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- PDB-6igz: Structure of PSI-LHCI -

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Basic information

Entry
Database: PDB / ID: 6igz
TitleStructure of PSI-LHCI
Components
  • Lhca-a
  • Lhca-b
  • Lhca-c
  • Lhca-d
  • Lhca-g
  • Lhca-h
  • Lhca-i
  • Lhca-j
  • Photosystem I reaction center subunit XII
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaG
  • PsaH
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
KeywordsPLANT PROTEIN / PSI-LHCI
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosynthetic electron transport in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosynthetic electron transport in photosystem I / photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / 4 iron, 4 sulfur cluster binding / : / electron transfer activity / oxidoreductase activity / integral component of membrane / metal ion binding
Similarity search - Function
: / Photosystem I, reaction centre, subunit PsaF / Photosystem I PsaD, reaction center subunit II / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaA/PsaB / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Single helix bin / Photosystem I reaction center subunit psaK, plant ...: / Photosystem I, reaction centre, subunit PsaF / Photosystem I PsaD, reaction center subunit II / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaA/PsaB / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Single helix bin / Photosystem I reaction center subunit psaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / SH3 type barrels. - #50 / Photosystem I psaG / psaK / Photosystem I reaction center subunit V/PsaK / Chlorophyll A-B binding protein, plant and chromista / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Chlorophyll A-B binding protein / Photosystem I PsaL, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit VIII superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / 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 / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaE, reaction centre subunit IV / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Photosystem I PsaA/PsaB / Alpha-Beta Plaits - #20 / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PsaH / Chlorophyll a-b binding protein, chloroplastic / PSI-F / PsaE / PsaD / 9 kDa polypeptide / Chlorophyll a-b binding protein, chloroplastic ...Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PsaH / Chlorophyll a-b binding protein, chloroplastic / PSI-F / PsaE / PsaD / 9 kDa polypeptide / Chlorophyll a-b binding protein, chloroplastic / Photosystem I / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chem-8CT / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / PsaK / PSI-J / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit XII / CHLOROPHYLL B / Chem-XAT / IRON/SULFUR CLUSTER / PHYLLOQUINONE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / CHLOROPHYLL A / Photosystem I reaction center subunit VIII
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsXiong, P. / Xiaochun, Q.
CitationJournal: Nat Plants / Year: 2019
Title: Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.
Authors: Xiaochun Qin / Xiong Pi / Wenda Wang / Guangye Han / Lixia Zhu / Mingmei Liu / Linpeng Cheng / Jian-Ren Shen / Tingyun Kuang / Sen-Fang Sui /
Abstract: Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an ...Photosystem I (PSI) is a highly efficient natural light-energy converter, and has diverse light-harvesting antennas associated with its core in different photosynthetic organisms. In green algae, an extremely large light-harvesting complex I (LHCI) captures and transfers energy to the PSI core. Here, we report the structure of PSI-LHCI from a green alga Bryopsis corticulans at 3.49 Å resolution, obtained by single-particle cryo-electron microscopy, which revealed 13 core subunits including subunits characteristic of both prokaryotes and eukaryotes, and 10 light-harvesting complex a (Lhca) antennas that form a double semi-ring and an additional Lhca dimer, including a novel four-transmembrane-helix Lhca. In total, 244 chlorophylls were identified, some of which were located at key positions for the fast energy transfer. These results provide a firm structural basis for unravelling the mechanisms of light-energy harvesting, transfer and quenching in the green algal PSI-LHCI, and important clues as to how PSI-LHCI has changed during evolution.
History
DepositionSep 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2019Group: Advisory / Data collection / Category: database_PDB_caveat / pdbx_validate_chiral
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.4Mar 4, 2020Group: Source and taxonomy / Category: entity_src_nat
Item: _entity_src_nat.common_name / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.5Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

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Assembly

Deposited unit
A: PsaA
B: PsaB
C: PsaC
D: PsaD
E: PsaE
F: PsaF
G: PsaG
H: PsaH
I: PsaI
J: PsaJ
K: PsaK
L: PsaL
1: Lhca-a
2: Lhca-c
3: Lhca-d
4: Lhca-b
6: Lhca-g
5: Lhca-a
7: Lhca-h
8: Lhca-b
9: Lhca-i
0: Lhca-j
M: Photosystem I reaction center subunit XII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)841,704343
Polymers579,24923
Non-polymers262,455320
Water0
1


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

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Components

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Protein , 18 types, 20 molecules ABCDEFGHKL1523486790

#1: Protein PsaA


Mass: 83412.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ2*PLUS
#2: Protein PsaB


Mass: 82164.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H003*PLUS
#3: Protein PsaC


Mass: 8880.307 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H005*PLUS
#4: Protein PsaD


Mass: 21733.045 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H006*PLUS
#5: Protein PsaE


Mass: 10096.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H007*PLUS
#6: Protein PsaF


Mass: 25129.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H008*PLUS
#7: Protein PsaG


Mass: 18226.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant)
#8: Protein PsaH


Mass: 14400.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H009*PLUS
#11: Protein PsaK


Mass: 12487.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ4*PLUS
#12: Protein PsaL


Mass: 21338.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ5*PLUS
#13: Protein Lhca-a


Mass: 24458.012 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ6*PLUS
#14: Protein Lhca-c


Mass: 27808.264 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ7*PLUS
#15: Protein Lhca-d


Mass: 30409.689 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ8*PLUS
#16: Protein Lhca-b


Mass: 26575.912 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ9*PLUS
#17: Protein Lhca-g


Mass: 29300.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H000*PLUS
#18: Protein Lhca-h


Mass: 28621.643 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H001*PLUS
#19: Protein Lhca-i


Mass: 24152.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H002*PLUS
#20: Protein Lhca-j


Mass: 26910.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H004*PLUS

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Protein/peptide , 3 types, 3 molecules IJM

#9: Protein/peptide PsaI


Mass: 3859.615 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8H010*PLUS
#10: Protein/peptide PsaJ


Mass: 4744.679 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A4V8GZZ3*PLUS
#21: Protein/peptide Photosystem I reaction center subunit XII / / PsaM / PSI-M


Mass: 3505.114 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bryopsis corticulans (plant) / References: UniProt: A0A0D6E2L8

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Sugars , 2 types, 3 molecules

#26: Sugar ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#28: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 8 types, 317 molecules

#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 218 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE / Phytomenadione


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#24: 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
#25: Chemical...
ChemComp-8CT / (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene


Mass: 536.873 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: C40H56
#27: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#29: Chemical...
ChemComp-CHL / CHLOROPHYLL B / Chlorophyll b


Mass: 907.472 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#30: 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.: 20 / Source method: obtained synthetically / Formula: C40H56O4
#31: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10

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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 / Type: COMPLEX / Entity ID: #1-#21 / Source: NATURAL
Source (natural)Organism: Bryopsis corticulans (plant)
Buffer solutionpH: 7.8
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.852 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: image acquisition
CTF correctionType: NONE
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 59525 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00954746
ELECTRON MICROSCOPYf_angle_d1.96678218
ELECTRON MICROSCOPYf_dihedral_angle_d15.14832460
ELECTRON MICROSCOPYf_chiral_restr0.1126449
ELECTRON MICROSCOPYf_plane_restr0.00610222

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