4XK8

Crystal structure of plant photosystem I-LHCI super-complex at 2.8 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for energy transfer pathways in the plant PSI-LHCI supercomplex

Qin, X.Suga, M.Kuang, T.Shen, J.R.

(2015) Science 348: 989-995

  • DOI: 10.1126/science.aab0214

  • PubMed Abstract: 
  • Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that cap ...

    Photosynthesis converts solar energy to chemical energy by means of two large pigment-protein complexes: photosystem I (PSI) and photosystem II (PSII). In higher plants, the PSI core is surrounded by a large light-harvesting complex I (LHCI) that captures sunlight and transfers the excitation energy to the core with extremely high efficiency. We report the structure of PSI-LHCI, a 600-kilodalton membrane protein supercomplex, from Pisum sativum (pea) at a resolution of 2.8 angstroms. The structure reveals the detailed arrangement of pigments and other cofactors—especially within LHCI—as well as numerous specific interactions between the PSI core and LHCI. These results provide a firm structural basis for our understanding on the energy transfer and photoprotection mechanisms within the PSI-LHCI supercomplex.


    Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China. Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Tsushima Naka 3-1-1, Okayama 700-8530, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A, a
742Pisum sativumMutation(s): 0 
Gene Names: psaA (psaA1)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P05310 (Pisum sativum)
Go to UniProtKB:  P05310
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B, b
733Pisum sativumMutation(s): 0 
Gene Names: psaB (psaA2)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P05311 (Pisum sativum)
Go to UniProtKB:  P05311
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C, c
80Pisum sativumMutation(s): 0 
Gene Names: psaC (frxA)
EC: 1.97.1.12
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P10793 (Pisum sativum)
Go to UniProtKB:  P10793
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized protein
D, d
141Glycine maxMutation(s): 0 
Gene Names: psaD (100101915)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for A5Z2K3 (Glycine max)
Go to UniProtKB:  A5Z2K3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
E, e
64Pisum sativumMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for E1C9K6 (Pisum sativum)
Go to UniProtKB:  E1C9K6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit III, chloroplastic
F, f
151Spinacia oleraceaMutation(s): 0 
Gene Names: PSAF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P12355 (Spinacia oleracea)
Go to UniProtKB:  P12355
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit V, chloroplastic
G, g
95Spinacia oleraceaMutation(s): 0 
Gene Names: PSAG
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P12357 (Spinacia oleracea)
Go to UniProtKB:  P12357
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
H, h
90Glycine maxMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for C6T221 (Glycine max)
Go to UniProtKB:  C6T221
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit VIII
I, i
30Pisum sativumMutation(s): 0 
Gene Names: psaI
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for P17227 (Pisum sativum)
Go to UniProtKB:  P17227
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J, j
39Phaseolus vulgarisMutation(s): 0 
Gene Names: psaJ
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for A4GGC6 (Phaseolus vulgaris)
Go to UniProtKB:  A4GGC6
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit X psaK
K, k
84Pisum sativumMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for E1C9L3 (Pisum sativum)
Go to UniProtKB:  E1C9L3
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
L, l
153Pisum sativumMutation(s): 0 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for E1C9L1 (Pisum sativum)
Go to UniProtKB:  E1C9L1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein 6, chloroplastic
1, 6
195Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA1 (CAB6)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q01667 (Arabidopsis thaliana)
Go to UniProtKB:  Q01667
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Type II chlorophyll a/b binding protein from photosystem I
2, 7
206Pisum sativumMutation(s): 0 
Gene Names: lhaB
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q41038 (Pisum sativum)
Go to UniProtKB:  Q41038
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein 3, chloroplastic
3, 8
218Pisum sativumMutation(s): 0 
Gene Names: lhca3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q32904 (Pisum sativum)
Go to UniProtKB:  Q32904
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein P4, chloroplastic
4, 9
196Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Photosystems
Protein: 
Photosystem I (plant)
Find proteins for Q9SQL2 (Pisum sativum)
Go to UniProtKB:  Q9SQL2
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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Download CCD File 
A, a, c, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
PQN
Query on PQN

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Download CCD File 
a, A, B, b
PHYLLOQUINONE
VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
LUT
Query on LUT

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1, 2, 3, 4, 6, 7, 8, 9
(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
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
CLA
Query on CLA

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1, 2, 3, 4, 6, 7, 8, 9, a, A, b, B, f, F, g, G, j, J, k, K, L, l
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
XAT
Query on XAT

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Download CCD File 
1, 2, 3, 4, 6, 7, 8, 9
(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
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
 Ligand Interaction
HTG
Query on HTG

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Download CCD File 
a, A, f, F, j, J
HEPTYL 1-THIOHEXOPYRANOSIDE
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
 Ligand Interaction
DGD
Query on DGD

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Download CCD File 
b, B
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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Download CCD File 
4, 6, 9, G
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
1, 2, 3, 4, 6, 7, 8, 9, a, A, b, B, f, F, g, G, i, I, j, J, K, k, L, l
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
B
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
CHL
Query on CHL

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Download CCD File 
1, 2, 3, 4, 6, 7, 8, 9
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-YFMFQLGVDX
 Ligand Interaction
LHG
Query on LHG

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Download CCD File 
1, 2, 3, 6, 7, A, a
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 165.624α = 90.00
b = 192.220β = 91.41
c = 175.089γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Type: Derived calculations