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- EMDB-0936: Cryo-EM structure of the air-oxidized photosynthetic alternative ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0936
TitleCryo-EM structure of the air-oxidized photosynthetic alternative complex III from Roseiflexus castenholzii
Map data
Sample
  • Complex: Air-oxidized alternative complex III
    • Protein or peptide: MULTIHEME_CYTC domain-containing protein
    • Protein or peptide: Fe-S-cluster-containing hydrogenase components 1-like protein
    • Protein or peptide: Polysulphide reductase NrfD
    • Protein or peptide: Uncharacterized protein ActD
    • Protein or peptide: Uncharacterized protein ActF
  • Protein or peptide: Cytochrome c domain-containing protein
  • Ligand: HEME C
  • Ligand: [(2S)-2-octadecanoyloxypropyl] octadecanoate
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER
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 / 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
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 (strain DSM 13941 / HLO8) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShi Y / Xin YY / Wang C / Blankenship RE / Sun F / Xu XL
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31570738 China
National Natural Science Foundation of China (NSFC)31400630 China
National Natural Science Foundation of China (NSFC)31870740 China
Ministry of Science and Technology (MoST, China)2017YFA0504700 China
Chinese Academy of SciencesXDB08030202 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, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateNov 4, 2020-
Current statusNov 4, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6lod
  • Surface level: 0.0398
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0936.png

Downloads & links

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Map

FileDownload / File: emd_0936.map.gz / Format: CCP4 / Size: 28.7 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 196 pix.
= 203.84 Å		1.04 Å/pix.
x 196 pix.
= 203.84 Å		1.04 Å/pix.
x 196 pix.
= 203.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0398 / Movie #1: 0.0398
Minimum - Maximum-0.16421944 - 0.3866216
Average (Standard dev.)0.0022115703 (±0.012172763)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 203.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z203.840203.840203.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.1640.3870.002

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Supplemental data

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Sample components

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Entire : Air-oxidized alternative complex III

EntireName: Air-oxidized alternative complex III
Components
  • Complex: Air-oxidized alternative complex III
    • Protein or peptide: MULTIHEME_CYTC domain-containing protein
    • Protein or peptide: Fe-S-cluster-containing hydrogenase components 1-like protein
    • Protein or peptide: Polysulphide reductase NrfD
    • Protein or peptide: Uncharacterized protein ActD
    • Protein or peptide: Uncharacterized protein ActF
  • Protein or peptide: Cytochrome c domain-containing protein
  • Ligand: HEME C
  • Ligand: [(2S)-2-octadecanoyloxypropyl] octadecanoate
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE3-S4 CLUSTER

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Supramolecule #1: Air-oxidized alternative complex III

SupramoleculeName: Air-oxidized alternative complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)

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Macromolecule #1: MULTIHEME_CYTC domain-containing protein

MacromoleculeName: MULTIHEME_CYTC domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 26.076992 KDa
SequenceString: MLERRPMAQV FDRRANTLAR VSIFAGIPLV LAILGGVWWL FGWSDWHRDV GVEIPQPGGG FNHQLHVALG MDCRYCHTAV EVSAHANIP PTETCMGCHS QIISRSEKVA FVWQSWETGT SIQWNKVHDL PKFVYFNHSI HVAKGVGCST CHGRIDQMRV V YKTQPLFM ...String:
MLERRPMAQV FDRRANTLAR VSIFAGIPLV LAILGGVWWL FGWSDWHRDV GVEIPQPGGG FNHQLHVALG MDCRYCHTAV EVSAHANIP PTETCMGCHS QIISRSEKVA FVWQSWETGT SIQWNKVHDL PKFVYFNHSI HVAKGVGCST CHGRIDQMRV V YKTQPLFM SWCLDCHRNP EKYVRPREEV FNMAWTPPPN QLEVGRRLVQ EYEIRSSWEL TNCAICHR

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Macromolecule #2: Fe-S-cluster-containing hydrogenase components 1-like protein

MacromoleculeName: Fe-S-cluster-containing hydrogenase components 1-like protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 102.515883 KDa
SequenceString: CQFALKQPQE KIVPYVRQPE EIIHGRPLFF ATAVTFAGFG VGLLVESHEG RPTKIEGNPD HPASLGSTDL ITQAMILTMY DPDRSQAPT NAGQETTWDA FVAAATAAMQ AQTAKQGAGL RVLSGSLTSP TLIAQKQQLL TQFPQAKWYE YEPVGRDNAN A GARLAFGA ...String:
CQFALKQPQE KIVPYVRQPE EIIHGRPLFF ATAVTFAGFG VGLLVESHEG RPTKIEGNPD HPASLGSTDL ITQAMILTMY DPDRSQAPT NAGQETTWDA FVAAATAAMQ AQTAKQGAGL RVLSGSLTSP TLIAQKQQLL TQFPQAKWYE YEPVGRDNAN A GARLAFGA DVHTIYRLDT AKVIVGFDAD FTAPSPTGVR MARQLADGRR IRKGTKEVNR LYLAESTPSI TGLLADHRLP VR SSQIEHL VRALATLVGV PNVAAGAPLS DTEKKWVEAA AKDLQANRGA CVVLVGESQP PVVHALGHAI NAQLGNVGST VVY TEPVED DPSGGIAALS ALTQEMNAGT VEVLLMIESN PVYNAPADIP FAEALAKVPL SMHVGLYRDE TAQQSVWHIN GAHF LEAWG DVRAFDGTTT IVQPLIAPLY NGKSAIEVLN VLLGKPQETG YQTLTAYWQT QDASGNFRVF WNTALHDGVI TATQA RSRQ VTLQQGFADA APPAPTQGLE IVFRPDPSLW DGAFANNAWL QETPKPYTKL TWDNVALMSV RTANALGLKN GDVVRL TYQ GRSVDAPVWV QPGHADDSVT VHFGFGRTAA GRVGNNVGFN AYRLRTSATP WFGVGLEVAK VGENYKLAST QGHFLME GR KKDLVRYGTL AEYVEDEKFL QVEKEEPISL IGEYEYNGYK WGMSIDLNVC NSCNACVVAC QSENNIPVVG KDEVWLGR E MHWIRIDQYY VGDEHTPNVY NMVMLCQQCE HAPCEIVCPV AATVHDAEGL NNMVYNRCVG TKYCSNNCPY KVRRFNFLQ YQDVPYRSPI DASTENDSIP VLKMMRNPDV TVRARGVMEK CTFCVQRINE ARIQARTENR RIADGEIMTA CQQVCPTQAI VFGDLNDPQ ARVVDLKEQP LKYTSLDKLN TKPRVSYLAK IKNLNPDLAE EKTA

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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: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 53.938129 KDa
SequenceString: MASQPAQKSA YGKMLEELLG PKQTYESVTR TIGDIVLTPI RKTPWGWPVG FVIAALGLLM YLFSLAVLFT VGVGVWGINI PVAWGFDII NFVWWIGIGH AGTLISAILL LFRQDWRTSI NRAAEAMTIF AVACAGIYPL VHTGRPWLDY WMLPYPGTLG M WPQFRSAL ...String:
MASQPAQKSA YGKMLEELLG PKQTYESVTR TIGDIVLTPI RKTPWGWPVG FVIAALGLLM YLFSLAVLFT VGVGVWGINI PVAWGFDII NFVWWIGIGH AGTLISAILL LFRQDWRTSI NRAAEAMTIF AVACAGIYPL VHTGRPWLDY WMLPYPGTLG M WPQFRSAL EWDVFAISTY ATVSILFWYL GLIPDLASLR DRATNIWVKR FYGFLALGWR GGARDWNRYE VASLILAGLS TP LVLSVHS IISLDFAISQ LPGWHVTVFP PYFVAGAVYC GFAMVILLLV PLRRWYKLHD LITIKHFDLM GKVMLASGLV VAY GYFAEI FYAWYSANIY EYFLITNRTM GPYAWSYWAL IVLNVAIPQL LWFKRFRVSL PWLFFISICI NIGMWFERWV IIVL SLHRD FLPSSWGYYT PSVWDISLYA GSFGWFFFLF FLFIRLLPAI SIFEVRDLVH KTETEKALAH GSAGHH

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Macromolecule #4: Uncharacterized protein ActD

MacromoleculeName: Uncharacterized protein ActD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 21.070332 KDa
SequenceString: MLKRNARQPK ALKVSTGPTL YGLMAEFDDA EALLAAAEKT RDAGYKQFEA YTPMPIHGLD EAVGYRGTRL PWVIFGAGLL GASGMFALQ TWINLVEYPL NIGGRPLFSW PAFIPATFEG MVLLSAFAAV FGMIAACGLP RPYHPVFNAP NFERASVDRF F LCIEAADP ...String:
MLKRNARQPK ALKVSTGPTL YGLMAEFDDA EALLAAAEKT RDAGYKQFEA YTPMPIHGLD EAVGYRGTRL PWVIFGAGLL GASGMFALQ TWINLVEYPL NIGGRPLFSW PAFIPATFEG MVLLSAFAAV FGMIAACGLP RPYHPVFNAP NFERASVDRF F LCIEAADP KFELKQTRQF LESLGPLAVS TVDN

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Macromolecule #5: Cytochrome c domain-containing protein

MacromoleculeName: Cytochrome c domain-containing protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 18.252623 KDa
SequenceString:
(ACE)CHLEMYDQA KYKPQQASEI FADGASARPL VEHTVARGRL RIDATSTGRV DGDPNGAYVT TIPIRITPEL LERGAQ RYR IYCAVCHGVN GNGRGQVGLL LNPRPPSFYD QRLLDMPDGE YYDVLVNGRR TMYPYGYRVQ SISDRWAIVA HIRELQK NP PPQN

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Macromolecule #6: Uncharacterized protein ActF

MacromoleculeName: Uncharacterized protein ActF / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Roseiflexus castenholzii (strain DSM 13941 / HLO8) (bacteria)
Molecular weightTheoretical: 46.545816 KDa
SequenceString: MIAQEPAALR PALGRLQQVA LIVGGVAMLL AVAGAFLGAA QFFHSYIFAY FFWMALSLGG LLVLMINHLT QGVWGLMLRR LLEAAALTL PLMAILFLPI AAETLMGTHY LFPWTNPEVV ANDEVVALKT PYLNVPFFLA RAVIYFVLFI GMAYLLRQWS L EEDAKGFS ...String:
MIAQEPAALR PALGRLQQVA LIVGGVAMLL AVAGAFLGAA QFFHSYIFAY FFWMALSLGG LLVLMINHLT QGVWGLMLRR LLEAAALTL PLMAILFLPI AAETLMGTHY LFPWTNPEVV ANDEVVALKT PYLNVPFFLA RAVIYFVLFI GMAYLLRQWS L EEDAKGFS DDLRGRFQRL SGPGIVVLVM AWTFAATDWG MSLEPEWFSS MYPVTYIASM LILTFGGGII ALAVLKSRNL LP FGIPVDR LHDLGKFLFA FVAVWAYVNF SEYLIIWSGN VPELTPWHGH RSAGGWEILG IVMIFGHFLL PFMLLLSRFA KRR LANLTA IAIYLYLIEI VWYFWKIMPA FHPDGFHIHW LDLVTLIAIG GLWLGVFAWN LQRAPLLAPN DYRVPLLRRQ EASG HGHGH HGKATAEHH

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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

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Macromolecule #8: [(2S)-2-octadecanoyloxypropyl] octadecanoate

MacromoleculeName: [(2S)-2-octadecanoyloxypropyl] octadecanoate / type: ligand / ID: 8 / Number of copies: 2 / Formula: EL6
Molecular weightTheoretical: 609.018 Da
Chemical component information

ChemComp-EL6:
[(2S)-2-octadecanoyloxypropyl] octadecanoate

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #10: FE3-S4 CLUSTER

MacromoleculeName: FE3-S4 CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: F3S
Molecular weightTheoretical: 295.795 Da
Chemical component information

ChemComp-F3S:
FE3-S4 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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 59.0 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

Particle selectionNumber selected: 257815
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 177489
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING

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