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- EMDB-32464: Subcomplexes B,M and L in the Cylic electron transfer supercomple... -

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Basic information

Entry
Database: EMDB / ID: EMD-32464
TitleSubcomplexes B,M and L in the Cylic electron transfer supercomplex NDH-PSI from Arabidopsis
Map data
Sample
  • Complex: Cylic electron transfer supercomplex from Arabidopsis
    • Protein or peptide: x 17 types
  • Ligand: x 3 types
KeywordsSubcomplex B / subcomplex M / subcomplex L / Arabidopisis / plant / cyclic electron transport supercomplex / ELECTRON TRANSPORT
Function / homology
Function and homology information


NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / protein histidine kinase binding / chloroplast membrane / ubiquinone biosynthetic process / P450-containing electron transport chain ...NAD(P)H dehydrogenase complex assembly / nitrite reductase complex [NAD(P)H] / NAD(P)H dehydrogenase complex (plastoquinone) / glucose-6-phosphate 1-epimerase activity / chloroplast stromal thylakoid / thylakoid lumen / protein histidine kinase binding / chloroplast membrane / ubiquinone biosynthetic process / P450-containing electron transport chain / chloroplast thylakoid / NADPH dehydrogenase activity / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosystem II oxygen evolving complex / photosynthetic electron transport in photosystem I / thylakoid / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / plastid / extrinsic component of membrane / photosynthesis, light reaction / chloroplast thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / NADH dehydrogenase activity / NADH dehydrogenase (ubiquinone) activity / ATP synthesis coupled electron transport / quinone binding / photosynthesis / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 2 iron, 2 sulfur cluster binding / protein folding / carbohydrate binding / response to oxidative stress / carbohydrate metabolic process / calcium ion binding / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus ...Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / : / PsbP, C-terminal / PsbP / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / NADH-quinone oxidoreductase chain 4 / Mog1/PsbP, alpha/beta/alpha sandwich / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / Adrenodoxin / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Glycoside hydrolase-type carbohydrate-binding / 2Fe-2S iron-sulfur cluster binding domain / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-plastoquinone oxidoreductase, chain 5 subgroup / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / NADH-quinone oxidoreductase, chain M/4 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-quinone oxidoreductase, chain 5-like / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / NADH:ubiquinone oxidoreductase / Galactose mutarotase-like domain superfamily / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Cyclophilin-like domain superfamily / Proton-conducting membrane transporter / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Beta-grasp domain superfamily / Peptidyl-prolyl cis-trans isomerase domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily
Similarity search - Domain/homology
NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NDH dependent flow 6 / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic ...NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NDH dependent flow 6 / Photosynthetic NDH subunit of lumenal location 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / Photosynthetic NDH subunit of subcomplex B 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / Photosynthetic NDH subunit of lumenal location 5, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of subcomplex B 3, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Photosynthetic NDH subunit of lumenal location 4, chloroplastic / Photosynthetic NDH subunit of lumenal location 3, chloroplastic / Photosynthetic NDH subunit of lumenal location 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsPan XW / Li M
Funding support China, 5 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)31770778 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)31970264 China
CitationJournal: Mol Plant / Year: 2022
Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.
Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li /
Abstract: Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane- ...Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.
History
DepositionDec 26, 2021-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7wff
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7wff
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_32464.png

Downloads & links

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Map

FileDownload / File: emd_32464.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å		1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.10214657 - 0.16794679
Average (Standard dev.)0.0003227866 (±0.005448986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ139118109
NX/NY/NZ123164187
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.1020.1680.000

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Supplemental data

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Sample components

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Entire : Cylic electron transfer supercomplex from Arabidopsis

EntireName: Cylic electron transfer supercomplex from Arabidopsis
Components
  • Complex: Cylic electron transfer supercomplex from Arabidopsis
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
    • Protein or peptide: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
    • Protein or peptide: NDH dependent flow 6
    • Protein or peptide: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
    • Protein or peptide: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
    • Protein or peptide: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: FE2/S2 (INORGANIC) CLUSTER

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Supramolecule #1: Cylic electron transfer supercomplex from Arabidopsis

SupramoleculeName: Cylic electron transfer supercomplex from Arabidopsis / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 40.041859 KDa
SequenceString: MIIYATAVQT INSFVKLESL KEVYGLIWIF VPIFSLVLGI ITGVLVIVWL EREISAGIQQ RIGPEYAGPL GILQALADGT KLLFKENLR PSRGNTPLFS IGPSIAVISI LLSYSVIPFS NHLVLADLNI GIFLWIAISS IAPIGLLMSG YGSNNKYSFL G GLRAAAQS ...String:
MIIYATAVQT INSFVKLESL KEVYGLIWIF VPIFSLVLGI ITGVLVIVWL EREISAGIQQ RIGPEYAGPL GILQALADGT KLLFKENLR PSRGNTPLFS IGPSIAVISI LLSYSVIPFS NHLVLADLNI GIFLWIAISS IAPIGLLMSG YGSNNKYSFL G GLRAAAQS ISYEIPLTLC VLSISLLSNS LSTVDIVEAQ SKYGFWGWNL WRQPIGFIIF LISSLAECER LPFDLPEAEE EL IAGYQTE YSGIKFGLFY VASYLNLLIS SLFVTVLYLG GWNISIPYIS ILELFQRDQI FGTTIGIFIT LAKTYLFLFV SIA TRWTLP RLRMDQLLNL GWKFLLPISL GNLLLTTSFQ LFSL

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

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

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 57.018625 KDa
SequenceString: MIWHVQNENF ILDSTRIFMK AFHLLLFDGS FIFPECILIF GLILLLMIDS TSDQKDIPWL YFISSTSFVM SITALLFRWR EEPMISFSG NFQTNNFNEI FQFLILLCST LCIPLSVEYI ECTEMAITEF LLFILTATLG GMFLCGANDL ITIFVAPECF S LCSYLLSG ...String:
MIWHVQNENF ILDSTRIFMK AFHLLLFDGS FIFPECILIF GLILLLMIDS TSDQKDIPWL YFISSTSFVM SITALLFRWR EEPMISFSG NFQTNNFNEI FQFLILLCST LCIPLSVEYI ECTEMAITEF LLFILTATLG GMFLCGANDL ITIFVAPECF S LCSYLLSG YTKKDIRSNE ATMKYLLMGG ASSSILVHGF SWLYGSSGGE IELQEIVNGL INTQMYNSPG ISIALIFITV GI GFKLSLA PSHQWTPDVY EDSPTPVVAF LSVTSKVAAS ASATRIFDIP FYFSSNEWHL LLEILAILSM IFGNLIAITQ TSM KRMLAY SSIGQIGYVI IGIIVGDSNG GYASMITYML FYIAMNLGTF ACIILFGLRT GTDNIRDYAG LYTKDPFLAL SLAL CLLSL GGLPPLAGFF GKLHLFWCGW QAGLYFLVSI GLLTSVLSIY YYLKIIKLLM TGRNQEITPH MRNYRISPLR SNNSI ELSM IVCVIASTIP GISMNPIIAI AQDTLFSF

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

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

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 13.846332 KDa
SequenceString:
MFLLYEYDIF WAFLLISSAI PVLAFLISGV LSPIRKGPEK LSSYESGIEP IGDAWLQFRI RYYMFALVFV VFDVETVFLY PWAMSFDVL GVSAFIEAFI FVLILILGLV YAWRKGALEW S

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

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Macromolecule #4: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic

MacromoleculeName: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / 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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 56.992473 KDa
SequenceString: MYLVFTTNDF PWLTIIVVFP ISAGSLMLFL PHRGNKVNKW YTICICILEL LLTTYAFCYN FKMDDPLIQL SEDYKWIDFF DFYWRMGID GLSIGTILLT GFITTLATLA AFPVTRDSRF FHFLMLAMYS GQIGSFSSRD LLLFFIMWEL ELIPVYLLLS M WGGKKRLY ...String:
MYLVFTTNDF PWLTIIVVFP ISAGSLMLFL PHRGNKVNKW YTICICILEL LLTTYAFCYN FKMDDPLIQL SEDYKWIDFF DFYWRMGID GLSIGTILLT GFITTLATLA AFPVTRDSRF FHFLMLAMYS GQIGSFSSRD LLLFFIMWEL ELIPVYLLLS M WGGKKRLY SATKFILYTA GSSIFLLIGV LGISLYGSNE PTLNLELLAN KSYPVTLEIL FYIGFLIAFA VKSPIIPLHT WL PDTHGEA HYSTCMLLAG ILLKMGAYGL VRINMELLPH AHSMFSPWLL VVGTIQIIYA ASTSPGQRNL KKRIAYSSVS HMG FIIIGI SSITDPGLNG AILQIISHGF IGAALFFLAG TSYDRIRLVY LDEMGGMAIS IPKIFTMFTI LSMASLALPG MSGF IAEFI VFFGIITSQK YFLISKIFII FVMAIGMILT PIYLLSMLRQ MFYGYKLINI KNFSFFDSGP RELFLSISIL LPIIG IGIY PDFVLSLASD KVESILSNYF YG

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

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

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 11.297439 KDa
SequenceString:
MILEHVLVLS AYLFLIGLYG LITSRNMVRA LMCLELILNA VNMNFVTFSD FFDNSQLKGE IFCIFVIAIA AAEAAIGLAI VSSIYRNRK SIRINQSTLL NK

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

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Macromolecule #6: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
EC number: Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 85.300836 KDa
SequenceString: MEHTYQYSWI IPFIPLPVPI LLGVGLLLFP TATKNLRRMW TFLSIFLLSI VMIFSIYLSI QQIFLSCIHQ NVWSWTINNE FSFEFGYFI DPLTSIMSIL ITTVGILVLI YSDNYMSHDQ GYLRFFAYMG FFNTSMLGLV TSSNLIQVYF FWELVGMCSY L LIGFWFTR ...String:
MEHTYQYSWI IPFIPLPVPI LLGVGLLLFP TATKNLRRMW TFLSIFLLSI VMIFSIYLSI QQIFLSCIHQ NVWSWTINNE FSFEFGYFI DPLTSIMSIL ITTVGILVLI YSDNYMSHDQ GYLRFFAYMG FFNTSMLGLV TSSNLIQVYF FWELVGMCSY L LIGFWFTR PIAANACQKA FVTNRVGDFG LLLGILGLYW ITGSFEFQDL FEIFNNLILN NRVNLLFLTL CAFLLFVGPI AK SAQFPLH VWLPDAMEGP TPISALIHAA TMVAAGIFLV ARLLPLFIVI PSIMYIISLI GIITVLLGAT LALAQKDIKR GLA YSTMSQ LGYMMLALGM GSYRSALFHL ITHAYSKALL FLGSGSIIHS MEAIVGYSPD KSQNMILMGG LTKHVPITKT AFLI GTLSL CGIPPLACFW SKDEILNDSL LFSPIFAIIA CSTAGLTAFY MFRIYLLTFE GHLNTYFLNY SGKKSGSFYS LSLWG KEEE KKLNKNFGLV PLLTMNNTKR ASFFCNKTYK ISNNVRNQIF ITVENFGLNT RTFYYPHESD NTILFPMLIL VLFTLF IGA IGIPFNQEGI DFDILSKFFT PSINLLHKNS QNFVDWYEFL RNATFSVSIA FFGIFIAYCL YKPFYSSLLN LTLLNSF QK WNSKRIHWEK LINFVYNWSY NRGYIDSFFK TSLIESIRRL AKQTTFFDKR IIDGITNGVG ITSFFVGEVT KYIGGSRI S SYLFLYLSYV LIFLMILFFF YFEKF

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic

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Macromolecule #7: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic

MacromoleculeName: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
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: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 19.218639 KDa
SequenceString:
MDLPGPIHDF LLVFLGSGLL VGGLGVVLLP NPIFSAFSLG FVLVCISLLY ILSNSHFVAA AQLLIYVGAI NVLIIFAVMF MNDSEYSTD FNLWTIGNGI TSLVCTTILF LLMSTILDTS WYGVIWTTKL NQILEQDLIS NSQQIGIHLS TDFFLPFELI S IILLVALI GAISVARQ

UniProtKB: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic

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Macromolecule #8: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 51.080168 KDa
SequenceString: MASSLPLLPK PISPFFKTPP FSTSKPLVFL NFQTRLTSRS SDVSVNLKKK NNPWLDPFDS GEDPDNEYGS LFADGKQDED PRPPDNPDN PYGFLKFPKG YTVELASLPL KIRGDVRRCC CVISGGVYEN LLFFPTIQLI KDRYPGVQVD ILTTERGKQT Y ELNKNVRW ...String:
MASSLPLLPK PISPFFKTPP FSTSKPLVFL NFQTRLTSRS SDVSVNLKKK NNPWLDPFDS GEDPDNEYGS LFADGKQDED PRPPDNPDN PYGFLKFPKG YTVELASLPL KIRGDVRRCC CVISGGVYEN LLFFPTIQLI KDRYPGVQVD ILTTERGKQT Y ELNKNVRW ANVYDPDDHW PEPAEYTDMI GLLKGRYYDM VLSTKLAGLG HAAFLFMTTA RDRVSYIYPN VNSAGAGLML SE TFTAENT NLSELGYSMY TQMEDWLGRP FRSVPRTPLL PLRVSISRKV KEVVAAKYRN AGAVTGKFIV IHGIESDSKA SMQ SKGDAD SLLSLEKWAK IIKGVRGFKP VFVIPHEKER ENVEDFVGDD TSIVFITTPG QLAALINDSA GVIATNTAAI QLAN ARDKP CIGLFSSEEK GKLFVPYAEE KSNCVIIASK TGKLADIDIG TVKNAMQVFE GSLALV

UniProtKB: Photosynthetic NDH subunit of subcomplex B 1, chloroplastic

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Macromolecule #9: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic
type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.048492 KDa
SequenceString: MASLISFSLL PKPKAVRSSI SAPQTQTINT EKLEDKFGRK GIKFSESNNI PMVELKVRNG SSLKLSLSDA HVLSYKPKVY WKDEGFEEV LYTVDGDESR GGVGVVIVNG EEPKGGSSVI SGCDWSVKDT DSDAIDALQI ELSCTAGVLD ITYIVSLYPV S MATALVVK ...String:
MASLISFSLL PKPKAVRSSI SAPQTQTINT EKLEDKFGRK GIKFSESNNI PMVELKVRNG SSLKLSLSDA HVLSYKPKVY WKDEGFEEV LYTVDGDESR GGVGVVIVNG EEPKGGSSVI SGCDWSVKDT DSDAIDALQI ELSCTAGVLD ITYIVSLYPV S MATALVVK NNGRKPVTLK PGIMSYLRFK KRSGAGIQGL KGCSYCPNPP LSSPFELLSP SEAMKAESSG WFGSEEGEKP GI WAVEDSV ITLLEKKMSR IYGAPPAERL KAVYNTPPSK FETIDQGRGL FFRMIRIGFE EMYVGSPGSM WDKYGKQHYF VCT GPTSML VPVDVASGET WRGAMVIEHD NL

UniProtKB: Photosynthetic NDH subunit of subcomplex B 2, chloroplastic

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Macromolecule #10: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic
type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.448355 KDa
SequenceString: MGSVQLSGSG LVASLPPNHS FSHKTKLNKP NSYFFRSKHN AARTKTVRAI STAPASQPPA ADEPDEPPAV DFAFVHSVLL PDGTPDVHW RRANGGQKLR DIMLDSNIEL YGPYSKPLSN CAGVGTCATC MVEIVNGKEL LNPRTDIEKE KLKRKPKNWR L ACQTNVGN ...String:
MGSVQLSGSG LVASLPPNHS FSHKTKLNKP NSYFFRSKHN AARTKTVRAI STAPASQPPA ADEPDEPPAV DFAFVHSVLL PDGTPDVHW RRANGGQKLR DIMLDSNIEL YGPYSKPLSN CAGVGTCATC MVEIVNGKEL LNPRTDIEKE KLKRKPKNWR L ACQTNVGN PDSTGLVVIQ QLPEWKAHEW NIPKNIPNDD DLETST

UniProtKB: Photosynthetic NDH subunit of subcomplex B 3, chloroplastic

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Macromolecule #11: NDH dependent flow 6

MacromoleculeName: NDH dependent flow 6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 18.699324 KDa
SequenceString:
MAEAFTSFTF TNLHIPSSYN HSPKQNSGPN HGYWLSNVNE KRERNLMRGS LCVRKALPHD LPLMAVMVQQ IEGMRDIITE KHVWHLSDK AIKNVYMFYI MFTCWGCLYF GSAKDPFYDS EEYRGDGGDG TGYWVYETVC ISPFLILLGK KEKNLEMHTN Y N

UniProtKB: NDH dependent flow 6

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Macromolecule #12: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.767838 KDa
SequenceString: MATVTILSPK SIPKVTDSKF GARVSDQIVN VVKCGKSGRR LKLAKLVSAA GLSQIEPDIN EDPIGQFETN SIEMEDFKYG YYDGAHTYY EGEVQKGTFW GAIADDIAAV DQTNGFQGLI SCMFLPAIAL GMYFDAPGEY LFIGAALFTV VFCIIEMDKP D QPHNFEPQ ...String:
MATVTILSPK SIPKVTDSKF GARVSDQIVN VVKCGKSGRR LKLAKLVSAA GLSQIEPDIN EDPIGQFETN SIEMEDFKYG YYDGAHTYY EGEVQKGTFW GAIADDIAAV DQTNGFQGLI SCMFLPAIAL GMYFDAPGEY LFIGAALFTV VFCIIEMDKP D QPHNFEPQ IYKLERGARD KLINDYNTMS IWDFNDKYGD VWDFTIEKDD IATR

UniProtKB: Photosynthetic NDH subunit of subcomplex B 5, chloroplastic

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Macromolecule #13: Photosynthetic NDH subunit of lumenal location 1, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of lumenal location 1, chloroplastic
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 26.997619 KDa
SequenceString: MAVSSLSIRC GGFSPTISHK TEILCPNPSL KACCLLSSGG KADSSESTYQ KGSGNNWKRR QALVGVGTLV ATSIPATLLL AEEIPKSYS PFVDREDGYS YYYPSDWREF DFRAHDSAFK DRYLQLQNVR VRFIPTEKND IHEVGPMEEV VYDLVKHKFA A PNQVATIY ...String:
MAVSSLSIRC GGFSPTISHK TEILCPNPSL KACCLLSSGG KADSSESTYQ KGSGNNWKRR QALVGVGTLV ATSIPATLLL AEEIPKSYS PFVDREDGYS YYYPSDWREF DFRAHDSAFK DRYLQLQNVR VRFIPTEKND IHEVGPMEEV VYDLVKHKFA A PNQVATIY DMKERVEDGK NYYTFEYGLR TPIYATTSFA TVAVGNNRYY TLIVGANERR WRKVKKQLQV VADSLKILQI

UniProtKB: Photosynthetic NDH subunit of lumenal location 1, chloroplastic

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Macromolecule #14: Photosynthetic NDH subunit of lumenal location 2, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of lumenal location 2, chloroplastic
type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 22.183342 KDa
SequenceString:
MSSFTTTNTP PPYLLRKIYH RRVNQPFSVV CCTGEPQQDI FTRRRTLTSL ITFTVIGGAT SSALAQEKWG TRSFIKEKYF MPGLSPEDA AARIKQTAEG LRDMREMLDH MSWRYVIFYI RLKQAYLSQD LTNAMNILPE SRRNDYVQAA NELVENMSEL D FYVRTPKV YESYLYYEKT LKSIDNVVEF LA

UniProtKB: Photosynthetic NDH subunit of lumenal location 2, chloroplastic

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Macromolecule #15: Photosynthetic NDH subunit of lumenal location 3, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of lumenal location 3, chloroplastic
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 24.811402 KDa
SequenceString: MAHFIDLNSL TNTLPSLPKL PESRKTGKSS GFACRRTEEF QEPDSVQITR RMTLGFAVSI GLTGILGENN VSLAQDNGFW IDGPLPIPP IYNNIVNEKT GTRTFIKKGV YVADIGTKGR MYRVKKNAFD LLAMEDLIGP DTLNYVKKYL RLKSTFLFYD F DNLISAAA ...String:
MAHFIDLNSL TNTLPSLPKL PESRKTGKSS GFACRRTEEF QEPDSVQITR RMTLGFAVSI GLTGILGENN VSLAQDNGFW IDGPLPIPP IYNNIVNEKT GTRTFIKKGV YVADIGTKGR MYRVKKNAFD LLAMEDLIGP DTLNYVKKYL RLKSTFLFYD F DNLISAAA SEDKQPLTDL ANRLFDNFEK LEDAAKTKNL AETESCYKDT KFLLQEVMTR MA

UniProtKB: Photosynthetic NDH subunit of lumenal location 3, chloroplastic

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Macromolecule #16: Photosynthetic NDH subunit of lumenal location 4, chloroplastic

MacromoleculeName: Photosynthetic NDH subunit of lumenal location 4, chloroplastic
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 23.282547 KDa
SequenceString: MAISTLTLTQ SLYTRSFRPT IFFSSSSSSS FSCLCSSSSD CEPKLSVKKR VFGVGLGFLA SSILSLTPLD ADATRIDYYA TVGDPLCEY SYAKSGLGFC DLDVGFGDEA PRGVLVNIHY TARFADGTLF DSSYKRARPL TMRIGVGKVI RGLDQGILGG E GVPPMRVG ...String:
MAISTLTLTQ SLYTRSFRPT IFFSSSSSSS FSCLCSSSSD CEPKLSVKKR VFGVGLGFLA SSILSLTPLD ADATRIDYYA TVGDPLCEY SYAKSGLGFC DLDVGFGDEA PRGVLVNIHY TARFADGTLF DSSYKRARPL TMRIGVGKVI RGLDQGILGG E GVPPMRVG GKRKLQIPPK LAYGPEPAGC FSGDCNIPGN ATLLYDINFV EIYPGSNTR

UniProtKB: Photosynthetic NDH subunit of lumenal location 4, chloroplastic

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Macromolecule #17: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, ch...

MacromoleculeName: Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplastic
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 27.915635 KDa
SequenceString: MATLSMTLSL SAPPRRLSPI NTSAFTSTSF RLRTKSSFDS ISFSSSTPFS ASSLLLHTSY TKRNHRCFSV QSNAEVVTEP QSKITHKVY FDISVGNPVG KLAGRIVIGL YGDDVPQTVE NFRALCTGEK GFGYKGSTFH RVIRDFMIQG GDFEKGNGTG G KSVYGRTF ...String:
MATLSMTLSL SAPPRRLSPI NTSAFTSTSF RLRTKSSFDS ISFSSSTPFS ASSLLLHTSY TKRNHRCFSV QSNAEVVTEP QSKITHKVY FDISVGNPVG KLAGRIVIGL YGDDVPQTVE NFRALCTGEK GFGYKGSTFH RVIRDFMIQG GDFEKGNGTG G KSVYGRTF KDENFKLSHV GPGVLSMANA GPNTNGSQFF ICTIKTSWLD GRHVVFGQVI EGMEVVKLIE EQETDRGDRP RK KVVIADC GQLPMSEA

UniProtKB: Photosynthetic NDH subunit of lumenal location 5, chloroplastic

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Macromolecule #18: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 18 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #19: 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: 19 / Number of copies: 1 / 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 #20: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 20 / 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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6khj

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136022
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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