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- PDB-7ew6: Barley photosystem I-LHCI-Lhca5 supercomplex -

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Basic information

Entry
Database: PDB / ID: 7ew6
TitleBarley photosystem I-LHCI-Lhca5 supercomplex
Components
  • (Chlorophyll a-b binding protein ...) x 2
  • (Chlorophyll a-b binding protein, ...) x 2
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 8
  • Photosystem I iron-sulfur center
KeywordsPHOTOSYNTHESIS / Photosystem I / Light-harvesting complex / Lhca5
Function / homology
Function and homology information


: / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding ...: / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
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 / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI ...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 / Photosystem I psaG and psaK proteins signature. / 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 PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / 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 / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
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 / Chlorophyll a-b binding protein, chloroplastic / 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 / Chlorophyll a-b binding protein, chloroplastic / Photosystem I iron-sulfur center / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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
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: Qin, X.C. / Suga, M. / Kuang, T.Y. / Shen, J.R.
History
DepositionMay 24, 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
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)570,498214
Polymers407,75815
Non-polymers162,740199
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: 83217.219 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: 82693.914 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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Photosystem I reaction center subunit ... , 8 types, 8 molecules DEFHIJKL

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


Mass: 21958.137 Da / Num. of mol.: 1 / 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.: 1 / 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.: 1 / 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.: 1 / 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.: 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 / 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 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.: 1 / 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.: 1 / 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 ... , 2 types, 2 molecules 15

#12: Protein Chlorophyll a-b binding protein Lhca1


Mass: 26691.438 Da / Num. of mol.: 1 / 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)

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Chlorophyll a-b binding protein, ... , 2 types, 2 molecules 23

#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.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: F2DAN8

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Protein / Sugars , 2 types, 3 molecules C

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


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15
#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.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4YZ47, photosystem I

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Non-polymers , 10 types, 197 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.: 136 / 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.: 5 / 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.: 12 / 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
Has protein modificationY

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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-Lhca5 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
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT

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