[English] 日本語
Yorodumi
- EMDB-32464: Subcomplexes B,M and L in the Cylic electron transfer supercomple... -

+
Open data


ID or keywords:

Loading...

-
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
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 / P450-containing electron transport chain / chloroplast thylakoid ...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 / P450-containing electron transport chain / chloroplast thylakoid / ubiquinone biosynthetic process / 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 / NADH dehydrogenase activity / photosynthetic electron transport chain / oxidoreductase activity, acting on NAD(P)H / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / electron transport coupled proton transport / plastid / cyclosporin A binding / extrinsic component of membrane / chloroplast thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transport chain / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / protein peptidyl-prolyl isomerization / aerobic respiration / photosynthesis / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / 2 iron, 2 sulfur cluster binding / protein folding / carbohydrate binding / response to oxidative stress / electron transfer activity / membrane => GO:0016020 / carbohydrate metabolic process / calcium ion binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / 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 / Oxygen-evolving enhancer protein 3 ...Photosynthetic NDH subunit of subcomplex B 4, chloroplastic / Photosynthetic NDH subunit of subcomplex B 1, chloroplastic / Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / Photosynthetic NDH subunit of lumenal location 4-like / 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 / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 (PsbQ) / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / Mog1/PsbP, alpha/beta/alpha sandwich / 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-plastoquinone oxidoreductase, chain 5 subgroup / 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-quinone oxidoreductase, chain 5-like / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / 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 / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / Proton-conducting membrane transporter / 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 / Cyclophilin-like domain superfamily / Galactose mutarotase-like domain superfamily / 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) / thale cress (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-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_32464.png

Downloads & links

-
Map

FileDownload / File: emd_32464.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
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

-
Supplemental data

-
Sample components

+
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

+
Supramolecule #1: Cylic electron transfer supercomplex from Arabidopsis

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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (thale cress)
Molecular weightTheoretical: 13.846332 KDa
SequenceString:
MFLLYEYDIF WAFLLISSAI PVLAFLISGV LSPIRKGPEK LSSYESGIEP IGDAWLQFRI RYYMFALVFV VFDVETVFLY PWAMSFDVL GVSAFIEAFI FVLILILGLV YAWRKGALEW S

+
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: thale cress (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

+
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: thale cress (thale cress)
Molecular weightTheoretical: 11.297439 KDa
SequenceString:
MILEHVLVLS AYLFLIGLYG LITSRNMVRA LMCLELILNA VNMNFVTFSD FFDNSQLKGE IFCIFVIAIA AAEAAIGLAI VSSIYRNRK SIRINQSTLL NK

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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: thale cress (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

+
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 / Phosphatidylglycerol

+
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

+
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 / Iron–sulfur cluster

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

6khj

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more