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- EMDB-0425: T.elongatus NDH (data-set 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-0425
TitleT.elongatus NDH (data-set 2)
Map datapixel spacing resized to match EMD-415
Sample
  • Complex: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus
    • Protein or peptide: x 17 types
  • Protein or peptide: x 1 types
  • Ligand: x 1 types
Keywordsphotosynthesis / bioenergetics / membrane protein complex / OXIDOREDUCTASE
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase 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 / transmembrane transporter complex / NADH dehydrogenase activity ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase 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 / transmembrane transporter complex / 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 / membrane / plasma membrane
Similarity search - Function
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 ...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 / 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-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 / [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 / 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 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 / 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
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria) / Thermosynechococcus elongatus (strain BP-1) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLaughlin TG / Bayne A
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-O5CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM007232-38 United States
Department of Energy (DOE, United States)DE-SC00016240 United States
CitationJournal: Nature / Year: 2019
Title: Structure of the complex I-like molecule NDH of oxygenic photosynthesis.
Authors: Thomas G Laughlin / Andrew N Bayne / Jean-François Trempe / David F Savage / Karen M Davies /
Abstract: Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like ...Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP molecule reduced. NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants. However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH, and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin. Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical.
History
DepositionDec 10, 2018-
Header (metadata) releaseJan 23, 2019-
Map releaseFeb 27, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 5.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nbx
  • Surface level: 5.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0425.png

Downloads & links

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Map

FileDownload / File: emd_0425.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpixel spacing resized to match EMD-415
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5 / Movie #1: 5.5
Minimum - Maximum-14.495347000000001 - 41.702187000000002
Average (Standard dev.)-0.0021918472 (±0.8420073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.480384.480384.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-14.49541.702-0.002

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Supplemental data

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Mask #1

Fileemd_0425_msk_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: binned relative to original particle images

Fileemd_0425_half_map_1.map
Annotationbinned relative to original particle images
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: em-half-volume P2

Fileemd_0425_half_map_2.map
Annotationem-half-volume_P2
Projections & Slices
AxesZYX

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Sample components

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Entire : NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus

EntireName: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus
Components
  • Complex: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus
    • 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 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: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
    • Protein or peptide: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
    • Protein or peptide: Tlr0636 protein
  • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit I
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus

SupramoleculeName: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L)from T.elongatus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8, #10-#18
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 420 KDa

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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)
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 (strain 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 (strain 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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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 (strain 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: NADH dehydrogenase (quinone)
Source (natural)Organism: Thermosynechococcus elongatus (strain 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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
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: Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
Source (natural)Organism: Thermosynechococcus elongatus (strain 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

+
Macromolecule #16: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP

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

UniProtKB: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP

+
Macromolecule #17: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ

MacromoleculeName: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (bacteria)
Strain: BP-1
Molecular weightTheoretical: 4.844698 KDa
SequenceString:
MATDFNRGIM KFDGADSPAM IAISAVLILG FIAGLIWWAL HTAYA

+
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)
Strain: BP-1
Molecular weightTheoretical: 12.462559 KDa
SequenceString:
MIRPIADTYP LLPLSKAQMG QRQEIINSHK RLWDKTMATD LIMTILPGMT VKVTNPNDTY YQFQGIVQRI TDGKVAVLFE GGNWDKLVT FQASELEPVV VTPKEKAKAK K

UniProtKB: Tlr0636 protein

+
Macromolecule #19: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 19 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.03 mg/mL
BufferpH: 6
Component:
ConcentrationName
20.0 mMBis-Tris
100.0 mMsodium chloride
0.03 %B-dodecyl-maltoside
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 7 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: incubate on grid for 30 seconds and blot 2.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 25 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 1385 / Average exposure time: 0.2 sec. / Average electron dose: 60.0 e/Å2 / Details: Three image per hole, focusing once per hole.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
Particle selectionNumber selected: 98145
Startup modelType of model: OTHER / Details: Ab initio from cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.b2) / Number images used: 34655
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.b2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.b2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6nbq


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 20 / Target criteria: Corelation coefficient
Output model

PDB-6nbx:
T.elongatus NDH (data-set 2)

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