4XK8 | pdb_00004xk8

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 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 3.1 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: https://doi.org/10.1126/science.aab0214
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 1,046.38 kDa 
  • Atom Count: 71,157 
  • Modeled Residue Count: 6,350 
  • Deposited Residue Count: 6,434 
  • Unique protein chains: 16

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A,
Q [auth a]		742Lathyrus oleraceusMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B,
R [auth b]		733Lathyrus oleraceusMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC,
S [auth c]		80Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P10793 (Pisum sativum)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized proteinD,
T [auth d]		141Lathyrus oleraceusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinE,
U [auth e]		64Lathyrus oleraceusMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticF,
V [auth f]		151Lathyrus oleraceusMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG,
W [auth g]		95Lathyrus oleraceusMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinH,
X [auth h]		90Lathyrus oleraceusMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIII,
Y [auth i]		30Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJ,
Z [auth j]		39Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A4GGC6 (Phaseolus vulgaris)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKAA [auth k],
K		84Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L3 (Pisum sativum)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinBA [auth l],
L		153Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticCA [auth 6],
M [auth 1]		195Lathyrus oleraceusMutation(s): 0 
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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]		206Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticEA [auth 8],
O [auth 3]		218Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticFA [auth 9],
P [auth 4]		196Lathyrus oleraceusMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


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

Query on CHL


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
GE [auth B]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
BM [auth b],
XB [auth A],
ZD [auth B],
ZJ [auth a]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
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
  • Version 3.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.1: 2026-09-16
    Changes: Structure summary