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- EMDB-7286: Cryo-EM density map of Alternative Complex III from Flavobacteriu... -

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Basic information

Entry
Database: EMDB / ID: EMD-7286
TitleCryo-EM density map of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)
Map dataStructure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type), primary map
Sample
  • Complex: ACIII-cyt aa3 supercomplex
    • Protein or peptide: x 4 types
  • Protein or peptide: x 2 types
  • Ligand: x 5 types
KeywordsElectron transport chain / triacylated cysteine / heme c domain / iron-sulfur cluster / MEMBRANE PROTEIN
Function / homology
Function and homology information


electron transfer activity / membrane => GO:0016020 / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Menaquinone reductase, multiheme cytochrome c subunit / 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 / Multiheme cytochrome c family profile. ...Menaquinone reductase, multiheme cytochrome c subunit / 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 / Multiheme cytochrome c family profile. / Cytochrome C oxidase, cbb3-type, subunit III / Multiheme cytochrome superfamily / Cytochrome c / 4Fe-4S dicluster domain / 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
Similarity search - Domain/homology
Uncharacterized protein / Cytochrome c, class I / 4Fe-4S ferredoxin, iron-sulfur binding domain protein / Polysulphide reductase, NrfD / Uncharacterized protein / Hypothetical lipoprotein
Similarity search - Component
Biological speciesFlavobacterium johnsoniae UW101 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBenlekbir S / Rubinstein JL
Funding support United States, Canada, 8 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01-HL16101 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41-GM104601 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM087519 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123455 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/Office of the DirectorOD019994 United States
Simons Foundation349247 United States
Canadian Institutes of Health Research (CIHR)MOP-81294 Canada
CitationJournal: Nature / Year: 2018
Title: Structure of the alternative complex III in a supercomplex with cytochrome oxidase.
Authors: Chang Sun / Samir Benlekbir / Padmaja Venkatakrishnan / Yuhang Wang / Sangjin Hong / Jonathan Hosler / Emad Tajkhorshid / John L Rubinstein / Robert B Gennis /
Abstract: Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII ...Alternative complex III (ACIII) is a key component of the respiratory and/or photosynthetic electron transport chains of many bacteria. Like complex III (also known as the bc complex), ACIII catalyses the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. However, the two complexes have no structural similarity. Although ACIII has eluded structural characterization, several of its subunits are known to be homologous to members of the complex iron-sulfur molybdoenzyme (CISM) superfamily , including the proton pump polysulfide reductase. We isolated the ACIII from Flavobacterium johnsoniae with native lipids using styrene maleic acid copolymer, both as an independent enzyme and as a functional 1:1 supercomplex with an aa-type cytochrome c oxidase (cyt aa). We determined the structure of ACIII to 3.4 Å resolution by cryo-electron microscopy and constructed an atomic model for its six subunits. The structure, which contains a [3Fe-4S] cluster, a [4Fe-4S] cluster and six haem c units, shows that ACIII uses known elements from other electron transport complexes arranged in a previously unknown manner. Modelling of the cyt aa component of the supercomplex revealed that it is structurally modified to facilitate association with ACIII, illustrating the importance of the supercomplex in this electron transport chain. The structure also resolves two of the subunits of ACIII that are anchored to the lipid bilayer with N-terminal triacylated cysteine residues, an important post-translational modification found in numerous prokaryotic membrane proteins that has not previously been observed structurally in a lipid bilayer.
History
DepositionDec 7, 2017-
Header (metadata) releaseFeb 28, 2018-
Map releaseMay 9, 2018-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.39
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.39
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6btm
  • Surface level: 0.39
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7286.png

Downloads & links

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Map

FileDownload / File: emd_7286.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type), primary map
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.39 / Movie #1: 0.39
Minimum - Maximum-1.6055999 - 5.340569
Average (Standard dev.)0.004662092 (±0.117458634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z281.600281.600281.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.6065.3410.005

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Supplemental data

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Additional map: 3.6-angstrom map for the Alternative Complex III: cyt...

Fileemd_7286_additional_1.map
Annotation3.6-angstrom map for the Alternative Complex III: cyt aa3 oxidase supercomplex from Flavobacterium johnsoniae
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3.6-angstrom map for the Alternative Complex III from...

Fileemd_7286_additional_2.map
Annotation3.6-angstrom map for the Alternative Complex III from Flavobacterium johnsoniae
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ACIII-cyt aa3 supercomplex

EntireName: ACIII-cyt aa3 supercomplex
Components
  • Complex: ACIII-cyt aa3 supercomplex
    • Protein or peptide: Alternative Complex III subunit A
    • Protein or peptide: Alternative Complex III subunit C
    • Protein or peptide: Alternative Complex III subunit D
    • Protein or peptide: Alternative Complex III subunit F
  • Protein or peptide: Alternative Complex III subunit B
  • Protein or peptide: Alternative Complex III subunit E
  • Ligand: HEME C
  • Ligand: FE3-S4 CLUSTER
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DECANOIC ACIDCapric acid
  • Ligand: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate

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Supramolecule #1: ACIII-cyt aa3 supercomplex

SupramoleculeName: ACIII-cyt aa3 supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #3-#4, #6
Details: Alternative complex III-- cytochrome aa3 oxidase supercomplex purified with styrene maleic acid copolymer
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria)

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Macromolecule #1: Alternative Complex III subunit A

MacromoleculeName: Alternative Complex III subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 48.23625 KDa
SequenceString: MKKVGNHNSI SRKLLLSLSL TLIFSLTSFA QDPAAAPAAT EAAAPAAASG GDPVKGKELF NANCAACHKL DAKSTGPALR GVASKHDMA WIYKWVHNSS DMIKSGDPVA VKLFEENNKA VMTSFPQLST GDIDNIIAYT SEVKAEPAAA AGGAATPPGT N VEGGGISN ...String:
MKKVGNHNSI SRKLLLSLSL TLIFSLTSFA QDPAAAPAAT EAAAPAAASG GDPVKGKELF NANCAACHKL DAKSTGPALR GVASKHDMA WIYKWVHNSS DMIKSGDPVA VKLFEENNKA VMTSFPQLST GDIDNIIAYT SEVKAEPAAA AGGAATPPGT N VEGGGISN NIILGALALV MAILVVMLFM VNKVLTKVAS NNGIEVAPKE GRTPIWKAFA KNQFLVLVTS IFLLLASGYF VY GYLMQVG VDQNYEPIQP IHYSHKIHAG DNEINCKYCH SAARVSKTAG IPSLNVCMNC HKNISEVAET TATAEYSKAF YDA QIQKLY DAVGWDKTKQ AYTGKTQPVK WVRIHNLPDF VYFNHSQHVS VAGVECQTCH GPVQEFEIMK QYSKLTMGWC VDCH RKTDV KMEGNAYYEK IHAELSKKYG VEKLTAAQMG GLECGKCHY

UniProtKB: Cytochrome c, class I

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Macromolecule #2: Alternative Complex III subunit B

MacromoleculeName: Alternative Complex III subunit B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 102.911984 KDa
SequenceString: CEGPVHKSIP YVLQPEQIIP GVADYYATTV FDGFDFANLL VKTREGRPIK IENNTIAGAK FSANARIHAS ILGLYDSMRL KEPKLDGKN SSWSAVDLKI KSSLADAKAK GGQVVLLTNT LASPTTEKLI GEFIAKNPNA KHVVYDAVSS SDALDAFETV Y GERALVDY ...String:
CEGPVHKSIP YVLQPEQIIP GVADYYATTV FDGFDFANLL VKTREGRPIK IENNTIAGAK FSANARIHAS ILGLYDSMRL KEPKLDGKN SSWSAVDLKI KSSLADAKAK GGQVVLLTNT LASPTTEKLI GEFIAKNPNA KHVVYDAVSS SDALDAFETV Y GERALVDY DFSKASLIVS VGADFLGDWQ GGGYDAGYAK GRIPQNGKMS RHFQFESNMT LSGAAADKRV PMTTADQKQA LV QIYNIVV GASVPVSLDA KFKAEVVKAA QQLKAAGTKG ILVSGIEDKN AQLLVLAINQ ALASEAFSTA GTRQIRKGSN AVV AQLIKD MNAGSVHTLI MSGVNPVYTL ADSASFVSGL KKVKTSVAFS LKEDETAAVS TIAAAAPHYL ESWGDVEITK GTYS LTQPT IRPIFDTKQF QDVLLSVNGT PGNFYDYLKA NSGAIIAGSS WNKVLHDGIF VVGSAALAGG SYDFAGAASL LSKAK SSGE LELVLYTKTG MGDGQHANNP WLQEFPDPIT RVSWDNYVTV SNADAKKFNL SNEIVANGGL NGSYATITTA DGNKLE NVP VIVQPGQAVG TVGLAVGYGR KAALKEEMQV GINAYALYKN FNSVQSITLA KANGEHEFAC VQGQKTLMGR GDIIKET TL EIFNTQDAKH WNEQPMVSLD HQEVEATTVD LWESFDRTTG HHFNLSIDLN ACTGCGACVI ACHAENNVPV VGKAEVRR S RDMHWLRIDR YYSSESTFEG DNERKEGIAG LSSSLSTFNE MEKPGDNPQV AFQPVMCQHC NHAPCETVCP VAATSHGRQ GQNHMAYNRC VGTRYCANNC PYKVRRFNWF LYNKNSEFDY HMNDDLGRMV LNPDVNVRSR GVMEKCSFCI QSTQAVILEA KRQGRVVGK DEFNNACACS AACSSGAMVF GDVNDKESEV AKLAESERMY HLLEHVGTKP NVFYHVKVRN

UniProtKB: 4Fe-4S ferredoxin, iron-sulfur binding domain protein

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Macromolecule #3: Alternative Complex III subunit C

MacromoleculeName: Alternative Complex III subunit C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 53.269992 KDa
SequenceString: MSSHYEAPIR KPLVIGDKSY HDVTVDVAAP VEGPANKQWW IVFTIALVAF LWGLGCIIYT VSTGIGTWGL NKTVGWAWDI TNFVWWVGI GHAGTLISAV LLLFRQRWRM AINRSAEAMT IFSVVQAGLF PIIHMGRPWL AYWVLPIPNQ FGSLWVNFNS P LLWDVFAI ...String:
MSSHYEAPIR KPLVIGDKSY HDVTVDVAAP VEGPANKQWW IVFTIALVAF LWGLGCIIYT VSTGIGTWGL NKTVGWAWDI TNFVWWVGI GHAGTLISAV LLLFRQRWRM AINRSAEAMT IFSVVQAGLF PIIHMGRPWL AYWVLPIPNQ FGSLWVNFNS P LLWDVFAI STYLSVSLVF WWTGLLPDFA MLRDRAITPF NKRVYSILSF GWSGRAKDWQ RFEEVSLVLA GLATPLVLSV HT IVSMDFA TSVIPGWHTT IFPPYFVAGA VFSGFAMVNT LLIVMRKVSN LEAYITLQHI ELMNIIIMIT GSIVGVAYIT ELF VAWYSG VEYEQYAFLN RATGPYWWAY WSMMTCNVFS PQFMWFKKLR TSIMFSFIIS IVVNIGMWFE RFVIIVTSLH RDYL PSSWT MFSPTFVDIG IFIGTIGFFF VLFLLYSRTF PVIAQAEVKT ILKGTGDNYI RERANKDSHH E

UniProtKB: Polysulphide reductase, NrfD

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Macromolecule #4: Alternative Complex III subunit D

MacromoleculeName: Alternative Complex III subunit D / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 19.72082 KDa
SequenceString:
MSNKVIYAIY NDDDVLMNAV KKTRAAHHHI EEVFTPFPVH GLDKAMGLAP TRLAICAFLY GCVGISVATT MMSYIMIHDW PQDIGGKPS FSFIQNMPSF VPIMFEMTVF FAAHLMVITF YMRSRLWPFK QAENPDVRTT DDHFLIEVAV NDNEAELVSF F EGTGAVEV KVIEKN

UniProtKB: Uncharacterized protein

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Macromolecule #5: Alternative Complex III subunit E

MacromoleculeName: Alternative Complex III subunit E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 18.17927 KDa
SequenceString:
CHNNSAPNYQ YFPNMYESVA YEPYTEAKIF KGGKEGQLPV EGTINRGFEP YEYENSTAGY ELAKANLKSP LTEEEKNSGK GKELFEIYC ISCHGAAGNG KGKLVEREKF LGVPSYKDRE ITEGSIFHVE TYGLNAMGSH ANQLSAHERW LVADYVLKLK S QL

UniProtKB: Hypothetical lipoprotein

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Macromolecule #6: Alternative Complex III subunit F

MacromoleculeName: Alternative Complex III subunit F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Flavobacterium johnsoniae UW101 (bacteria) / Strain: ATCC 17061 / DSM 2064 / UW101
Molecular weightTheoretical: 52.926332 KDa
SequenceString: MYTFSSKLKT FSIILMVLGL LGIGYGFLSA PKDIQEVEKI LAADAHGAHG TAHGESAEAS HKEAGHHEAA EASHEEHKGG EHAKVGAAD EHTEHLNHVL HQLQNKPWSA LYVACIFFLL LSMGVLAFYA IQQVAQAGWS PVLFRVMQGI TAYLPAGSII F FIILVLCG ...String:
MYTFSSKLKT FSIILMVLGL LGIGYGFLSA PKDIQEVEKI LAADAHGAHG TAHGESAEAS HKEAGHHEAA EASHEEHKGG EHAKVGAAD EHTEHLNHVL HQLQNKPWSA LYVACIFFLL LSMGVLAFYA IQQVAQAGWS PVLFRVMQGI TAYLPAGSII F FIILVLCG LHFNHIFVWL GEGVTDPKSP NYDAIIAGKS GYLNFPFWIV RAFIFLLGWN IYRHFSRKNC LAQDEANDDL YY KKNFKIS AGFLVFFIVS ESIMAWDWIM SFDPHWFSTL FAWYVFASFF VSGITSIALI TIYLKSKGYL EYVNTSHIHD LAK FMFGIS VFWTYLWFSQ FMLIWYANIP EEVTYFVTRI QLYNLPFFGA VVMNFVFPLL ILINTDFKRL NWVVVMAGIV ILLG HYVDF FNMIMPGTVG DKWFIGVPEI ASILFFLGLF IFVVFTALTK SPLLAKRNPF IEESKHFHY

UniProtKB: Uncharacterized protein

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Macromolecule #7: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 7 / Number of copies: 6 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #8: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 8 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 CLUSTER / Iron–sulfur cluster

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #10: DECANOIC ACID

MacromoleculeName: DECANOIC ACID / type: ligand / ID: 10 / Number of copies: 2 / Formula: DKA
Molecular weightTheoretical: 172.265 Da
Chemical component information

ChemComp-DKA:
DECANOIC ACID / Capric acid

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Macromolecule #11: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate

MacromoleculeName: (2S)-3-hydroxypropane-1,2-diyl ditetradecanoate / type: ligand / ID: 11 / Number of copies: 2 / Formula: FAW
Molecular weightTheoretical: 512.805 Da
Chemical component information

ChemComp-FAW:
(2S)-3-hydroxypropane-1,2-diyl ditetradecanoate

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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

Concentration3 mg/mL
BufferpH: 8
GridMaterial: GOLD
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 2017 / Average exposure time: 10.0 sec. / Average electron dose: 61.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3044
Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 164239

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6btm:
Structure of Alternative Complex III from Flavobacterium johnsoniae (Wild Type)

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