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- PDB-7ewk: Barley photosystem I-LHCI-Lhca6 supercomplex -

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Basic information

Entry
Database: PDB / ID: 7ewk
TitleBarley photosystem I-LHCI-Lhca6 supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 3
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Chlorophyll a-b binding protein, chloroplastic
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / Light-harvesting complex / Lhca6 / cyclic electron transport
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosynthesis, light harvesting in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding
Similarity search - Function
Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaA ...Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / 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
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-XAT / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2
Similarity search - Component
Biological speciesHordeum vulgare subsp. spontaneum (wild barley)
Hordeum vulgare (barley)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å
AuthorsWang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Zhang, X. / Shen, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
CitationJournal: 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.
History
DepositionMay 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: 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
Revision 1.2Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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 D
E: Photosystem I reaction center subunit E
F: Photosystem I reaction center subunit F
H: Photosystem I reaction center subunit H
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: Photosystem I reaction center subunit K
L: Photosystem I reaction center subunit L
1: Chlorophyll a-b binding protein Lhca1
3: Chlorophyll a-b binding protein Lhca3
4: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein Lhca6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)505,186211
Polymers344,82115
Non-polymers160,365196
Water00
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, 2 molecules AB

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


Mass: 82292.070 Da / Num. of mol.: 1 / 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: 82562.719 Da / Num. of mol.: 1 / 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 , 2 types, 2 molecules C4

#3: Protein Photosystem I iron-sulfur center


Mass: 8909.345 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#14: Protein 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 (barley) / References: UniProt: Q9LKC7

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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFHIJKL

#4: Protein Photosystem I reaction center subunit D


Mass: 15801.046 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#5: Protein Photosystem I reaction center subunit E


Mass: 7679.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#6: Protein Photosystem I reaction center subunit F


Mass: 17488.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#7: Protein Photosystem I reaction center subunit H


Mass: 6431.653 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#8: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3338.116 Da / Num. of mol.: 1 / 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 / Photosystem I reaction center subunit J / PSI-J


Mass: 4747.620 Da / Num. of mol.: 1 / 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 K


Mass: 8502.845 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#11: Protein Photosystem I reaction center subunit L


Mass: 15512.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)

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Chlorophyll a-b binding protein ... , 3 types, 3 molecules 136

#12: Protein Chlorophyll a-b binding protein Lhca1


Mass: 21278.209 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#13: Protein Chlorophyll a-b binding protein Lhca3


Mass: 24395.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#15: Protein Chlorophyll a-b binding protein Lhca6


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

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Sugars , 1 types, 2 molecules

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 10 types, 194 molecules

#16: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 137 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


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


Mass: 722.970 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#23: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10
#24: 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


Mass: 568.871 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H56O2
#25: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#26: 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


Mass: 600.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O4

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Details

Has ligand of interestN

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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-LHCI-Lhca6 supercomplex of Barley / Type: COMPLEX / Entity ID: #1-#15 / 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 2000 nm
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: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT

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