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- EMDB-0849: cryo-EM structure of cyanobacteria Fd-NDH-1L complex -

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Basic information

Entry
Database: EMDB / ID: EMD-0849
Titlecryo-EM structure of cyanobacteria Fd-NDH-1L complex
Map dataNone
Sample
  • Complex: Fd-NDH-1L complex
    • Protein or peptide: x 20 types
  • Ligand: x 8 types
Keywordsphotosystem I / cyclic electron transfer / PHOTOSYNTHESIS
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 / electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NAD(P)H-quinone oxidoreductase subunit O / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L ...Protein of unknown function DUF2996 / Protein of unknown function (DUF2996) / NADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NAD(P)H-quinone oxidoreductase subunit O / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / 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 / NADH-quinone oxidoreductase chain 4 / 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 / Ferredoxin [2Fe-2S], plant / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 2Fe-2S ferredoxin, iron-sulphur binding site / 2Fe-2S ferredoxin-type iron-sulfur binding region signature. / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-plastoquinone oxidoreductase, chain 5 subgroup / 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 / Beta-grasp domain superfamily / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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
Ferredoxin-1 / 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 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit 4L ...Ferredoxin-1 / 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 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase chain 4 1 / 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 / Tlr0472 protein / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O / Proton-translocating NADH-quinone dehydrogenase subunit P NdhP / Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang C / Shuai J
CitationJournal: Nat Commun / Year: 2020
Title: Structural insights into NDH-1 mediated cyclic electron transfer.
Authors: Chunli Zhang / Jin Shuai / Zhaoxing Ran / Jiaohong Zhao / Zhenfang Wu / Rijing Liao / Jian Wu / Weimin Ma / Ming Lei /
Abstract: NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution ...NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment.
History
DepositionNov 2, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6l7o
  • Surface level: 0.038
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0849.png

Downloads & links

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Map

FileDownload / File: emd_0849.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å		1.09 Å/pix.
x 300 pix.
= 327. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.16719173 - 0.4012762
Average (Standard dev.)0.000029895496 (±0.008296943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 327.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z327.000327.000327.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1670.4010.000

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Supplemental data

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Sample components

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Entire : Fd-NDH-1L complex

EntireName: Fd-NDH-1L complex
Components
  • Complex: Fd-NDH-1L complex
    • 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: NAD(P)H-quinone oxidoreductase chain 4 1
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 4L
    • Protein or peptide: NADH dehydrogenase subunit 5
    • Protein or peptide: NADH-quinone oxidoreductase subunit J
    • 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: NAD(P)H-quinone oxidoreductase subunit P
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit Q
    • Protein or peptide: Ferredoxin-1
    • Protein or peptide: Tlr0636 protein
    • Protein or peptide: Tlr0472 protein
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: Digitonin
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Fd-NDH-1L complex

SupramoleculeName: Fd-NDH-1L complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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: NAD(P)H-quinone oxidoreductase chain 4 1

MacromoleculeName: NAD(P)H-quinone oxidoreductase chain 4 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 57.847504 KDa
SequenceString: MSTFPWLTTI ILFPIVAALA IPFIPDPTGK GRPIRWYALA VGLIDFALIV YAFTNFYDLN TPGMQLWESY DWIPEIGLRW SVGADGLSM PLILLTGFIT TLAILAAWPV TLKPRLFYFL MLAMYGGQIA VFAVQDMLVF FLAWELELIP VYLLLAIWGG H KRQYAATK ...String:
MSTFPWLTTI ILFPIVAALA IPFIPDPTGK GRPIRWYALA VGLIDFALIV YAFTNFYDLN TPGMQLWESY DWIPEIGLRW SVGADGLSM PLILLTGFIT TLAILAAWPV TLKPRLFYFL MLAMYGGQIA VFAVQDMLVF FLAWELELIP VYLLLAIWGG H KRQYAATK FILYTAGSSL FILVAGLAMA FYGDTVSFDM QTLAAKDYAL GFQLLVYAGF LVAYGVKLPI VPLHTWLPDA HG EATAPVH MLLAGILLKM GGYALIRMNV DMLPAAHAKF APVLVILGVV NIIYAALTSY AQRNLKRKIA YSSISHIGFV LIG IASFTN LGMSGAVLQM VSHGLIGASL FFLVGATYDR THTLILEEMG GVGQKMKKIF AMFTACSLAS LALPGMSGFV AELM VFIGF ATSDAYSLPF RVIVVFLAAV GVILTPIYLL SMLREIFYGP ENKELVEHEA LVDAEPREVF IIACLLVPII GIGLY PKLL TQIYDATTGQ VIARAREVLP TLAQQTEQPL GILPMVAPQL KANAQ

UniProtKB: NAD(P)H-quinone oxidoreductase chain 4 1

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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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 72.025352 KDa
SequenceString: MEPLYQYAWL IPVLPLLGAL IVGFGLIAFS ETTSKLRRPS AIFIMALMAI AMGHSLTLFW SQVQGHLPYT QMIEWAAAGN LHIAMGYVI DPLAALMLVI VTTVAFLVML YSDGYMAHDP GYVRFFAYLS LFGSSMLGLV VSPNLVQVYI FWELVGMCSY L LIGFWYDR ...String:
MEPLYQYAWL IPVLPLLGAL IVGFGLIAFS ETTSKLRRPS AIFIMALMAI AMGHSLTLFW SQVQGHLPYT QMIEWAAAGN LHIAMGYVI DPLAALMLVI VTTVAFLVML YSDGYMAHDP GYVRFFAYLS LFGSSMLGLV VSPNLVQVYI FWELVGMCSY L LIGFWYDR KSAAEAAQKA FVTNRVGDFG LLLGMVGLFW ATGTFDFAGM GDRLTELVNT GLLSPSLAAI LAILVFLGPV AK SAQFPLH VWLPDAMEGP TPISALIHAA TMVAAGVFLI ARMFPVFEQL PQVMTTIAWT GAFTAFMGAT IAITQNDIKK SLA YSTISQ LGYMVMGMGV GAYSAGLFHL MTHAYFKAML FLGSGSVIHS MEGVVGHNPD LAQDMRYMGG LRKYMPITGA TFLV GCLAI SGVPPFAGFW SKDEILGAVF HANPAMWLLT WLTAGLTAFY MFRMYFMTFE GKFRNVPPER QEHHDHHSHH AAVPH ESPW TMTLPLVVLA IPSTLIGFVG TPFNNLFEVF IHAPGEEKVA EHAVDLTEFL ILGGSSVGIG LMGITVAYLM YLKGTP SPQ AIAKAIQPLY QFSLHKWYFD ELYEAVFIKG CRRLARQVLE VDYNVVDGVV NLTGFVTMVT GEGLKYLQNG RAQFYAL IV LLAVLGFVIF SVQT

UniProtKB: NADH dehydrogenase subunit 5

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Macromolecule #7: NADH-quinone oxidoreductase subunit J

MacromoleculeName: NADH-quinone oxidoreductase subunit J / 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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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 BP-1 (bacteria) / Strain: BP-1
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: NAD(P)H-quinone oxidoreductase subunit P

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit P / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 4.878649 KDa
SequenceString:
MDAVISVKPI LLAMTPVFIL LCLFFGTRNG FYDTDQYHGN GSAH

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Macromolecule #17: NAD(P)H-quinone oxidoreductase subunit Q

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit Q / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 4.844698 KDa
SequenceString:
MATDFNRGIM KFDGADSPAM IAISAVLILG FIAGLIWWAL HTAYA

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Macromolecule #18: Ferredoxin-1

MacromoleculeName: Ferredoxin-1 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 10.853959 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MATYKVTLVR PDGSETTIDV PEDEYILDVA EEQGLDLPFS CRAGACSTCA GKLLEGEVDQ SDQSFLDDDQ IEKGFVLTCV AYPRSDCKI LTNQEEELY

UniProtKB: Ferredoxin-1

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Macromolecule #19: Tlr0636 protein

MacromoleculeName: Tlr0636 protein / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
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 #20: Tlr0472 protein

MacromoleculeName: Tlr0472 protein / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 16.016489 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MAVACKGECY HAEEMVPCRS AMAEETPTQA PKKEKPPAIE DKPFAEFINE AFLPALKNAL SAKVGDVTLR LEGNTVMGEW GKGMYQFRL YFLEGNIQGP KVFVCSSGGI APSTLEPFLG DERKVTLDLL VFGVMQRLNG QKWLGGN

UniProtKB: Tlr0472 protein

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Macromolecule #21: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 21 / Number of copies: 3 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 9 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM

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Macromolecule #23: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 23 / 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 #24: Digitonin

MacromoleculeName: Digitonin / type: ligand / ID: 24 / Number of copies: 60 / Formula: AJP
Molecular weightTheoretical: 1.229312 KDa
Chemical component information

ChemComp-AJP:
Digitonin / detergent*YM

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Macromolecule #25: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 25 / Number of copies: 1 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #26: 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: 26 / Number of copies: 4 / 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 #27: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 27 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #28: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 28 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) 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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338822
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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