7DKZ | pdb_00007dkz

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 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7DKZ

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 543.37 kDa 
  • Atom Count: 36,093 
  • Modeled Residue Count: 3,200 
  • Deposited Residue Count: 3,377 
  • Unique protein chains: 16

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]195Lathyrus oleraceusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]269Lathyrus oleraceusMutation(s): 0 
Gene Names: lhaB
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
Explore Q41038 
Go to UniProtKB:  Q41038
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41038
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticC [auth 3]275Lathyrus oleraceusMutation(s): 0 
Gene Names: lhca3
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
Explore Q32904 
Go to UniProtKB:  Q32904
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ32904
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticD [auth 4]198Lathyrus oleraceusMutation(s): 0 
Gene Names: lhcA-P4
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
Explore Q9SQL2 
Go to UniProtKB:  Q9SQL2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQL2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]758Lathyrus oleraceusMutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
Explore P05310 
Go to UniProtKB:  P05310
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05310
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Lathyrus oleraceusMutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A0F6NGI2 (Pisum sativum)
Explore A0A0F6NGI2 
Go to UniProtKB:  A0A0F6NGI2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F6NGI2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Lathyrus oleraceusMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
Explore P10793 
Go to UniProtKB:  P10793
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10793
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaDH [auth D]143Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
Explore E1C9K8 
Go to UniProtKB:  E1C9K8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K8
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaEI [auth E]66Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
Explore E1C9K6 
Go to UniProtKB:  E1C9K6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9K6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-FJ [auth F]154Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
Explore A0A0M3KL12 
Go to UniProtKB:  A0A0M3KL12
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL12
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaGK [auth G]97Lathyrus oleraceusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaHL [auth H]88Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
Explore A0A0M3KL10 
Go to UniProtKB:  A0A0M3KL10
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KL10
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]40Lathyrus oleraceusMutation(s): 0 
Gene Names: psaI
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
Explore P17227 
Go to UniProtKB:  P17227
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17227
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]42Lathyrus oleraceusMutation(s): 0 
Gene Names: psaJ
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
Explore D5MAL3 
Go to UniProtKB:  D5MAL3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5MAL3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaLO [auth L]157Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
Explore E1C9L1 
Go to UniProtKB:  E1C9L1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9L1
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-KP [auth K]80Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
Explore E1C9L3 
Go to UniProtKB:  E1C9L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE1C9L3
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
MC [auth 4],
NG [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PE [auth A],
YA [auth 2]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
CE [auth A],
GG [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
ME [auth A],
QG [auth C],
RG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG

Query on HTG



Download:Ideal Coordinates CCD File
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 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
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

View Full Validation Report



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