6IGZ

Structure of PSI-LHCI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structure of a green algal photosystem I in complex with a large number of light-harvesting complex I subunits.

Qin, X.Pi, X.Wang, W.Han, G.Zhu, L.Liu, M.Cheng, L.Shen, J.R.Kuang, T.Sui, S.F.

(2019) Nat Plants 5: 263-272

  • DOI: https://doi.org/10.1038/s41477-019-0379-y
  • Primary Citation of Related Structures:  
    6IGZ

  • PubMed 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 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.


  • Organizational Affiliation

    School of Biological Science and Technology, University of Jinan, Jinan, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PsaA751Bryopsis corticulansMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V8GZZ2 (Bryopsis corticulans)
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UniProt GroupA0A4V8GZZ2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PsaB734Bryopsis corticulansMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A4V8H003
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PsaC81Bryopsis corticulansMutation(s): 0 
EC: 1.97.1.12
UniProt
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UniProt GroupA0A4V8H005
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsaD198Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsaE91Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsaF236Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsaG167Bryopsis corticulansMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaH133Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaI36Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaJ41Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V8GZZ3 (Bryopsis corticulans)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaK123Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V8GZZ4 (Bryopsis corticulans)
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UniProt GroupA0A4V8GZZ4
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaL204Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V8GZZ5 (Bryopsis corticulans)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-aM [auth 1],
R [auth 5]
226Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-cN [auth 2]256Bryopsis corticulansMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-dO [auth 3]281Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-bP [auth 4],
T [auth 8]
248Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A4V8GZZ9 (Bryopsis corticulans)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-gQ [auth 6]267Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-hS [auth 7]264Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-iU [auth 9]222Bryopsis corticulansMutation(s): 0 
UniProt
Find proteins for A0A4V8H002 (Bryopsis corticulans)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca-jV [auth 0]245Bryopsis corticulansMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIW [auth M]32Bryopsis corticulansMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0D6E2L8 (Bryopsis plumosa)
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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VD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AI [auth 6]
AL [auth 9]
BH [auth 4]
CF [auth 1]
FH [auth 4]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AD [auth B]
AF [auth 1]
AG [auth 2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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IJ [auth 5],
SH [auth 4],
YK [auth 8]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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DM [auth 0]
EK [auth 7]
GG [auth 2]
HJ [auth 5]
OB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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BK [auth 7]
BM [auth 0]
CK [auth 7]
CM [auth 0]
DG [auth 2]
(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
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
8CT
Query on 8CT

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CC [auth B]
CE [auth F]
DK [auth 7]
FG [auth 2]
FK [auth 7]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
PQN
Query on PQN

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MB [auth A],
OD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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AC [auth B],
AE [auth C],
ZD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG
Query on HTG

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KE [auth J],
VB [auth A]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-01
    Changes: Advisory, Data collection
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other
  • Version 1.4: 2020-03-04
    Changes: Source and taxonomy
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary