 298.08 Å		1.04 Å/pix.
x 288 pix.
= 298.08 Å		1.04 Å/pix.
x 288 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.035 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.10377691 - 0.3312479
Average (Standard dev.)0.000036377565 (±0.0060736933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 298.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z298.080298.080298.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1040.3310.000

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Supplemental data

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Sample components

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Entire : Alternative complex III

EntireName: Alternative complex III
Components
  • Complex: Alternative complex III
    • Protein or peptide: Cytochrome c family protein
    • Protein or peptide: Fe-S-cluster-containing hydrogenase
    • Protein or peptide: Polysulphide reductase NrfD
    • Protein or peptide: ActD
    • Protein or peptide: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit
    • Protein or peptide: ActF
    • Protein or peptide: ActH
  • Ligand: HEME C
  • Ligand: FE3-S4 CLUSTER
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: Alternative complex III

SupramoleculeName: Alternative complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Rhodothermus marinus (bacteria) / Strain: PRQ-62B
Molecular weightTheoretical: 300 kDa/nm

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Macromolecule #1: Cytochrome c family protein

MacromoleculeName: Cytochrome c family protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 24.245594 KDa
SequenceString: MPQIFSRKTN RLPALSLAGS VFGGVLAVFL VWYYFSPEFY EVGYAPPYSH RIHVGKLGLD CRYCHNWVEV SDKANIPPTQ TCINCHSQI LTDSPRLQAV RDSWATDRSI EWVKVHHLPD YAHFSHASHV NNGVGCETCH GRIDQMDVVR LVEPLSMGWC L ECHRQPEL ...String:
MPQIFSRKTN RLPALSLAGS VFGGVLAVFL VWYYFSPEFY EVGYAPPYSH RIHVGKLGLD CRYCHNWVEV SDKANIPPTQ TCINCHSQI LTDSPRLQAV RDSWATDRSI EWVKVHHLPD YAHFSHASHV NNGVGCETCH GRIDQMDVVR LVEPLSMGWC L ECHRQPEL YLRPQSEITT MGYQPPADYI ERNLERIRKE GIRPPTNCSA CHY

UniProtKB: Cytochrome c family protein

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Macromolecule #2: Fe-S-cluster-containing hydrogenase

MacromoleculeName: Fe-S-cluster-containing hydrogenase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 115.382617 KDa
SequenceString: MIELPVVNPD GAETPGSGKR LWRSTADLRR DPEWVKLAHD EFMPGVAEPP SGTSRRQFLQ IMGASMALAG LTACRRPVEK ILPYVRQPE EIIPGIPLYY ATAMPFRGSV RPLLVESHEG RPTKIEGNPD HPLSRGATGV FEQASLLNLY DPDRSQQVLR K GEPASWGD ...String:
MIELPVVNPD GAETPGSGKR LWRSTADLRR DPEWVKLAHD EFMPGVAEPP SGTSRRQFLQ IMGASMALAG LTACRRPVEK ILPYVRQPE EIIPGIPLYY ATAMPFRGSV RPLLVESHEG RPTKIEGNPD HPLSRGATGV FEQASLLNLY DPDRSQQVLR K GEPASWGD FVQFARSLAA EAGTKRLAVL CEPSSSPTLA ALRRELERRY AQVRWVTYRP EGDDHEALGL QQAFGRPVRA RY RFSEARV IVSLDADFLG PTDRNFVENT REFAASRRME RPEDEISRLY VIESTYTVTG GMADHRLRLR AGDIPAFAAA LAA ELGVGE LREAGARFAG HPYVVEIARD LRAAGARGVV LAGETQPPAV HALCAVINDL LGSLGRTVIL HALDEPATAQ HAAL AELVQ AMQAGAVDAL LLLNVNPVYD APAALGFAEA LAQVPEVIHL GLHVDETARR STWHLPSTHY LEAWGDGRAY DGTLS VIQP LIAPLYEAAH SPLEVLALLA TGEEQSAYDL VRNTWRRLLA GRGAFEQAWQ RVLHDGFLPD SGYPTVSLRP NRQALA DWP QAAEGGLEVV FRLDPTVLDG SFANNAWAQE LPDPITKIVW DNVAILSPKT AAALGVKAEY HKGVYIADVI ELSLDGR AV ELPVWVLPGH PDDSITVYLG YGREITSTRP ERKTPFFDLD DYTDIYGHGA IATGVGVNVA PLRRPDNTWV AYGAQVRK T GRTYKIVTTQ DHGSMVGRPL VRLATVEEFR KNPDFAKEAE PPLEGLEPWD QYPTLWEENH PSKQPAFQDS DYYRNQWAM VIDLNACTGC NACIVACDSE NNIPMVGKNE VGRGREMHWL RIDRYFVSDE AHADDPQIVV QPVPCMHCEN APCESVCPVA ATVHSPDGL NEMVYNRCIG TRYCSNNCPY KVRRFNWFNW VKTLPIQVQM AQNPDVTVRF RGVMEKCTYC VQRIREAQRQ A NIEKRPLR DGEVKTACQQ ACPAEAITFG DLNDPNNAVV KQRQNARRYE MLAALNVKPR TSYLARITNP NPRLLEQEPV A

UniProtKB: Fe-S-cluster-containing hydrogenase

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Macromolecule #3: Polysulphide reductase NrfD

MacromoleculeName: Polysulphide reductase NrfD / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 55.256566 KDa
SequenceString: MAHATKDLSA LARTDEEVLV QGGLTFHDIT ELVAQHTEKK TPKAWWAAFS VAFLGMLTLV AMLAYQVWNG VGVWGNNIPV GWGWPIVNF VFWVGIGHAG TLISAILFLF RQRWRTSINR AAEAMTIFAV ICALIFPTFH VGRVWAIYWT LPIPNQMEMW P QFKSPLLW ...String:
MAHATKDLSA LARTDEEVLV QGGLTFHDIT ELVAQHTEKK TPKAWWAAFS VAFLGMLTLV AMLAYQVWNG VGVWGNNIPV GWGWPIVNF VFWVGIGHAG TLISAILFLF RQRWRTSINR AAEAMTIFAV ICALIFPTFH VGRVWAIYWT LPIPNQMEMW P QFKSPLLW DVFAVSSYFI VSLVFWYVGL IPDLATLRDR AALMGRRLRA KILGFFALGW CGANRHWRNY EKVYMLLAGL AT PLVLSVH SVVSFDFAVS IIPGWHTTIF PPYFVAGAIF SGFAMVVTLM VIARKAYGLE NVITIDHLEK MNIIMLVTGT MVG FAYITE FFIAWYSGVP YEQYAFINRA TGPYAWAYWT MMSCNLIFPQ FFWIKKLRRN IPFMFIASIV VNIGMWFERF VITI TSLHR DYLPSSWDYF VPTWVDVLTL IGSFGLFFTL FLLFLRFVPM VAIAEVKGVL PEADPHFYET HGDGHSRPAE VQVNR GRSS

UniProtKB: Polysulphide reductase NrfD

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Macromolecule #4: ActD

MacromoleculeName: ActD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 23.796275 KDa
SequenceString: MLKELLRSLK ASMGIYEARD GSIYGLLAEF SDPAALLHAA RQVRKAGYRH FDAHSPFPIH GMDEAMGLGN SKVAFITFFT GTIAGFALA WWMQWWMGAV DYPLNISGKP FFALPPSVPI IFELTILFSA LAGVATMLAL NGLPRPYNPL FYSKNFMRVT D DGFFLFVA ...String:
MLKELLRSLK ASMGIYEARD GSIYGLLAEF SDPAALLHAA RQVRKAGYRH FDAHSPFPIH GMDEAMGLGN SKVAFITFFT GTIAGFALA WWMQWWMGAV DYPLNISGKP FFALPPSVPI IFELTILFSA LAGVATMLAL NGLPRPYNPL FYSKNFMRVT D DGFFLFVA ASDPKFDPTA TRQLLEQLGG YNIEVIEDRG EEDVTPATAP AAEAAVTTS

UniProtKB: DUF3341 domain-containing protein

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Macromolecule #5: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit

MacromoleculeName: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 23.336631 KDa
SequenceString: MQNITAMPRT IWTGLLLGLL LAGCRGMISS KPPVHPNLNM DFQEKFEAQE LNPFFADRRA MRPPVPGTVP RGLLKEDTPF YFGKTADGA YVERIPVAVT PELVARGRER YNIYCAVCHG QAGDGQGIIM RGNYGYTPAP SFHDDRLRNV EDGYIFDVIS H GVRNMPAY ...String:
MQNITAMPRT IWTGLLLGLL LAGCRGMISS KPPVHPNLNM DFQEKFEAQE LNPFFADRRA MRPPVPGTVP RGLLKEDTPF YFGKTADGA YVERIPVAVT PELVARGRER YNIYCAVCHG QAGDGQGIIM RGNYGYTPAP SFHDDRLRNV EDGYIFDVIS H GVRNMPAY GHQIPVADRW AIVAYVRALQ RSQHATAADV PEEVRARLQG E

UniProtKB: Quinol:cytochrome c oxidoreductase monoheme cytochrome subunit

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Macromolecule #6: ActF

MacromoleculeName: ActF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 48.536781 KDa
SequenceString: MAEVKANGFP GWLLDPLRPT REKAEPRYRL PEDVRIWAVP LAIGVGLLIV SLVGWAIDAR QFYFSYLVGW TFCLTLALGS LFFVMIQHL TRAQWVVAVR RLPEALVWTF PVLIVLFIPI LFGLHDLYHW THHELYDPSS PEYDPILAGK HAYLNVPFFL V RIAFYFFI ...String:
MAEVKANGFP GWLLDPLRPT REKAEPRYRL PEDVRIWAVP LAIGVGLLIV SLVGWAIDAR QFYFSYLVGW TFCLTLALGS LFFVMIQHL TRAQWVVAVR RLPEALVWTF PVLIVLFIPI LFGLHDLYHW THHELYDPSS PEYDPILAGK HAYLNVPFFL V RIAFYFFI WTLLAYKLYT LSVRQDVDPD PSIPAQQRKV SAWGMPLYGV TVAFASYDFL MSLDPHWYST IFGVYFFAGS FF VALGFIT TCYAILVRRG TLQGIVRAPH FQDLGKLMFG FTAFWAYIAF SQYMLIWYGN LPEETLWYRH RLEHGWEVLS QVL IWGHFV LPFLILLPWA AKRTPVLVGT MGIWFAIIHW IDLFWVAMPV LHTEHMTFHW LDVTCWLGLF GVVVGLFFYR ISRH SLVPQ NDPYLARSLA LH

UniProtKB: Quinol:cytochrome c oxidoreductase quinone-binding subunit 2

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Macromolecule #7: ActH

MacromoleculeName: ActH / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10) (bacteria)
Strain: ATCC 43812 / DSM 4252 / R-10
Molecular weightTheoretical: 20.219014 KDa
SequenceString:
MKRYPGLIGL LVVLVSVAGC RFYGYPGGVA LTLAQIEAAS EQVAQDLEQA LAELEALRLL ARRDETLAPY VAQYEAILEA HQQAVLEFE HWKEQVAAHP GDYRRANRTL GAITARHEAL LQQYADVAWA VAQHVNPALL ARAYTSSGPR FFFYVVPPQY A RQVNEQAV PPLQVVRYLA AQLS

UniProtKB: LemA family protein

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Macromolecule #8: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 8 / Number of copies: 6 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #9: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER

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Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 72.0 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: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 52386
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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