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- PDB-7f9o: PSI-NDH supercomplex of Barley -

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Basic information

Entry
Database: PDB / ID: 7f9o
TitlePSI-NDH supercomplex of Barley
Components
  • (Chlorophyll a-b binding protein ...Light-harvesting complexes of green plants) x 3
  • (Chlorophyll a-b binding protein, ...Light-harvesting complexes of green plants) x 3
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • (Photosynthetic NDH subunit of subcomplex ...) x 10
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
  • NADH-plastoquinone oxidoreductase subunit 5
  • Photosystem I iron-sulfur center
  • Unidentified stromal protein
KeywordsPHOTOSYNTHESIS / Photosystem I / NDH
Function / homology
Function and homology information


NADH dehydrogenase complex (plastoquinone) assembly / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthesis, light harvesting / photosystem II oxygen evolving complex / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I ...NADH dehydrogenase complex (plastoquinone) assembly / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / photosynthesis, light harvesting / photosystem II oxygen evolving complex / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / thylakoid / photosystem I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / photosystem II / extrinsic component of membrane / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis, light reaction / iron-sulfur cluster binding / response to light stimulus / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / defense response to fungus / catalytic activity / photosynthesis / chloroplast / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / mitochondrial membrane / NAD binding / protein folding / 4 iron, 4 sulfur cluster binding / carbohydrate binding / response to oxidative stress / electron transfer activity / membrane => GO:0016020 / carbohydrate metabolic process / iron ion binding / calcium ion binding / magnesium ion binding / metal ion binding
Similarity search - Function
Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / 4Fe-4S dicluster domain / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / 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 ...Photosynthetic NDH subunit of subcomplex B 5, chloroplastic / 4Fe-4S dicluster domain / : / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / 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 / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 (PsbQ) / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / PsbQ-like domain superfamily / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / Photosystem I psaG and psaK proteins signature. / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / Glycoside hydrolase-type carbohydrate-binding / 2Fe-2S iron-sulfur cluster binding domain / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH dehydrogenase, subunit C / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / 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, 30kDa subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH-quinone oxidoreductase, chain 5-like / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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 / 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
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 5, chloroplastic / Peptidyl-prolyl cis-trans isomerase / Predicted protein / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / NAD(P)H dehydrogenase subunit M / Predicted protein / Predicted protein / Chlorophyll a-b binding protein, chloroplastic / Predicted protein / Predicted protein / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A1 / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
Similarity search - Component
Biological speciesHordeum vulgare subsp. spontaneum (wild barley)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Shen, J.R. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
Citation
Journal: Nature / Year: 2022
Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.
Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang /
Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.
#1: Journal: Science / Year: 2015
Title: Photosynthesis. Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex.
Authors: Xiaochun Qin / Michihiro Suga / Tingyun Kuang / Jian-Ren Shen /
Abstract: Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by ...Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.
#2: Journal: Nat Commun / Year: 2020
Title: Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.
Authors: Pan, X. / Cao, D. / Xie, F. / Xu, F. / Su, X. / Mi, H. / Zhang, X. / Li, M.
History
DepositionJul 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction center subunit IV, chloroplastic
F: Photosystem I reaction center subunit III, chloroplastic
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit psaK, chloroplastic
L: Photosystem I reaction center subunit XI, chloroplastic
1: Chlorophyll a-b binding protein Lhca1
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein Lhca5
G: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
M: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
N: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
O: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
P: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
Q: NADH-plastoquinone oxidoreductase subunit 5
R: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
S: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
T: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
U: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
V: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
W: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
X: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
Y: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
Z: Unidentified stromal protein
a: Photosynthetic NDH subunit of subcomplex L1
b: Photosynthetic NDH subunit of subcomplex L2
c: Photosynthetic NDH subunit of subcomplex L2
4: Photosynthetic NDH subunit of subcomplex L4
d: Photosynthetic NDH subunit of subcomplex L5
6: Photosynthetic NDH subunit of subcomplex B1
7: Photosynthetic NDH subunit of subcomplex B2
8: Photosynthetic NDH subunit of subcomplex B3
9: Photosynthetic NDH subunit of subcomplex B4
0: Photosynthetic NDH subunit of subcomplex B5
e: Photosystem I P700 chlorophyll a apoprotein A1
f: Photosystem I P700 chlorophyll a apoprotein A2
g: Photosystem I iron-sulfur center
h: Photosystem I reaction center subunit II, chloroplastic
i: Photosystem I reaction center subunit IV, chloroplastic
j: Photosystem I reaction center subunit III, chloroplastic
k: Photosystem I reaction center subunit VI, chloroplastic
l: Photosystem I reaction center subunit VIII
m: Photosystem I reaction center subunit IX
n: Photosystem I reaction center subunit psaK, chloroplastic
o: Photosystem I reaction center subunit XI, chloroplastic
p: Chlorophyll a-b binding protein Lhca1
q: Chlorophyll a-b binding protein, chloroplastic
r: Chlorophyll a-b binding protein Lhca4
s: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,837,449455
Polymers1,511,14355
Non-polymers326,306400
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 4 molecules AeBf

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / / PSI-A / PsaA


Mass: 83217.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1K7, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / / PSI-B / PsaB


Mass: 82693.914 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z289, photosystem I

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Protein , 4 types, 5 molecules CgOQZ

#3: Protein Photosystem I iron-sulfur center / / Photosystem I reaction center subunit PSI-C / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8909.345 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4YZ47, photosystem I
#19: Protein NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H-quinone oxidoreductase chain D / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone ...NAD(P)H-quinone oxidoreductase chain D / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone oxidoreductase chain 4


Mass: 56222.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z8N2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#21: Protein NADH-plastoquinone oxidoreductase subunit 5 / NAD(P)H-quinone oxidoreductase subunit F / chloroplastic


Mass: 87552.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A7T7JN26
#30: Protein Unidentified stromal protein


Mass: 5209.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)

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Photosystem I reaction center subunit ... , 8 types, 16 molecules DhEiFjHkIlJmKnLo

#4: Protein Photosystem I reaction center subunit II, chloroplastic / / Photosystem I 20 kDa subunit / PSI-D


Mass: 21958.137 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P36213
#5: Protein Photosystem I reaction center subunit IV, chloroplastic / / PSI-E / Photosystem I 10.8 kDa polypeptide


Mass: 15476.541 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P13194
#6: Protein Photosystem I reaction center subunit III, chloroplastic / / PSI-F / Light-harvesting complex I 17 kDa protein


Mass: 24866.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P13192
#7: Protein Photosystem I reaction center subunit VI, chloroplastic / / PSI-H / Light-harvesting complex I 11 kDa protein


Mass: 14900.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P20143
#8: Protein/peptide Photosystem I reaction center subunit VIII / / PSI-I


Mass: 4010.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1D9
#9: Protein/peptide Photosystem I reaction center subunit IX / / PSI-J


Mass: 4747.620 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1E9
#10: Protein Photosystem I reaction center subunit psaK, chloroplastic / / Photosystem I reaction center subunit PSI-K / Light-harvesting complex I 7 kDa protein / PSI-K / ...Photosystem I reaction center subunit PSI-K / Light-harvesting complex I 7 kDa protein / PSI-K / Photosystem I subunit X


Mass: 13742.934 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P36886
#11: Protein Photosystem I reaction center subunit XI, chloroplastic / / PSI-L / PSI subunit V


Mass: 22229.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P23993

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Chlorophyll a-b binding protein ... , 3 types, 4 molecules 1p5r

#12: Protein Chlorophyll a-b binding protein Lhca1


Mass: 26691.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A287WC32
#15: Protein Chlorophyll a-b binding protein Lhca5


Mass: 27618.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#41: Protein Chlorophyll a-b binding protein Lhca4 / Chlorophyll a-b binding protein / chloroplastic


Mass: 21976.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: Q9LKC7

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Chlorophyll a-b binding protein, ... , 3 types, 4 molecules 23qs

#13: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27320.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: Q43485
#14: Protein Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein Lhca3


Mass: 29374.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2DAN8
#42: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23904.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2D0D5

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NAD(P)H-quinone oxidoreductase subunit ... , 12 types, 12 molecules GMNPRSTUVWXY

#16: Protein NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit A / NAD(P)H dehydrogenase subunit 1 / NDH subunit 1 / NADH- ...NAD(P)H-quinone oxidoreductase subunit A / NAD(P)H dehydrogenase subunit 1 / NDH subunit 1 / NADH-plastoquinone oxidoreductase subunit 1


Mass: 38544.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: P92432, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#17: Protein NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit B / NAD(P)H dehydrogenase / subunit 2 / NADH-plastoquinone ...NAD(P)H-quinone oxidoreductase subunit B / NAD(P)H dehydrogenase / subunit 2 / NADH-plastoquinone oxidoreductase subunit 2


Mass: 53452.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z268, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#18: Protein NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit C / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone ...NAD(P)H-quinone oxidoreductase subunit C / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3


Mass: 13299.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1L1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#20: Protein NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit E / / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone ...NAD(P)H-quinone oxidoreductase subunit E / / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L


Mass: 11199.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1I1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#22: Protein NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit G / chloroplastic


Mass: 19587.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A4Y5SEJ9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#23: Protein NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H dehydrogenase / subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH- ...NAD(P)H dehydrogenase / subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH-plastoquinone oxidoreductase subunit H


Mass: 44563.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z272, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#24: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H dehydrogenase subunit I / NDH subunit I / NADH-plastoquinone oxidoreductase subunit I


Mass: 19271.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A218LNN1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#25: Protein NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J


Mass: 18733.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: Q7GT16, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#26: Protein NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H dehydrogenase subunit K / NADH-plastoquinone oxidoreductase subunit K


Mass: 27568.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z232, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#27: Protein NAD(P)H-quinone oxidoreductase subunit L, chloroplastic


Mass: 22240.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2CUR7
#28: Protein NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H dehydrogenase subunit M / NADH-plastoquinone oxidoreductase subunit M


Mass: 24051.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2D138
#29: Protein NAD(P)H-quinone oxidoreductase subunit N, chloroplastic


Mass: 25928.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A287M953

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Photosynthetic NDH subunit of subcomplex ... , 10 types, 10 molecules abc4d67890

#31: Protein Photosynthetic NDH subunit of subcomplex L1


Mass: 17835.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#32: Protein Photosynthetic NDH subunit of subcomplex L2


Mass: 23946.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2CTW7
#33: Protein Photosynthetic NDH subunit of subcomplex L2


Mass: 24733.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#34: Protein Photosynthetic NDH subunit of subcomplex L4


Mass: 13954.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#35: Protein Photosynthetic NDH subunit of subcomplex L5


Mass: 25818.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2CTD7
#36: Protein Photosynthetic NDH subunit of subcomplex B1


Mass: 51675.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2D3G1
#37: Protein Photosynthetic NDH subunit of subcomplex B2


Mass: 38079.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2D932
#38: Protein Photosynthetic NDH subunit of subcomplex B3


Mass: 13313.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2DD79
#39: Protein Photosynthetic NDH subunit of subcomplex B4


Mass: 9756.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#40: Protein Photosynthetic NDH subunit of subcomplex B5


Mass: 18146.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2DWH9

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Sugars , 1 types, 4 molecules

#49: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 11 types, 396 molecules

#43: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#44: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 273 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#45: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2
#46: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#47: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 51 / Source method: obtained synthetically / Formula: C40H56
#48: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe4S4
#50: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#51: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN / Lutein


Mass: 568.871 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H56O2
#52: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#53: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN / Violaxanthin


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4
#54: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S

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Details

Has ligand of interestN
Sequence detailsUniProt database assigns these position to UNK. Author determined these residues.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-NDH supercomplex of Barley / Type: COMPLEX / Entity ID: #1-#42 / Source: NATURAL
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT

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