5L8R | pdb_00005l8r

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 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 564.88 kDa 
  • Atom Count: 37,583 
  • Modeled Residue Count: 3,230 
  • Deposited Residue Count: 3,375 
  • Unique protein chains: 16

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]193Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]269Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticC [auth 3]275Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticD [auth 4]198Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]758Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaDH [auth D]143Lathyrus oleraceusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinI [auth E]66Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth F]154Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL12 (Pisum sativum)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaGK [auth G]97Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIL [auth H]88Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]40Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]42Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKO [auth K]80Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinP [auth L]157Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
AD [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA

Query on CLA


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


Download:Ideal Coordinates CCD File
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


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

Query on SF4


Download:Ideal Coordinates CCD File
IH [auth C],
JH [auth C],
QE [auth A]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
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 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
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