3LW5 | pdb_00003lw5

Improved model of plant photosystem I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.383 (Depositor), 0.375 (DCC) 
  • R-Value Work: 
    0.349 (Depositor), 0.353 (DCC) 
  • R-Value Observed: 
    0.351 (Depositor) 

Starting Model: experimental
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Literature

Structure determination and improved model of plant photosystem I

Amunts, A., Toporik, H., Borovikova, A., Nelson, N.

(2010) J Biological Chem 285: 3478-3486

  • DOI: https://doi.org/10.1074/jbc.M109.072645
  • Primary Citation Related Structures: 
    2WSC, 2WSE, 2WSF, 3LW5

  • PubMed Abstract: 

    Photosystem I functions as a sunlight energy converter, catalyzing one of the initial steps in driving oxygenic photosynthesis in cyanobacteria, algae, and higher plants. Functionally, Photosystem I captures sunlight and transfers the excitation energy through an intricate and precisely organized antenna system, consisting of a pigment network, to the center of the molecule, where it is used in the transmembrane electron transfer reaction. Our current understanding of the sophisticated mechanisms underlying these processes has profited greatly from elucidation of the crystal structures of the Photosystem I complex. In this report, we describe the developments that ultimately led to enhanced structural information of plant Photosystem I. In addition, we report an improved crystallographic model at 3.3-A resolution, which allows analysis of the structure in more detail. An improved electron density map yielded identification and tracing of subunit PsaK. The location of an additional ten beta-carotenes as well as five chlorophylls and several loop regions, which were previously uninterpretable, are now modeled. This represents the most complete plant Photosystem I structure obtained thus far, revealing the locations of and interactions among 17 protein subunits and 193 non-covalently bound photochemical cofactors. Using the new crystal structure, we examine the network of contacts among the protein subunits from the structural perspective, which provide the basis for elucidating the functional organization of the complex.

    • Organizational Affiliation: 
    • Biochemistry Department, George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Macromolecule Content 

  • Total Structure Weight: 550.2 kDa 
  • Atom Count: 36,370 
  • Modeled Residue Count: 3,182 
  • Deposited Residue Count: 3,211 
  • Unique protein chains: 18

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1738Lathyrus oleraceusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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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): 0 
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 iron-sulfur center81Lathyrus 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
Putative uncharacterized protein138Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for E1C9K8 (Pisum sativum)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein64Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K6 (Pisum sativum)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic154Lathyrus 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 protein95Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P20120 (Pisum sativum)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein69Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for E1C9K9 (Pisum sativum)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII30Lathyrus 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 IX42Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit X psaK84Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative uncharacterized protein161Lathyrus 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-N subunitM [auth N]85Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
CHAIN RN [auth R]53unidentifiedMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
AT3g54890O [auth 1]170Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IP [auth 2]176Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticQ [auth 3]172Lathyrus 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: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein P4, chloroplasticR [auth 4]166Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AH [auth 2]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AH [auth 2],
AI [auth 3],
AJ [auth 4],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BF [auth J],
BH [auth 2],
BI [auth 3],
BJ [auth 4],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth J],
CH [auth 2],
CI [auth 3],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth F],
DH [auth 2],
DI [auth 3],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth F],
EF [auth K],
EG [auth 1],
EH [auth 2],
EI [auth 3],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth F],
FF [auth K],
FG [auth 1],
FH [auth 2],
FI [auth 3],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth K],
GG [auth 1],
GH [auth 2],
GI [auth 3],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth K],
HG [auth 1],
HH [auth 2],
HI [auth 3],
IA [auth A],
IC [auth B],
ID [auth B],
IG [auth 1],
IH [auth 2],
JA [auth A],
JC [auth B],
JD [auth B],
JE [auth G],
JG [auth 1],
JH [auth 2],
KA [auth A],
KC [auth B],
KD [auth B],
KG [auth 1],
KH [auth 2],
LA [auth A],
LC [auth B],
LG [auth 1],
LI [auth 4],
MA [auth A],
MC [auth B],
MF [auth L],
MG [auth 1],
MI [auth 4],
NA [auth A],
NC [auth B],
NE [auth H],
NF [auth L],
NG [auth 1],
NI [auth 4],
OA [auth A],
OC [auth B],
OE [auth H],
OF [auth L],
OG [auth 1],
OI [auth 4],
PA [auth A],
PC [auth B],
PE [auth H],
PF [auth L],
PG [auth 1],
PH [auth 3],
PI [auth 4],
QA [auth A],
QC [auth B],
QE [auth H],
QF [auth L],
QG [auth 1],
QH [auth 3],
QI [auth 4],
RA [auth A],
RC [auth B],
RF [auth L],
RG [auth 1],
RH [auth 3],
RI [auth 4],
S [auth A],
SA [auth A],
SC [auth B],
SG [auth 1],
SH [auth 3],
SI [auth 4],
T [auth A],
TA [auth A],
TC [auth B],
TH [auth 3],
TI [auth 4],
U [auth A],
UA [auth A],
UC [auth B],
UH [auth 3],
UI [auth 4],
V [auth A],
VA [auth A],
VB [auth A],
VC [auth B],
VF [auth R],
VH [auth 3],
VI [auth 4],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth R],
WG [auth 2],
WH [auth 3],
WI [auth 4],
X [auth A],
XA [auth A],
XB [auth A],
XC [auth B],
XG [auth 2],
XH [auth 3],
XI [auth 4],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YE [auth I],
YG [auth 2],
YH [auth 3],
YI [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZG [auth 2],
ZH [auth 3],
ZI [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG


Download:Ideal Coordinates CCD File
VD [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
BCR

Query on BCR


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AF [auth I]
DF [auth J]
GE [auth F]
HE [auth F]
II [auth 3]
AF [auth I],
DF [auth J],
GE [auth F],
HE [auth F],
II [auth 3],
JB [auth A],
KB [auth A],
LB [auth A],
MB [auth A],
MD [auth B],
NB [auth A],
ND [auth B],
OD [auth B],
PD [auth B],
QD [auth B],
RD [auth B],
SF [auth L],
TG [auth 1],
ZE [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU


Download:Ideal Coordinates CCD File
AE [auth D]
AG [auth R]
BE [auth E]
BG [auth R]
CE [auth E]
AE [auth D],
AG [auth R],
BE [auth E],
BG [auth R],
CE [auth E],
CG [auth R],
CJ [auth 4],
DG [auth R],
DJ [auth 4],
EJ [auth 4],
FJ [auth 4],
GJ [auth 4],
HJ [auth 4],
IE [auth F],
IF [auth K],
IJ [auth 4],
JF [auth K],
JI [auth 3],
JJ [auth 4],
KE [auth G],
KF [auth K],
KI [auth 3],
LE [auth G],
LF [auth K],
LH [auth 2],
ME [auth G],
MH [auth 2],
NH [auth 2],
OB [auth A],
OH [auth 2],
PB [auth A],
QB [auth A],
RB [auth A],
RE [auth H],
SB [auth A],
SD [auth B],
SE [auth H],
TB [auth A],
TD [auth B],
TE [auth H],
TF [auth L],
UD [auth B],
UE [auth H],
UF [auth N],
UG [auth 1],
VE [auth H],
VG [auth 1],
WE [auth H],
XD [auth C],
XE [auth H],
XF [auth R],
YF [auth R],
ZF [auth R]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN


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

Query on SF4


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UB [auth A],
YD [auth C],
ZD [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.383 (Depositor), 0.375 (DCC) 
  • R-Value Work:  0.349 (Depositor), 0.353 (DCC) 
  • R-Value Observed: 0.351 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.655α = 90
b = 189.086β = 91.24
c = 129.388γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-08-01
    Changes: Non-polymer description
  • Version 1.3: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 2.0: 2021-09-22
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2023-11-01
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary