4Y28 | pdb_00004y28

The structure of plant photosystem I super-complex at 2.8 angstrom resolution.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.259 (DCC) 
  • R-Value Work: 
    0.259 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

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Ligand Structure Quality Assessment 


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

Literature

The structure of plant photosystem I super-complex at 2.8 angstrom resolution.

Mazor, Y., Borovikova, A., Nelson, N.

(2015) Elife 4: e07433-e07433

  • DOI: https://doi.org/10.7554/eLife.07433
  • Primary Citation Related Structures: 
    4Y28

  • PubMed Abstract: 

    Most life forms on Earth are supported by solar energy harnessed by oxygenic photosynthesis. In eukaryotes, photosynthesis is achieved by large membrane-embedded super-complexes, containing reaction centers and connected antennae. Here, we report the structure of the higher plant PSI-LHCI super-complex determined at 2.8 Å resolution. The structure includes 16 subunits and more than 200 prosthetic groups, which are mostly light harvesting pigments. The complete structures of the four LhcA subunits of LHCI include 52 chlorophyll a and 9 chlorophyll b molecules, as well as 10 carotenoids and 4 lipids. The structure of PSI-LHCI includes detailed protein pigments and pigment-pigment interactions, essential for the mechanism of excitation energy transfer and its modulation in one of nature's most efficient photochemical machines.

    • Organizational Affiliation: 
    • Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Macromolecule Content 

  • Total Structure Weight: 554.63 kDa 
  • Atom Count: 35,653 
  • Modeled Residue Count: 3,187 
  • Deposited Residue Count: 3,492 
  • Unique protein chains: 16

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1758Lathyrus oleraceusMutation(s): 4 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Lathyrus oleraceusMutation(s): 7 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05311 (Pisum sativum)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIC [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: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXD [auth J]42Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D5MAL3 (Pisum sativum)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIE [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: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
photosystem I reaction centerF [auth G]97Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized proteinG [auth L]167Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerH [auth C]81Lathyrus 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: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticI [auth D]147Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplasticJ [auth E]66Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for E1C9K6 (Pisum sativum)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIK [auth H]90Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL10 (Pisum sativum)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaKL [auth K]129Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M3KL11 (Pisum sativum)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IM [auth 2]269Lathyrus oleraceusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticN [auth 4]252Lathyrus oleraceusMutation(s): 1 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Light-harvesting complex I chlorophyll A/B-binding proteinO [auth 1]202Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticP [auth 3]275Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q32904 (Pisum sativum)
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Reference Sequence

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


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

Query on CHL


Download:Ideal Coordinates CCD File
AG [auth 4]
DF [auth 2]
EF [auth 2]
GF [auth 2]
IH [auth 3]
AG [auth 4],
DF [auth 2],
EF [auth 2],
GF [auth 2],
IH [auth 3],
QG [auth 1],
RG [auth 1],
XF [auth 4],
YF [auth 4]
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 2]
AH [auth 3]
BB [auth A]
AB [auth A],
AD [auth B],
AF [auth 2],
AH [auth 3],
BB [auth A],
BD [auth B],
BE [auth F],
BF [auth 2],
BG [auth 4],
BH [auth 3],
CB [auth A],
CD [auth B],
CE [auth F],
CF [auth 2],
CG [auth 4],
CH [auth 3],
DA [auth A],
DB [auth A],
DD [auth B],
DH [auth 3],
EA [auth A],
EB [auth A],
ED [auth B],
EH [auth 3],
FA [auth A],
FB [auth A],
FD [auth B],
FF [auth 2],
FH [auth 3],
GA [auth A],
GB [auth A],
GD [auth B],
GE [auth G],
GH [auth 3],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth G],
HF [auth 2],
HH [auth 3],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth G],
IG [auth 1],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JG [auth 1],
JH [auth 3],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KG [auth 1],
KH [auth 3],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LG [auth 1],
LH [auth 3],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth L],
MF [auth 2],
MG [auth 1],
MH [auth 3],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth L],
NF [auth 2],
NG [auth 1],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth L],
OF [auth 4],
OG [auth 1],
PA [auth A],
PC [auth B],
PD [auth B],
PF [auth 4],
PG [auth 1],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth 4],
QH [auth 3],
R [auth A],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RF [auth 4],
S [auth A],
SA [auth A],
SB [auth A],
SC [auth B],
SE [auth H],
SF [auth 4],
SG [auth 1],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TF [auth 4],
TG [auth 1],
UA [auth A],
UB [auth B],
UC [auth B],
UE [auth K],
UF [auth 4],
UG [auth 1],
VA [auth A],
VB [auth B],
VE [auth 2],
VF [auth 4],
VG [auth 1],
WA [auth A],
WB [auth B],
WD [auth J],
WE [auth 2],
WF [auth 4],
XA [auth A],
XB [auth B],
XE [auth 2],
YA [auth A],
YB [auth B],
YC [auth B],
YE [auth 2],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZE [auth 2],
ZF [auth 4],
ZG [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0


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

Query on LMG


Download:Ideal Coordinates CCD File
AE [auth F]
CC [auth B]
DE [auth F]
GG [auth 4]
KE [auth G]
AE [auth F],
CC [auth B],
DE [auth F],
GG [auth 4],
KE [auth G],
LF [auth 2],
XD [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG


Download:Ideal Coordinates CCD File
BC [auth B],
CA [auth A],
KF [auth 2],
W [auth A],
YG [auth 1]		1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
ZEX

Query on ZEX


Download:Ideal Coordinates CCD File
HG [auth 4](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
DG [auth 4]
EG [auth 4]
FG [auth 4]
IF [auth 2]
JF [auth 2]
DG [auth 4],
EG [auth 4],
FG [auth 4],
IF [auth 2],
JF [auth 2],
NH [auth 3],
OH [auth 3],
UD [auth I],
WG [auth 1],
XG [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
AA [auth A]
BA [auth A]
EC [auth B]
EE [auth F]
FC [auth B]
AA [auth A],
BA [auth A],
EC [auth B],
EE [auth F],
FC [auth B],
FE [auth F],
GC [auth B],
JE [auth G],
LE [auth L],
PB [auth A],
PE [auth L],
PH [auth 3],
TE [auth K],
VC [auth B],
VD [auth I],
WC [auth B],
X [auth A],
Y [auth A],
YD [auth J],
Z [auth A],
ZD [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU


Download:Ideal Coordinates CCD File
SD [auth B],
TD [auth B]		DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN


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

Query on SF4


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

Query on CA


Download:Ideal Coordinates CCD File
DC [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.259 (DCC) 
  • R-Value Work:  0.259 (Depositor), 0.246 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 189α = 90
b = 201.9β = 90
c = 213.2γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
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: 2015-08-19
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Advisory, Derived calculations, Structure summary
  • Version 1.3: 2018-09-19
    Changes: Data collection
  • Version 1.4: 2019-04-24
    Changes: Advisory, Data collection, Source and taxonomy
  • Version 2.0: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary