7DKZ

Structure of plant photosystem I-light harvesting complex I supercomplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Literature

Structure of plant photosystem I-light harvesting complex I supercomplex at 2.4 angstrom resolution.

Wang, J.Yu, L.J.Wang, W.Yan, Q.Kuang, T.Qin, X.Shen, J.R.

(2021) J Integr Plant Biol 63: 1367-1381

  • DOI: https://doi.org/10.1111/jipb.13095
  • Primary Citation of Related Structures:  
    7DKZ

  • PubMed Abstract: 

    Photosystem I (PSI) is one of the two photosystems in photosynthesis, and performs a series of electron transfer reactions leading to the reduction of ferredoxin. In higher plants, PSI is surrounded by four light-harvesting complex I (LHCI) subunits, which harvest and transfer energy efficiently to the PSI core. The crystal structure of PSI-LHCI supercomplex has been analyzed up to 2.6 Å resolution, providing much information on the arrangement of proteins and cofactors in this complicated supercomplex. Here we have optimized crystallization conditions, and analyzed the crystal structure of PSI-LHCI at 2.4 Å resolution. Our structure showed some shift of the LHCI, especially the Lhca4 subunit, away from the PSI core, suggesting the indirect connection and inefficiency of energy transfer from this Lhca subunit to the PSI core. We identified five new lipids in the structure, most of them are located in the gap region between the Lhca subunits and the PSI core. These lipid molecules may play important roles in binding of the Lhca subunits to the core, as well as in the assembly of the supercomplex. The present results thus provide novel information for the elucidation of the mechanisms for the light-energy harvesting, transfer and assembly of this supercomplex.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]195Pisum sativumMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]269Pisum sativumMutation(s): 0 
Gene Names: lhaB
UniProt
Find proteins for Q41038 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticC [auth 3]275Pisum sativumMutation(s): 0 
Gene Names: lhca3
UniProt
Find proteins for Q32904 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticD [auth 4]198Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]758Pisum sativumMutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
UniProt
Find proteins for P05310 (Pisum sativum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Pisum sativumMutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Pisum sativumMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
UniProt
Find proteins for P10793 (Pisum sativum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDH [auth D]143Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEI [auth E]66Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-FJ [auth F]154Pisum sativumMutation(s): 0 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaGK [auth G]97Pisum sativumMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaHL [auth H]88Pisum sativumMutation(s): 0 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]40Pisum sativumMutation(s): 0 
Gene Names: psaI
UniProt
Find proteins for P17227 (Pisum sativum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]42Pisum sativumMutation(s): 0 
Gene Names: psaJ
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaLO [auth L]157Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KP [auth K]80Pisum sativumMutation(s): 0 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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MC [auth 4],
NG [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AB [auth 3]
EC [auth 4]
GB [auth 3]
KA [auth 2]
LA [auth 2]
AB [auth 3],
EC [auth 4],
GB [auth 3],
KA [auth 2],
LA [auth 2],
MA [auth 2],
QB [auth 4],
TA [auth 2],
U [auth 1],
UB [auth 4],
VB [auth 4],
WB [auth 4]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth 1]
AC [auth 4]
AD [auth A]
AE [auth A]
AF [auth B]
AA [auth 1],
AC [auth 4],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
BA [auth 1],
BB [auth 3],
BC [auth 4],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
CA [auth 1],
CB [auth 3],
CC [auth 4],
CD [auth A],
CF [auth B],
CG [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
EB [auth 3],
ED [auth A],
EF [auth B],
EG [auth B],
EH [auth G],
FB [auth 3],
FD [auth A],
FF [auth B],
FG [auth B],
FH [auth G],
GD [auth A],
GF [auth B],
GH [auth G],
HA [auth 2],
HB [auth 3],
HD [auth A],
HF [auth B],
IA [auth 2],
IB [auth 3],
ID [auth A],
IF [auth B],
JA [auth 2],
JB [auth 3],
JD [auth A],
JF [auth B],
JH [auth J],
KB [auth 3],
KD [auth A],
KF [auth B],
LB [auth 3],
LD [auth A],
LF [auth B],
LH [auth J],
MB [auth 3],
MD [auth A],
MF [auth B],
NA [auth 2],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth B],
OA [auth 2],
OC [auth A],
OD [auth A],
OF [auth B],
PA [auth 2],
PC [auth A],
PD [auth A],
PF [auth B],
PH [auth L],
Q [auth 1],
QA [auth 2],
QC [auth A],
QD [auth A],
QF [auth B],
QH [auth L],
R [auth 1],
RA [auth 2],
RB [auth 4],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
RH [auth L],
S [auth 1],
SA [auth 2],
SB [auth 4],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
T [auth 1],
TB [auth 4],
TC [auth A],
TD [auth A],
TE [auth B],
TF [auth B],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
UH [auth K],
V [auth 1],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
VG [auth F],
VH [auth K],
W [auth 1],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
X [auth 1],
XB [auth 4],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
XG [auth F],
Y [auth 1],
YB [auth 4],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
YG [auth F],
Z [auth 1],
ZA [auth 2],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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AH [auth F],
CH [auth G],
IC [auth 4],
JC [auth 4],
PG [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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DH [auth G]
EE [auth A]
FE [auth A]
GA [auth 1]
QE [auth B]
DH [auth G],
EE [auth A],
FE [auth A],
GA [auth 1],
QE [auth B],
TG [auth F],
XA [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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EA [auth 1],
GC [auth 4],
OB [auth 3],
VA [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
LUT
Query on LUT

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DA [auth 1],
FC [auth 4],
NB [auth 3],
UA [auth 2]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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FA [auth 1]
GE [auth A]
HC [auth 4]
HE [auth A]
HG [auth B]
FA [auth 1],
GE [auth A],
HC [auth 4],
HE [auth A],
HG [auth B],
HH [auth G],
IE [auth A],
IG [auth B],
IH [auth I],
JE [auth A],
JG [auth B],
KE [auth A],
KG [auth B],
LE [auth A],
LG [auth B],
MG [auth B],
MH [auth J],
NH [auth J],
OH [auth L],
PB [auth 3],
SH [auth L],
TH [auth L],
UG [auth F],
WA [auth 2],
WH [auth K],
ZG [auth F]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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PE [auth A],
YA [auth 2]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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

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ME [auth A],
QG [auth C],
RG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG
Query on HTG

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BH [auth F]
KC [auth 4]
KH [auth J]
LC [auth 4]
OE [auth A]
BH [auth F],
KC [auth 4],
KH [auth J],
LC [auth 4],
OE [auth A],
OG [auth B],
SG [auth F],
WG [auth F]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 225.652α = 90
b = 168.952β = 121.39
c = 185.224γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 2.0: 2021-07-21
    Changes: Data collection, Database references, Non-polymer description
  • Version 2.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-10-09
    Changes: Database references, Structure summary