5L8R

The structure of plant photosystem I super-complex at 2.6 angstrom resolution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6ZXS


Literature

Structure of the plant photosystem I supercomplex at 2.6 angstrom resolution.

Mazor, Y., Borovikova, A., Caspy, I., Nelson, N.

(2017) Nat Plants 3: 17014-17014

  • DOI: https://doi.org/10.1038/nplants.2017.14
  • Primary Citation of Related Structures:  
    5L8R

  • PubMed Abstract: 

    Four elaborate membrane complexes carry out the light reaction of oxygenic photosynthesis. Photosystem I (PSI) is one of two large reaction centres responsible for converting light photons into the chemical energy needed to sustain life. In the thylakoid membranes of plants, PSI is found together with its integral light-harvesting antenna, light-harvesting complex I (LHCI), in a membrane supercomplex containing hundreds of light-harvesting pigments. Here, we report the crystal structure of plant PSI-LHCI at 2.6 Å resolution. The structure reveals the configuration of PsaK, a core subunit important for state transitions in plants, a conserved network of water molecules surrounding the electron transfer centres and an elaborate structure of lipids bridging PSI and its LHCI antenna. We discuss the implications of the structure for energy transfer and the evolution of PSI.

    • Organizational Affiliation: 

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]193Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L2 (Pisum sativum)
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UniProt GroupE1C9L2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]269Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
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 
EC: 1.97.1.12
Membrane Entity: Yes 
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 
EC: 1.97.1.12
Membrane Entity: Yes 
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 
EC: 1.97.1.12
Membrane Entity: Yes 
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
Putative uncharacterized proteinI [auth E]66Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth F]154Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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UniProt GroupA0A0M3KL12
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsaGK [auth G]97Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIL [auth H]88Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
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 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKO [auth K]80Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinP [auth L]157Pisum sativumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9L1 (Pisum sativum)
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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EF [auth B],
FH [auth B],
II [auth J],
WC [auth 4],
WH [auth G]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL
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AB [auth 2]
BA [auth 1]
DA [auth 1]
KA [auth 1]
KB [auth 2]
AB [auth 2],
BA [auth 1],
DA [auth 1],
KA [auth 1],
KB [auth 2],
QC [auth 4],
RC [auth 4],
TC [auth 4],
UC [auth 4],
WA [auth 2],
XA [auth 2],
YB [auth 3],
ZA [auth 2]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
Query on CL0
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AD [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA
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AA [auth 1]
AC [auth 3]
AE [auth A]
AG [auth B]
AI [auth H]
AA [auth 1],
AC [auth 3],
AE [auth A],
AG [auth B],
AI [auth H],
BC [auth 3],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth B],
CA [auth 1],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth B],
DD [auth A],
DE [auth A],
DG [auth B],
DI [auth J],
EA [auth 1],
ED [auth A],
EE [auth A],
EG [auth B],
EI [auth J],
FA [auth 1],
FD [auth A],
FE [auth A],
FG [auth B],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
HC [auth 4],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
HI [auth J],
IC [auth 4],
ID [auth A],
IE [auth A],
IF [auth B],
IG [auth B],
JC [auth 4],
JD [auth A],
JE [auth A],
JF [auth B],
JG [auth B],
KC [auth 4],
KD [auth A],
KE [auth A],
KF [auth B],
KG [auth B],
LC [auth 4],
LD [auth A],
LE [auth A],
LF [auth B],
LG [auth B],
LH [auth F],
MC [auth 4],
MD [auth A],
ME [auth A],
MF [auth B],
MG [auth B],
MH [auth F],
MI [auth K],
NC [auth 4],
ND [auth A],
NE [auth A],
NF [auth B],
NG [auth B],
NI [auth K],
OA [auth 2],
OC [auth 4],
OD [auth A],
OE [auth A],
OF [auth B],
OG [auth B],
OI [auth K],
PA [auth 2],
PB [auth 3],
PC [auth 4],
PD [auth A],
PE [auth A],
PF [auth B],
PG [auth B],
PI [auth K],
QA [auth 2],
QB [auth 3],
QD [auth A],
QF [auth B],
QG [auth B],
QH [auth G],
RA [auth 2],
RB [auth 3],
RD [auth A],
RF [auth B],
RG [auth B],
RH [auth G],
RI [auth L],
SA [auth 2],
SB [auth 3],
SC [auth 4],
SD [auth A],
SF [auth B],
SH [auth G],
T [auth 1],
TA [auth 2],
TB [auth 3],
TD [auth A],
TF [auth B],
TH [auth G],
TI [auth L],
U [auth 1],
UA [auth 2],
UB [auth 3],
UD [auth A],
UF [auth B],
UI [auth L],
V [auth 1],
VA [auth 2],
VB [auth 3],
VC [auth 4],
VD [auth A],
VF [auth B],
VI [auth L],
W [auth 1],
WB [auth 3],
WD [auth A],
WF [auth B],
X [auth 1],
XB [auth 3],
XD [auth A],
XF [auth B],
Y [auth 1],
YA [auth 2],
YD [auth A],
YF [auth B],
Z [auth 1],
ZB [auth 3],
ZD [auth A],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG
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CB [auth 2]
DB [auth 2]
EB [auth 2]
FB [auth 2]
FI [auth J]
CB [auth 2],
DB [auth 2],
EB [auth 2],
FB [auth 2],
FI [auth J],
GB [auth 2],
GI [auth J],
HA [auth 1],
IA [auth 1],
IB [auth 2],
JB [auth 2],
NH [auth F],
OH [auth F],
UE [auth A],
VG [auth B],
VH [auth G],
WG [auth B],
YC [auth 4],
ZC [auth 4],
ZH [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG
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AF [auth A]
BB [auth 2]
GA [auth 1]
JA [auth 1]
SE [auth A]
AF [auth A],
BB [auth 2],
GA [auth 1],
JA [auth 1],
SE [auth A],
TG [auth B],
UG [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT
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GC [auth 4],
MA [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
ZEX
Query on ZEX
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KH [auth F](1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
LUT
Query on LUT
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FC [auth 4]
LA [auth 2]
LB [auth 3]
LI [auth J]
MB [auth 3]
FC [auth 4],
LA [auth 2],
LB [auth 3],
LI [auth J],
MB [auth 3],
Q [auth 1],
R [auth 1]
(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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AH [auth B]
BH [auth B]
BI [auth I]
CH [auth B]
CI [auth I]
AH [auth B],
BH [auth B],
BI [auth I],
CH [auth B],
CI [auth I],
DF [auth A],
DH [auth B],
EC [auth 4],
EH [auth B],
FF [auth B],
HH [auth B],
KI [auth J],
NA [auth 2],
NB [auth 3],
OB [auth 3],
PH [auth F],
QI [auth K],
S [auth 1],
SI [auth L],
UH [auth G],
VE [auth A],
WE [auth A],
WI [auth L],
XE [auth A],
XI [auth L],
YE [auth A],
ZE [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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CC [auth 3]
GH [auth B]
HB [auth 2]
JI [auth J]
TE [auth A]
CC [auth 3],
GH [auth B],
HB [auth 2],
JI [auth J],
TE [auth A],
XC [auth 4],
XG [auth B],
XH [auth G],
YG [auth B],
YH [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN
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RE [auth A],
SG [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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IH [auth C],
JH [auth C],
QE [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA
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DC [auth 3],
ZG [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189.611α = 90
b = 200.994β = 90
c = 212.943γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilIsrael293579
ISFIsrael71/14
I-COREIsrael1775/12

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-15
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Structure summary
  • Version 1.2: 2017-11-29
    Changes: Database references
  • Version 1.3: 2019-04-24
    Changes: Advisory, Author supporting evidence, Data collection
  • Version 2.0: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary