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- PDB-5zgb: Cryo-EM structure of the red algal PSI-LHCR -

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Basic information

Entry
Database: PDB / ID: 5zgb
TitleCryo-EM structure of the red algal PSI-LHCR
Components
  • Lhcr1
  • Lhcr2
  • Lhcr3
  • PsaA
  • PsaB
  • PsaC
  • PsaD
  • PsaE
  • PsaF
  • PsaI
  • PsaJ
  • PsaK
  • PsaL
  • PsaM
  • PsaO
KeywordsPHOTOSYNTHESIS / super-complex / red alga / PSI-5Lhcr
Function / homology
Function and homology information


thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane ...thylakoid membrane / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / thylakoid / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre ...Photosystem I, reaction centre, subunit PsaF / Photosystem I p700 chlorophyll A apoprotein A1 / Photosystem I PsaA/PsaB / Photosystem 1 Reaction Centre Subunit Ii; Chain: D; / Photosystem I PsaD, reaction center subunit II / Photosystem I PsaO / Photosystem I reaction centre subunit PsaK / Photosystem I PsaM, reaction centre superfamily / SH3 type barrels. - #50 / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I reaction centre subunit PsaK superfamily / 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 / Alpha-Beta Plaits - #20 / 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. / Helicase, Ruva Protein; domain 3 / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 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
1-DODECANOL / (2S)-2,3-dihydroxypropyl octadecanoate / BETA-CAROTENE / beta-D-glucopyranose / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...1-DODECANOL / (2S)-2,3-dihydroxypropyl octadecanoate / BETA-CAROTENE / beta-D-glucopyranose / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-ZEX / Similar to chlorophyll a/b-binding protein, CP24 / Photosystem I subunit O / Similar to light harvesting protein / Photosystem I reaction center subunit XI / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit III / Photosystem I reaction center subunit II / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I iron-sulfur center subunit VII / Photosystem I iron-sulfur center / PSI-K / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
Cyanidioschyzon merolae strain 10D (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.63 Å
AuthorsPi, X.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Unique organization of photosystem I-light-harvesting supercomplex revealed by cryo-EM from a red alga.
Authors: Xiong Pi / Lirong Tian / Huai-En Dai / Xiaochun Qin / Lingpeng Cheng / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic ...Photosystem I (PSI) is one of the two photosystems present in oxygenic photosynthetic organisms and functions to harvest and convert light energy into chemical energy in photosynthesis. In eukaryotic algae and higher plants, PSI consists of a core surrounded by variable species and numbers of light-harvesting complex (LHC)I proteins, forming a PSI-LHCI supercomplex. Here, we report cryo-EM structures of PSI-LHCR from the red alga in two forms, one with three Lhcr subunits attached to the side, similar to that of higher plants, and the other with two additional Lhcr subunits attached to the opposite side, indicating an ancient form of PSI-LHCI. Furthermore, the red algal PSI core showed features of both cyanobacterial and higher plant PSI, suggesting an intermediate type during evolution from prokaryotes to eukaryotes. The structure of PsaO, existing in eukaryotic organisms, was identified in the PSI core and binds three chlorophylls and may be important in harvesting energy and in mediating energy transfer from LHCII to the PSI core under state-2 conditions. Individual attaching sites of LHCRs with the core subunits were identified, and each Lhcr was found to contain 11 to 13 chlorophylls and 5 zeaxanthins, which are apparently different from those of LHCs in plant PSI-LHCI. Together, our results reveal unique energy transfer pathways different from those of higher plant PSI-LHCI, its adaptation to the changing environment, and the possible changes of PSI-LHCI during evolution from prokaryotes to eukaryotes.
History
DepositionMar 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell / chem_comp
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 / _chem_comp.type
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _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
I: PsaI
J: PsaJ
K: PsaK
L: PsaL
M: PsaM
O: PsaO
1: Lhcr1
2: Lhcr2
3: Lhcr3
4: Lhcr1
5: Lhcr2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)546,074232
Polymers374,33017
Non-polymers171,744215
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, the molecular weight of complex is nearly equal to molecular weight of all subunits
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 14 molecules ABCDEFKLO14253

#1: Protein PsaA / PSI-A / PsaA


Mass: 82763.461 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY7, photosystem I
#2: Protein PsaB / PSI-B / PsaB


Mass: 82107.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY6, photosystem I
#3: Protein PsaC / PSI-C / PsaC


Mass: 8822.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G47, photosystem I
#4: Protein PsaD


Mass: 15698.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FY0
#5: Protein PsaE


Mass: 10545.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FZ1
#6: Protein PsaF


Mass: 21239.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FS9
#9: Protein PsaK


Mass: 6295.657 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G51
#10: Protein PsaL / PSI subunit V / PSI-L


Mass: 15157.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FP8
#12: Protein PsaO


Mass: 16744.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VFJ4
#13: Protein Lhcr1


Mass: 19808.818 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1VKK5
#14: Protein Lhcr2


Mass: 21960.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: M1UU36
#15: Protein Lhcr3


Mass: 20458.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae strain 10D (eukaryote)
Strain: 10D

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Protein/peptide , 3 types, 3 molecules IJM

#7: Protein/peptide PsaI


Mass: 3408.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FQ6
#8: Protein/peptide PsaJ / PSI-J


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85FS8
#11: Protein/peptide PsaM / PSI-M


Mass: 3139.878 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Cyanidioschyzon merolae (strain 10D) (eukaryote)
Strain: 10D / References: UniProt: Q85G73

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Sugars , 2 types, 2 molecules

#22: Sugar ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#23: 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 , 9 types, 213 molecules

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


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


Mass: 893.489 Da / Num. of mol.: 157 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#18: 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
#19: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#24: Chemical ChemComp-3XQ / (2S)-2,3-dihydroxypropyl octadecanoate


Mass: 358.556 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H42O4
#25: Chemical...
ChemComp-ZEX / (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol


Mass: 568.871 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C40H56O2
#26: Chemical ChemComp-1DO / 1-DODECANOL / Dodecanol


Mass: 186.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H26O

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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-5Lhcr / Type: COMPLEX / Entity ID: #1-#15 / Source: NATURAL
Source (natural)Organism: Cyanidioschyzon merolae (eukaryote)
Buffer solutionpH: 7.4
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN / 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 2.17 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM softwareName: RELION / Version: 1.4 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.63 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124279 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0137058
ELECTRON MICROSCOPYf_angle_d1.31152839
ELECTRON MICROSCOPYf_dihedral_angle_d14.83416840
ELECTRON MICROSCOPYf_chiral_restr0.0764591
ELECTRON MICROSCOPYf_plane_restr0.0075034

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