4XK8

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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This is version 2.0 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: https://doi.org/10.1126/science.aab0214
  • Primary Citation of Related Structures:  
    4XK8

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
Q [auth a]		742Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
R [auth b]		733Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05311 (Pisum sativum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
S [auth c]		80Pisum sativumMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Find proteins for P10793 (Pisum sativum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized proteinD,
T [auth d]		141Pisum sativumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinE,
U [auth e]		64Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9K6 (Pisum sativum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticF,
V [auth f]		151Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG,
W [auth g]		95Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinH,
X [auth h]		90Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIII,
Y [auth i]		30Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P17227 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJ,
Z [auth j]		39Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKAA [auth k],
K		84Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinBA [auth l],
L		153Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9L1 (Pisum sativum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticCA [auth 6],
M [auth 1]		195Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IDA [auth 7],
N [auth 2]		206Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q41038 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticEA [auth 8],
O [auth 3]		218Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q32904 (Pisum sativum)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticFA [auth 9],
P [auth 4]		196Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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HE [auth B],
IM [auth b]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL
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AH [auth 3]
AP [auth 8]
BI [auth 4]
CG [auth 2]
DO [auth 7]
AH [auth 3],
AP [auth 8],
BI [auth 4],
CG [auth 2],
DO [auth 7],
GG [auth 2],
HG [auth 2],
HO [auth 7],
IG [auth 2],
IO [auth 7],
JF [auth 1],
JO [auth 7],
KN [auth 6],
OF [auth 1],
PG [auth 2],
PN [auth 6],
PP [auth 9],
QO [auth 7],
QP [auth 9],
RH [auth 4],
RP [auth 9],
SH [auth 4],
TH [auth 4],
ZP [auth 9]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA
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AB [auth A]
AD [auth B]
AF [auth K]
AI [auth 4]
AJ [auth a]
AB [auth A],
AD [auth B],
AF [auth K],
AI [auth 4],
AJ [auth a],
AK [auth a],
AL [auth b],
AM [auth b],
AN [auth k],
BB [auth A],
BD [auth B],
BH [auth 3],
BJ [auth a],
BL [auth b],
BP [auth 8],
CB [auth A],
CD [auth B],
CH [auth 3],
CJ [auth a],
CL [auth b],
CP [auth 8],
DB [auth A],
DD [auth B],
DF [auth L],
DG [auth 2],
DH [auth 3],
DJ [auth a],
DL [auth b],
DN [auth l],
DP [auth 8],
EB [auth A],
ED [auth B],
EF [auth L],
EG [auth 2],
EH [auth 3],
EJ [auth a],
EL [auth b],
EN [auth l],
EO [auth 7],
EP [auth 8],
FB [auth A],
FD [auth B],
FF [auth L],
FG [auth 2],
FH [auth 3],
FJ [auth a],
FL [auth b],
FN [auth l],
FO [auth 7],
FP [auth 8],
GA [auth A],
GB [auth A],
GD [auth B],
GH [auth 3],
GJ [auth a],
GL [auth b],
GO [auth 7],
GP [auth 8],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth B],
HH [auth 3],
HI [auth a],
HJ [auth a],
HL [auth b],
HP [auth 8],
IA [auth A],
IB [auth A],
ID [auth B],
IH [auth 3],
II [auth a],
IJ [auth a],
IL [auth b],
JA [auth A],
JB [auth A],
JD [auth B],
JG [auth 2],
JI [auth a],
JJ [auth a],
JL [auth b],
KA [auth A],
KB [auth A],
KD [auth B],
KE [auth F],
KF [auth 1],
KG [auth 2],
KI [auth a],
KJ [auth a],
KK [auth a],
KL [auth b],
KO [auth 7],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth 1],
LG [auth 2],
LI [auth a],
LJ [auth a],
LL [auth b],
LN [auth 6],
LO [auth 7],
LP [auth 9],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MF [auth 1],
MG [auth 2],
MI [auth a],
MJ [auth a],
ML [auth b],
MM [auth f],
MN [auth 6],
MO [auth 7],
MP [auth 9],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth F],
NF [auth 1],
NG [auth 2],
NH [auth 4],
NI [auth a],
NJ [auth a],
NK [auth b],
NL [auth b],
NM [auth f],
NN [auth 6],
NO [auth 7],
NP [auth 9],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OG [auth 2],
OH [auth 4],
OI [auth a],
OJ [auth a],
OK [auth b],
OL [auth b],
ON [auth 6],
OO [auth 7],
OP [auth 9],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth G],
PF [auth 1],
PH [auth 4],
PI [auth a],
PJ [auth a],
PK [auth b],
PL [auth b],
PM [auth g],
PO [auth 7],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth 1],
QH [auth 4],
QI [auth a],
QJ [auth a],
QK [auth b],
QL [auth b],
QM [auth g],
QN [auth 6],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RF [auth 1],
RI [auth a],
RJ [auth a],
RK [auth b],
RL [auth b],
RM [auth g],
RN [auth 6],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SF [auth 1],
SI [auth a],
SJ [auth a],
SK [auth b],
SL [auth b],
SN [auth 6],
SP [auth 9],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth 1],
TI [auth a],
TJ [auth a],
TK [auth b],
TL [auth b],
TN [auth 6],
TP [auth 9],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth 1],
UG [auth 3],
UH [auth 4],
UI [auth a],
UJ [auth a],
UK [auth b],
UL [auth b],
UN [auth 6],
UP [auth 9],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth 1],
VG [auth 3],
VH [auth 4],
VI [auth a],
VJ [auth a],
VK [auth b],
VL [auth b],
VM [auth j],
VN [auth 6],
VO [auth 8],
VP [auth 9],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth J],
WF [auth 1],
WG [auth 3],
WH [auth 4],
WI [auth a],
WJ [auth a],
WK [auth b],
WL [auth b],
WN [auth 6],
WO [auth 8],
WP [auth 9],
XA [auth A],
XC [auth B],
XD [auth B],
XG [auth 3],
XH [auth 4],
XI [auth a],
XJ [auth a],
XK [auth b],
XL [auth b],
XN [auth 6],
XO [auth 8],
XP [auth 9],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YG [auth 3],
YH [auth 4],
YI [auth a],
YJ [auth a],
YK [auth b],
YL [auth b],
YM [auth k],
YO [auth 8],
YP [auth 9],
ZA [auth A],
ZC [auth B],
ZE [auth K],
ZG [auth 3],
ZH [auth 4],
ZI [auth a],
ZK [auth b],
ZL [auth b],
ZM [auth k],
ZO [auth 8]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG
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DQ [auth 9],
FI [auth 4],
GI [auth 4],
JN [auth 6],
QE [auth G]		1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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AC [auth A]
AG [auth 1]
BK [auth a]
BO [auth 6]
CK [auth a]
AC [auth A],
AG [auth 1],
BK [auth a],
BO [auth 6],
CK [auth a],
IF [auth 1],
IN [auth 6],
MH [auth 3],
TG [auth 2],
UO [auth 7],
ZB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT
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BQ [auth 9]
DI [auth 4]
JP [auth 8]
KH [auth 3]
RG [auth 2]
BQ [auth 9],
DI [auth 4],
JP [auth 8],
KH [auth 3],
RG [auth 2],
SO [auth 7],
YF [auth 1],
ZN [auth 6]
(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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AQ [auth 9]
BG [auth 1]
CI [auth 4]
CO [auth 6]
IP [auth 8]
AQ [auth 9],
BG [auth 1],
CI [auth 4],
CO [auth 6],
IP [auth 8],
JH [auth 3],
QG [auth 2],
RO [auth 7],
XF [auth 1],
YN [auth 6]
(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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AE [auth B]
AO [auth 6]
BC [auth A]
BE [auth B]
BF [auth K]
AE [auth B],
AO [auth 6],
BC [auth A],
BE [auth B],
BF [auth K],
BN [auth k],
CC [auth A],
CE [auth B],
CF [auth L],
CM [auth b],
CN [auth l],
CQ [auth 9],
DC [auth A],
DE [auth B],
DK [auth a],
DM [auth b],
EC [auth A],
EE [auth B],
EI [auth 4],
EK [auth a],
EM [auth b],
FC [auth A],
FE [auth B],
FK [auth a],
FM [auth b],
GF [auth L],
GK [auth a],
GM [auth b],
GN [auth l],
HF [auth L],
HK [auth a],
HM [auth b],
HN [auth l],
IK [auth a],
JC [auth A],
KC [auth B],
KP [auth 8],
LH [auth 3],
MK [auth b],
OE [auth F],
OM [auth f],
SG [auth 2],
SM [auth g],
TE [auth G],
TM [auth i],
TO [auth 7],
UE [auth I],
WM [auth j],
XE [auth J],
XM [auth j],
YE [auth K],
ZF [auth 1]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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GE [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN
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BM [auth b],
XB [auth A],
ZD [auth B],
ZJ [auth a]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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GC [auth A]
IE [auth C]
JE [auth C]
JK [auth a]
JM [auth c]
GC [auth A],
IE [auth C],
JE [auth C],
JK [auth a],
JM [auth c],
KM [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG
Query on HTG
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IC [auth A]
LE [auth F]
LK [auth a]
LM [auth f]
UM [auth j]
IC [auth A],
LE [auth F],
LK [auth a],
LM [auth f],
UM [auth j],
VE [auth J]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.624α = 90
b = 192.22β = 91.41
c = 175.089γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-07-08
    Changes: Derived calculations
  • Version 1.2: 2019-05-01
    Changes: Advisory, Data collection, Derived calculations, Source and taxonomy
  • Version 1.3: 2020-03-04
    Changes: Source and taxonomy, Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 2.0: 2024-11-20
    Changes: Data collection, Database references, Non-polymer description, Structure summary