6JO6

Structure of the green algal photosystem I supercomplex with light-harvesting complex I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the green algal photosystem I supercomplex with a decameric light-harvesting complex I.

Suga, M.Ozawa, S.I.Yoshida-Motomura, K.Akita, F.Miyazaki, N.Takahashi, Y.

(2019) Nat Plants 5: 626-636

  • DOI: 10.1038/s41477-019-0438-4
  • Primary Citation of Related Structures:  
    6JO5, 6JO6

  • PubMed Abstract: 
  • In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron microscopic structure of the PSI-LHCI supercomplex from the green alga Chlamydomonas reinhardtii ...

    In plants and green algae, the core of photosystem I (PSI) is surrounded by a peripheral antenna system consisting of light-harvesting complex I (LHCI). Here we report the cryo-electron microscopic structure of the PSI-LHCI supercomplex from the green alga Chlamydomonas reinhardtii. The structure reveals that eight Lhca proteins form two tetrameric LHCI belts attached to the PsaF side while the other two Lhca proteins form an additional Lhca2/Lhca9 heterodimer attached to the opposite side. The spatial arrangement of light-harvesting pigments reveals that Chlorophylls b are more abundant in the outer LHCI belt than in the inner LHCI belt and are absent from the core, thereby providing the downhill energy transfer pathways to the PSI core. PSI-LHCI is complexed with a plastocyanin on the patch of lysine residues of PsaF at the luminal side. The assembly provides a structural basis for understanding the mechanism of light-harvesting, excitation energy transfer of the PSI-LHCI supercomplex and electron transfer with plastocyanin.


    Organizational Affiliation

    Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan. taka@cc.okayama-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A751Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaAps1a1
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B755Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaBps1a2
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC81Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticD161Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaD
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplasticE73Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAE
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplasticF165Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG94Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAG
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth I]106Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAICHLRE_03g165100v5CHLREDRAFT_144056
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]41Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaJ
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticJ [auth K]87Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAK
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIK [auth L]156Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSALCHLRE_12g486300v5CHLREDRAFT_205935
Membrane Entity: Yes 
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Find proteins for A8IL32 (Chlamydomonas reinhardtii)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticL [auth 1], P [auth Z]194Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: cabI-1Lhca1LhcI-6CHLRE_06g283050v5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 3]268Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LHCA3CHLREDRAFT_153678
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 7]215Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcaCHLRE_16g687900v5
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 8]217Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-4LHCA8CHLRE_06g272650v5CHLREDRAFT_187025
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 4]236Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-1CHLRE_10g452050v5
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 5]229Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-3LHCA5CHLRE_10g425900v5CHLREDRAFT_186299
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 6]232Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-5LHCA6CHLRE_06g278213v5CHLREDRAFT_192961
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Find proteins for Q75VY6 (Chlamydomonas reinhardtii)
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Small Molecules
Ligands 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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TD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CHL (Subject of Investigation/LOI)
Query on CHL

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AK [auth 6] , BH [auth 8] , BK [auth 6] , CK [auth 6] , FJ [auth 5] , GJ [auth 5] , HG [auth 7] , KI [auth 4] , 
AK [auth 6], BH [auth 8], BK [auth 6], CK [auth 6], FJ [auth 5], GJ [auth 5], HG [auth 7], KI [auth 4], LI [auth 4], LK [auth 6], MI [auth 4], OF [auth 3], OH [auth Z], PJ [auth 5], RE [auth 1], TH [auth Z], UI [auth 4], WE [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth A] , AB [auth A] , AC [auth B] , AD [auth B] , AE [auth F] , AF [auth 1] , AH [auth 8] , AI [auth Z] , 
AA [auth A], AB [auth A], AC [auth B], AD [auth B], AE [auth F], AF [auth 1], AH [auth 8], AI [auth Z], AJ [auth 5], BA [auth A], BB [auth A], BC [auth B], BD [auth B], BF [auth 1], BI [auth Z], BJ [auth 5], CA [auth A], CB [auth A], CC [auth B], CD [auth B], CE [auth G], CF [auth 1], CG [auth 7], CH [auth 8], CJ [auth 5], DA [auth A], DB [auth A], DC [auth B], DD [auth B], DE [auth G], DF [auth 1], DG [auth 7], DH [auth 8], DJ [auth 5], DK [auth 6], EA [auth A], EB [auth A], EC [auth B], ED [auth B], EF [auth 1], EG [auth 7], EH [auth 8], EJ [auth 5], EK [auth 6], FA [auth A], FB [auth A], FC [auth B], FD [auth B], FG [auth 7], FH [auth 8], FK [auth 6], GA [auth A], GB [auth A], GC [auth B], GD [auth B], GG [auth 7], GH [auth 8], GI [auth 4], GK [auth 6], HA [auth A], HB [auth A], HC [auth B], HD [auth B], HE [auth J], HH [auth 8], HI [auth 4], HJ [auth 5], HK [auth 6], IA [auth A], IB [auth A], IC [auth B], ID [auth B], IG [auth 7], IH [auth 8], II [auth 4], IJ [auth 5], IK [auth 6], JA [auth A], JB [auth A], JC [auth B], JD [auth B], JF [auth 3], JG [auth 7], JH [auth 8], JI [auth 4], JJ [auth 5], JK [auth 6], KA [auth A], KC [auth B], KD [auth B], KE [auth K], KF [auth 3], KG [auth 7], KJ [auth 5], KK [auth 6], LA [auth A], LB [auth A], LC [auth B], LD [auth B], LE [auth K], LF [auth 3], LG [auth 7], LJ [auth 5], MA [auth A], MC [auth B], MF [auth 3], MG [auth 7], MJ [auth 5], NA [auth A], NC [auth B], NF [auth 3], NG [auth 7], NI [auth 4], NJ [auth 5], OA [auth A], OC [auth B], OE [auth L], OG [auth 7], OI [auth 4], OJ [auth 5], OK [auth 6], PA [auth A], PC [auth B], PE [auth L], PF [auth 3], PG [auth 7], PH [auth Z], PI [auth 4], QA [auth A], QC [auth B], QF [auth 3], QG [auth 7], QH [auth Z], QI [auth 4], RA [auth A], RC [auth B], RF [auth 3], RH [auth Z], RI [auth 4], RJ [auth 5], SA [auth A], SC [auth B], SE [auth 1], SF [auth 3], SH [auth Z], SI [auth 4], TA [auth A], TC [auth B], TE [auth 1], TF [auth 3], TI [auth 4], U [auth A], UA [auth A], UB [auth A], UC [auth B], UE [auth 1], UF [auth 3], UH [auth Z], V [auth A], VA [auth A], VC [auth B], VD [auth B], VE [auth 1], VF [auth 3], VH [auth Z], W [auth A], WA [auth A], WC [auth B], WF [auth 3], WG [auth 8], WH [auth Z], WJ [auth 6], X [auth A], XA [auth A], XC [auth B], XE [auth 1], XG [auth 8], XH [auth Z], XJ [auth 6], Y [auth A], YA [auth A], YB [auth B], YC [auth B], YD [auth F], YE [auth 1], YG [auth 8], YH [auth Z], YJ [auth 6], Z [auth A], ZA [auth A], ZB [auth B], ZC [auth B], ZD [auth F], ZE [auth 1], ZG [auth 8], ZH [auth Z], ZJ [auth 6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
CL0 (Subject of Investigation/LOI)
Query on CL0

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T [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
LMG (Subject of Investigation/LOI)
Query on LMG

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GE [auth J]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG (Subject of Investigation/LOI)
Query on LHG

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FI [auth Z] , IF [auth 1] , MB [auth A] , MK [auth 6] , NB [auth A] , NH [auth 8] , TJ [auth 5] , UD [auth B] , 
FI [auth Z], IF [auth 1], MB [auth A], MK [auth 6], NB [auth A], NH [auth 8], TJ [auth 5], UD [auth B], VB [auth A], VG [auth 7], YI [auth 4], ZI [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
LUT (Subject of Investigation/LOI)
Query on LUT

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CI [auth Z] , DI [auth Z] , EI [auth Z] , FF [auth 1] , GF [auth 1] , HF [auth 1] , KH [auth 8] , LH [auth 8] , 
CI [auth Z], DI [auth Z], EI [auth Z], FF [auth 1], GF [auth 1], HF [auth 1], KH [auth 8], LH [auth 8], NK [auth 6], QJ [auth 5], QK [auth 6], RG [auth 7], SG [auth 7], UJ [auth 5], VI [auth 4], WI [auth 4], XF [auth 3], YF [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
BCR (Subject of Investigation/LOI)
Query on BCR

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AG [auth 3] , BE [auth F] , BG [auth 3] , EE [auth G] , FE [auth I] , IE [auth J] , JE [auth K] , ME [auth K] , 
AG [auth 3], BE [auth F], BG [auth 3], EE [auth G], FE [auth I], IE [auth J], JE [auth K], ME [auth K], MH [auth 8], ND [auth B], NE [auth L], OB [auth A], OD [auth B], PB [auth A], PD [auth B], PK [auth 6], QB [auth A], QD [auth B], QE [auth L], RB [auth A], RD [auth B], RK [auth 6], SB [auth A], SD [auth B], SJ [auth 5], TG [auth 7], UG [auth 7], VJ [auth 5], WB [auth A], XB [auth B], XI [auth 4], ZF [auth 3]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PQN (Subject of Investigation/LOI)
Query on PQN

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KB [auth A], MD [auth B]PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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TB [auth A], WD [auth C], XD [auth C]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP16H06554
Japan Society for the Promotion of ScienceJapanJP16H06162
Japan Society for the Promotion of ScienceJapanJP16H06296

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-06-26
    Changes: Data collection, Database references