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- EMDB-10513: Structure of the NDH-1MS complex from Thermosynechococcus elongatus -

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Basic information

Entry
Database: EMDB / ID: EMD-10513
TitleStructure of the NDH-1MS complex from Thermosynechococcus elongatus
Map dataStructure of the NDH-1MS complex from Thermosynechococcus elongatus
Sample
  • Complex: NDH-1MS
    • Protein or peptide: x 18 types
  • Ligand: x 8 types
Keywordscarbon concentrating photosynthetic complex I / proton pump / MEMBRANE PROTEIN
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / transmembrane transporter complex / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / transmembrane transporter complex / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / electron transport coupled proton transport / NADH dehydrogenase activity / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / endomembrane system / aerobic respiration / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / extracellular space / membrane / plasma membrane
Similarity search - Function
NAD(P)H-quinone oxidoreductase subunit 5, organellar chromatophore 2 / CO2 hydration / CO2 hydration protein (ChpXY) / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NAD(P)H-quinone oxidoreductase subunit O / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N ...NAD(P)H-quinone oxidoreductase subunit 5, organellar chromatophore 2 / CO2 hydration / CO2 hydration protein (ChpXY) / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NAD(P)H-quinone oxidoreductase subunit O / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH-quinone oxidoreductase cyanobacterial subunit N / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / : / Fasciclin domain / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile. / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit N / Tlr0906 protein / NADH dehydrogenase subunit 4 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit 4L ...NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit N / Tlr0906 protein / NADH dehydrogenase subunit 4 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit 4L / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H-quinone oxidoreductase subunit 1 / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit M / Tll0220 protein / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria) / Thermosynechococcus elongatus (strain BP-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSchuller JM / Saura P
Funding support Germany, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)715311 Germany
German Research Foundation (DFG)836/3-2 Germany
German Research Foundation (DFG)836/4-1 Germany
German Research Foundation (DFG)836/1-1 Germany
CitationJournal: Nat Commun / Year: 2020
Title: Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.
Authors: Jan M Schuller / Patricia Saura / Jacqueline Thiemann / Sandra K Schuller / Ana P Gamiz-Hernandez / Genji Kurisu / Marc M Nowaczyk / Ville R I Kaila /
Abstract: Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, ...Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn active site, with connectivity to proton-pumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO conditions.
History
DepositionNov 27, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tjv
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10513.png

Downloads & links

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Map

FileDownload / File: emd_10513.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the NDH-1MS complex from Thermosynechococcus elongatus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 280 pix.
= 378. Å		1.35 Å/pix.
x 280 pix.
= 378. Å		1.35 Å/pix.
x 280 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.1075922 - 0.26671836
Average (Standard dev.)0.00010500534 (±0.0035816415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1080.2670.000

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Supplemental data

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Additional map: Structure of the NDH-1MS complex from Thermosynechococcus elongatus...

Fileemd_10513_additional.map
AnnotationStructure of the NDH-1MS complex from Thermosynechococcus elongatus (Local resolution filtered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NDH-1MS

EntireName: NDH-1MS
Components
  • Complex: NDH-1MS
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 1
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 2
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 3
    • Protein or peptide: NADH dehydrogenase subunit 4
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 4L
    • Protein or peptide: NADH dehydrogenase subunit 5
    • Protein or peptide: NADH dehydrogenase subunit 6
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit H
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit I
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit J
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit K
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit L
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit M
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit N
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit O
    • Protein or peptide: Tlr0906 protein
    • Protein or peptide: Tll0220 protein
    • Protein or peptide: Tlr0636 protein
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: BETA-CAROTENE
  • Ligand: CHLOROPHYLL A
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: NDH-1MS

SupramoleculeName: NDH-1MS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)

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Macromolecule #1: NAD(P)H-quinone oxidoreductase subunit 1

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 40.565984 KDa
SequenceString: MESGIDLQGQ FISALQSLGL SHDLAKLLWL PLPMLMMLIV ATVGVLVAVW LERKISAAVQ QRIGPEYIGP LGILAPLADG LKLIFKEDV LPANSDRWLF TLGPAVVVIP VFLSYIIVPF GQNLLISNLA MGVFLWIALS SIAPIGLLMA GYASNNKYSL L GGLRAAAQ ...String:
MESGIDLQGQ FISALQSLGL SHDLAKLLWL PLPMLMMLIV ATVGVLVAVW LERKISAAVQ QRIGPEYIGP LGILAPLADG LKLIFKEDV LPANSDRWLF TLGPAVVVIP VFLSYIIVPF GQNLLISNLA MGVFLWIALS SIAPIGLLMA GYASNNKYSL L GGLRAAAQ SISYEIPLAL AVLAVAMMSN GLGTVEIVEQ QSQYGILSWN VWRQPIGFLV FWIAALAECE RLPFDLPEAE EE LVAGYQT EYAGMKFALF YLGAYVNLVL SALLVSVLYF GGWSFPIPLE TIANLLGVSE TNPFLQIAFA VLGITMTLIK AYF FVFLAI LLRWTVPRVR IDQLLDLGWK FLLPVGLVNL LLTAGLKLAF PVAFGG

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 1

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Macromolecule #2: NAD(P)H-quinone oxidoreductase subunit 2

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 55.168543 KDa
SequenceString: MDLVTLAGQL NAGTILPETI LIVTLLVVLL ADLIQGRQAD RWTPYFAIVG LGGAIATMIP LWTQPATISF FGSFISDHLS LFFRGLIAL SALGTILMSI RYVEQTGSSL GEFMTILLTA TVGGMFIAGA QELVFIFVAL ETLSIASYLL TGYTKRDSRS N EAALKYLL ...String:
MDLVTLAGQL NAGTILPETI LIVTLLVVLL ADLIQGRQAD RWTPYFAIVG LGGAIATMIP LWTQPATISF FGSFISDHLS LFFRGLIAL SALGTILMSI RYVEQTGSSL GEFMTILLTA TVGGMFIAGA QELVFIFVAL ETLSIASYLL TGYTKRDSRS N EAALKYLL IGAASSAIFL YGSSLLYGLS GGHTQLPAIA QALSSESLGL VVALVFVIAG ISFKISAVPF HQWTPDVYEG AP TPVVAFL SVGSKAAGFA LAIRFLTLAF PSVTDQWQLI FTVLAILSMI LGNVVALAQT SMKRMLAYSS IGQAGFVMIG FVV GTEAGY ASMLFYLLVY LFMNLGAFTC VILFSLRTGT DQISEYAGLY QKDPLLTLGL SLCLLSLGGI PPLAGFFGKI YLFW AGWQA GAYGLVLLGL LTSVISIYYY IRVVKMMVVK EPQEMSEAVR NYPEVSWSSF GLRPLQVGLV MTVIATSLAG ILANP LFNL VNTAVWDVPQ LANQPTVMEV AYQALSPAGK S

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 2

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Macromolecule #3: NAD(P)H-quinone oxidoreductase subunit 3

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 15.013919 KDa
SequenceString:
MVAIPRLRDT ATVFVLSGYE YFLGFLIICS LVPVLALAAS ALLRPKSGRM IRLTTYESGM EPIGGAWIQF NVRYYMFALV FVIFDVETV FLYPWAVAFH QLGLLAFIEA LIFIAILVVA LVYAWRKRAL EWS

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 3

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Macromolecule #4: NADH dehydrogenase subunit 4

MacromoleculeName: NADH dehydrogenase subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 53.908137 KDa
SequenceString: MLHSLRFLPM LTLLIVLPVI GALLMPLLPE RVLRSVALVI AGLTFALSLW MLTQFDVHQS ALQFTEFVPW LLPLGLNYSL GVDGLSLPL IVLGTFLTLG VVFTGEKTGQ RLFYALVLLA NAGITGALAA QNLLLFFLFY ELELVPFYLL ILIWGGQRRE Q AAVKFLIY ...String:
MLHSLRFLPM LTLLIVLPVI GALLMPLLPE RVLRSVALVI AGLTFALSLW MLTQFDVHQS ALQFTEFVPW LLPLGLNYSL GVDGLSLPL IVLGTFLTLG VVFTGEKTGQ RLFYALVLLA NAGITGALAA QNLLLFFLFY ELELVPFYLL ILIWGGQRRE Q AAVKFLIY TAVSGILVLA AFLAMGWLTH APSFDSADIQ IAGLAPTTQG ILLLLLILGF GIKMPLVPLH SWLPDAYVEA ST PTAILLG GALAKLGAYG LVRFALGYFP EAWAQFSGLL AIVAAVGIAY GALAAIAQKD IKRMVAYSSI GHMSYVLLAA AAH THLSMV GAIAQMISHG LILALLFYLV GVIETKVGTR ELNVLNGLLN PLRGLPTTSA LLILGGMASA GIPGLVGFVA EFLI FQGSY GMFPLPTLVA VVGTGLTAVY FVIMINRTCF GRLDNRTAYY PRVVWSEKMP ALVLTLLIVF LGVQPTWLVR WSETT SAQI VAAVPRTNEL VATLAKR

UniProtKB: NADH dehydrogenase subunit 4

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Macromolecule #5: NAD(P)H-quinone oxidoreductase subunit 4L

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 4L / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 11.140265 KDa
SequenceString:
MQLTYVLILA ALLFCIGIYG LVTSRNAVRV LMSIELLLNA VNLNLIGFAN YLDGQQIKGQ VFAVFVITVA AAEAAVGLAI ILAIYRNRD TVDMEKFNLL KW

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 4L

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Macromolecule #6: NADH dehydrogenase subunit 5

MacromoleculeName: NADH dehydrogenase subunit 5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 66.283469 KDa
SequenceString: MLQSFADTVW LIPFYSLAGM VLSLIWSPGI TRKTGPRPAG YLNILLTFFS FVHALLATVA IANQPPQYLH WTWLDVAGLH LDIPVEISI LTTTALMLIT ALNLMAQVFA VGYMEMDWGW ARFFALLALF EGGMGALVLL DSLFFNYVVL EILTLATYLL I GLWFNQPL ...String:
MLQSFADTVW LIPFYSLAGM VLSLIWSPGI TRKTGPRPAG YLNILLTFFS FVHALLATVA IANQPPQYLH WTWLDVAGLH LDIPVEISI LTTTALMLIT ALNLMAQVFA VGYMEMDWGW ARFFALLALF EGGMGALVLL DSLFFNYVVL EILTLATYLL I GLWFNQPL VVTGARDAFL TKRVGDLVLL MGVLAIYPLA GSWNYDDLAA WAATAQVNST LITLICLALI AGPMGKCAQF PL HLWLDEA MEGPIPASIL RNAVVVATGA WVLVKLTPVL SLSPVALTAL LVIGSVTALG GTLIAIAQVD IKRALSYLVS AYM GWVFIA VGLKEPGLAF VFILTYSLAM AVLMMSIGSI IWNSVTQDLR LLGGLWSRRP ISGISFLVGS AGLLAVPPLA SFFP QAELL DTAFAQLPWV GGVLLLMNTF AAFSLGRTFC LVWGGEVKPM TARSPEVFWP MILPMTVDLG LVLHLPILMA RFDWV IWTQ PSLATAAALT ITALLGWGVA AWVYLGKAIP KPVQFPLPSV QNLLAYDFYT PKLYRATVVG VVDMISRITA WFDRTF VDG TGNAFGVVTL LGGDRLKYST TGQSQAYILT ILMGIAILVI AICWPLLA

UniProtKB: NADH dehydrogenase subunit 5

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Macromolecule #7: NADH dehydrogenase subunit 6

MacromoleculeName: NADH dehydrogenase subunit 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 21.580568 KDa
SequenceString: MDLATLTQTI TFFALAAAVI IAALGVVLLD NVVYSAFLLG GVFLSIAGLY ILMNADFVSA AQILIYVGAV NVLILFAIML VNKRETYTP VPGRWLRQGG AAVVSLGVFA LLTKMILQTP WQLSSVPPTP DSITTIGQHF FSDFLLPFEL ASVLLLMALI G AVVLARRE ...String:
MDLATLTQTI TFFALAAAVI IAALGVVLLD NVVYSAFLLG GVFLSIAGLY ILMNADFVSA AQILIYVGAV NVLILFAIML VNKRETYTP VPGRWLRQGG AAVVSLGVFA LLTKMILQTP WQLSSVPPTP DSITTIGQHF FSDFLLPFEL ASVLLLMALI G AVVLARRE LVLEPEPILG EEVVPPLELP ERPREPVALS EK

UniProtKB: NADH-quinone oxidoreductase subunit J

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Macromolecule #8: NAD(P)H-quinone oxidoreductase subunit H

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit H / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 45.271184 KDa
SequenceString: MPKIETRTEP MVINMGPHHP SMHGVLRLMV TLDGEDVIDC EPVIGYLHRG MEKIAENRTN IMFIPYVSRW DYAAGMFNEA VTVNAPEKL AGIPVPKRAS YIRVIMLELN RIANHLLWLG PFLADVGAQT PFFYIFRERE YIYDLFEAAT GMRFINNNYF R IGGVAADL ...String:
MPKIETRTEP MVINMGPHHP SMHGVLRLMV TLDGEDVIDC EPVIGYLHRG MEKIAENRTN IMFIPYVSRW DYAAGMFNEA VTVNAPEKL AGIPVPKRAS YIRVIMLELN RIANHLLWLG PFLADVGAQT PFFYIFRERE YIYDLFEAAT GMRFINNNYF R IGGVAADL TYGWVTKCRD FCDYFLPKVD EYERLITNNP IFVRRLQGVG KISREEAINW GLSGPMLRAS GVKWDLRKVD HY ECYDDFD WDVPVATEGD CLARYIVRIQ EMRESVKIIR QALDGLPGGP YENLEAKRML EGAKSEWNGF DYQYIGKKLS PTF KIPKGE HYVRVESGKG ELGIYLIGDD NVFPWRWKIR PPDFNNLQVL PQLLKGMKVA DIVAILGSID VIMGSVDR

UniProtKB: NAD(P)H-quinone oxidoreductase subunit H

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Macromolecule #9: NAD(P)H-quinone oxidoreductase subunit I

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit I / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 22.444801 KDa
SequenceString: MKFLNQITNY AKEAVQSAKY IGQGLSVTFD HMRRRPITVQ YPYEKLIPSE RFRGRIHFEF DKCIACEVCV RVCPINLPVV DWVFNKELK KKELKHYSID FGVCIFCANC VEYCPTNCLS VTEEYELATY DRHELNYDSV AMGRIPYKVT QDPMVTPIRE F AYLPAGVM ...String:
MKFLNQITNY AKEAVQSAKY IGQGLSVTFD HMRRRPITVQ YPYEKLIPSE RFRGRIHFEF DKCIACEVCV RVCPINLPVV DWVFNKELK KKELKHYSID FGVCIFCANC VEYCPTNCLS VTEEYELATY DRHELNYDSV AMGRIPYKVT QDPMVTPIRE F AYLPAGVM SGHDLPAGAQ RAGERPEAIA NTAKSSEN

UniProtKB: NAD(P)H-quinone oxidoreductase subunit I

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Macromolecule #10: NAD(P)H-quinone oxidoreductase subunit J

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit J / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 19.363789 KDa
SequenceString:
MSDTPEAPIV EAGPVGRLLQ SQNLSVESLG RDASGVEMIK VDRDRLLAVC QTLYADGFNY LRCQAAYDSG PGQDLVSTYH LIKLSDNAD RPPEVRIKVF VPRDDPRVPS VYWIWKTADW QERESYDMFG IVYEGHPNLK RILMPEDWVG WPLRKDYITP D FYELQEAY

UniProtKB: NAD(P)H-quinone oxidoreductase subunit J

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Macromolecule #11: NAD(P)H-quinone oxidoreductase subunit K

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit K / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 25.766998 KDa
SequenceString: MTNTTSPAIL NPIARPEVPQ ELAENIILTS LNDVYDWARL SSLWPLMYGT ACCFIEFAAM IGSRFDFDRF GLVPRNSPRQ ADLIITSGT ITMKMAPALV RLYEQMPSPK YVIAMGACTI TGGMFSSDSY SAVRGVDKLI PVDVYLPGCP PRPEAIMDAI V KLRKKIAN ...String:
MTNTTSPAIL NPIARPEVPQ ELAENIILTS LNDVYDWARL SSLWPLMYGT ACCFIEFAAM IGSRFDFDRF GLVPRNSPRQ ADLIITSGT ITMKMAPALV RLYEQMPSPK YVIAMGACTI TGGMFSSDSY SAVRGVDKLI PVDVYLPGCP PRPEAIMDAI V KLRKKIAN EHINERGNLA QTHRLFTAKH KMKPVPPILT GQYLNAPSRQ APPPALAAAM GIAVPALGEA VSETTSVAE

UniProtKB: NAD(P)H-quinone oxidoreductase subunit K

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Macromolecule #12: NAD(P)H-quinone oxidoreductase subunit L

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit L / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 8.575137 KDa
SequenceString:
MAVSTELLVL GVYGALAGLY LLVVPAIVYA YLNARWYVAS SFERAFMYFL VTFFFPGLLL LAPFINFRPQ PRSLNS

UniProtKB: NAD(P)H-quinone oxidoreductase subunit L

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Macromolecule #13: NAD(P)H-quinone oxidoreductase subunit M

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit M / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 12.584056 KDa
SequenceString:
MLLKSTTRHV HIYAGHVVDG EVHPDTETLT LNVDPDNELE WNEAALAKVE AKFRELVANA AGEDLTEYNL RRIGSDLEHF IRSLLMQGE IGYNLNSRVR NYSLGIPRVN HS

UniProtKB: NAD(P)H-quinone oxidoreductase subunit M

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Macromolecule #14: NAD(P)H-quinone oxidoreductase subunit N

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit N / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 16.656182 KDa
SequenceString:
MGLLAGYQFV KDLESAGALA LFVPPEGGFE GRYQRRLRSK GYTTLPMSAP GLGDLAAYLT QEHGIRPAHT GKEDIRVYFQ PPLVTYHLE NLPPNAKGLV LWLIDGKRLS KQEFAYLAQL TQTLPKFKVV VEVGGDRVVR WEPLADWVAA A

UniProtKB: NAD(P)H-quinone oxidoreductase subunit N

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Macromolecule #15: NAD(P)H-quinone oxidoreductase subunit O

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit O / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 7.877076 KDa
SequenceString:
MAIKKGDLVK VVAEKLANSL EALASDHRYP PYLFEGRGEV VDIRGDYAQI KFPVPTPTVW LRLDQLEVAQ

UniProtKB: NAD(P)H-quinone oxidoreductase subunit O

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Macromolecule #16: Tlr0906 protein

MacromoleculeName: Tlr0906 protein / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 51.00343 KDa
SequenceString: MVQAMERPSS AKLPPLDHPL ADIIYRLEAG GALIPDTPVN LMKIIGMYKA YSIPMDFYWR DLLYLGERVF INPFPFFKYF PTKEYFELP NHYAGDTADL RIWRGPAHAH PELMEFIEKG ETGKMPRLLH HLWHDRINME FSEDLARAMM WHRMGGQLDI Y LDSEEYKA ...String:
MVQAMERPSS AKLPPLDHPL ADIIYRLEAG GALIPDTPVN LMKIIGMYKA YSIPMDFYWR DLLYLGERVF INPFPFFKYF PTKEYFELP NHYAGDTADL RIWRGPAHAH PELMEFIEKG ETGKMPRLLH HLWHDRINME FSEDLARAMM WHRMGGQLDI Y LDSEEYKA AADKAIRAYF KRNPLMLGLY KLFPDLFLEQ ARQATYMNVL GLFWEVMAPV FFEISDRYDE GSITSVKDAM NF LVNGIFA IAGRPIYHHV YIDDEVHVLV PKEKGFMWLY EAAFPYVEAV FYRTSPFRGT KSYNAQANQV PTDQVDFHYG ILF ADKFPV GTAGIPPTLL HQDMYHFLPQ YLKDYFHQHC RGEDDILVQL GIAFQHAMYT VTSAVLQATR AAFYYPLDDP NPEH LMANR RFFVAQMDRF LRPQYGIAEA CKIRNVQDPN YL

UniProtKB: Tlr0906 protein

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Macromolecule #17: Tll0220 protein

MacromoleculeName: Tll0220 protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 15.785082 KDa
SequenceString:
MATIVDIAVN TPGFSTLVTA VKVANLVEAL QSPGPFTVFA PNDDAFAKLP DGTITSLVQN PPQLGRILKY HVVAGAYKAT DLKRMGIVT SLEGSTIPIH GDNPLEVKNA TVLAADIEAE NGIIHVIDTV ILMGLDPAHS FQETNIPYKV

UniProtKB: Tll0220 protein

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Macromolecule #18: Tlr0636 protein

MacromoleculeName: Tlr0636 protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Molecular weightTheoretical: 12.462559 KDa
SequenceString:
MIRPIADTYP LLPLSKAQMG QRQEIINSHK RLWDKTMATD LIMTILPGMT VKVTNPNDTY YQFQGIVQRI TDGKVAVLFE GGNWDKLVT FQASELEPVV VTPKEKAKAK K

UniProtKB: Tlr0636 protein

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Macromolecule #19: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 19 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #20: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 20 / Number of copies: 2 / Formula: PGT
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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Macromolecule #21: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 21 / Number of copies: 5 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 1 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #23: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 23 / Number of copies: 1 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #24: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 24 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #25: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 25 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #26: water

MacromoleculeName: water / type: ligand / ID: 26 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.2 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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170151
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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