2WSE | pdb_00002wse

Improved Model of Plant Photosystem I

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 
    0.375 (Depositor), 0.408 (DCC) 
  • R-Value Work: 
    0.369 (Depositor), 0.387 (DCC) 
  • R-Value Observed: 
    0.369 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2WSE

Ligand Structure Quality Assessment 


This is version 7.0 of the entry. See complete history. 

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: 651.64 kDa 
  • Atom Count: 36,461 
  • Modeled Residue Count: 3,186 
  • Deposited Residue Count: 4,161 
  • Unique protein chains: 18

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
AT3G54890A [auth 1]241Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q01667 (Arabidopsis thaliana)
Explore Q01667 
Go to UniProtKB:  Q01667
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01667
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM IB [auth 2]269Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41038 (Pisum sativum)
Explore Q41038 
Go to UniProtKB:  Q41038
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41038
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LHCA3C [auth 3]276Glycine maxMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for C6TEX2 (Glycine max)
Explore C6TEX2 
Go to UniProtKB:  C6TEX2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC6TEX2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTICD [auth 4]251Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SQL2 (Pisum sativum)
Explore Q9SQL2 
Go to UniProtKB:  Q9SQL2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SQL2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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 
UniProt
Find proteins for P05310 (Pisum sativum)
Explore P05310 
Go to UniProtKB:  P05310
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05310
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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
Find proteins for P05311 (Pisum sativum)
Explore P05311 
Go to UniProtKB:  P05311
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05311
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
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
Find proteins for P10793 (Pisum sativum)
Explore P10793 
Go to UniProtKB:  P10793
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10793
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTICH [auth D]212Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12353 (Spinacia oleracea)
Explore P12353 
Go to UniProtKB:  P12353
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12353
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTICI [auth E]143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9S831 (Arabidopsis thaliana)
Explore Q9S831 
Go to UniProtKB:  Q9S831
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S831
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTICJ [auth F]231Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12355 (Spinacia oleracea)
Explore P12355 
Go to UniProtKB:  P12355
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12355
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTICK [auth G]167Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12357 (Spinacia oleracea)
Explore P12357 
Go to UniProtKB:  P12357
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12357
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTICL [auth H]144Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P22179 (Spinacia oleracea)
Explore P22179 
Go to UniProtKB:  P22179
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22179
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT VIIIM [auth I]40Lathyrus oleraceusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17227 (Pisum sativum)
Explore P17227 
Go to UniProtKB:  P17227
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17227
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT IXN [auth J]44Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P17230 (Spinacia oleracea)
Explore P17230 
Go to UniProtKB:  P17230
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17230
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTICO [auth K]131Hordeum vulgareMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P36886 (Hordeum vulgare)
Explore P36886 
Go to UniProtKB:  P36886
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36886
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTICP [auth L]216Spinacia oleraceaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q41385 (Spinacia oleracea)
Explore Q41385 
Go to UniProtKB:  Q41385
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ41385
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNITQ [auth N]170Phaseolus vulgarisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q84U30 (Phaseolus vulgaris)
Explore Q84U30 
Go to UniProtKB:  Q84U30
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84U30
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOTOSYSTEM I-N SUBUNIT53Lathyrus oleraceusMutation(s): 0 

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth 2]
AC [auth 3]
AD [auth 4]
AE [auth A]
AG [auth B]
AB [auth 2],
AC [auth 3],
AD [auth 4],
AE [auth A],
AG [auth B],
AH [auth B],
BB [auth 2],
BC [auth 3],
BD [auth 4],
BE [auth A],
BG [auth B],
BH [auth B],
BI [auth G],
BJ [auth L],
CB [auth 2],
CC [auth 3],
CD [auth 4],
CE [auth A],
CG [auth B],
CH [auth B],
CI [auth H],
CJ [auth L],
DB [auth 2],
DC [auth 3],
DD [auth 4],
DE [auth A],
DG [auth B],
DI [auth H],
DJ [auth L],
EB [auth 2],
EC [auth 3],
EE [auth A],
EG [auth B],
EI [auth H],
FA [auth 1],
FB [auth 2],
FC [auth 3],
FD [auth 4],
FE [auth A],
FG [auth B],
GA [auth 1],
GB [auth 2],
GD [auth 4],
GE [auth A],
GG [auth B],
GJ [auth L],
HA [auth 1],
HB [auth 2],
HC [auth 3],
HE [auth A],
HF [auth A],
HG [auth B],
HJ [auth L],
IA [auth 1],
IB [auth 2],
IC [auth 3],
IE [auth A],
IF [auth A],
IG [auth B],
JA [auth 1],
JB [auth 2],
JC [auth 3],
JE [auth A],
JF [auth A],
JG [auth B],
KA [auth 1],
KB [auth 2],
KC [auth 3],
KD [auth A],
KE [auth A],
KG [auth B],
KI [auth H],
LA [auth 1],
LC [auth 3],
LD [auth A],
LE [auth A],
LG [auth B],
LH [auth B],
MA [auth 1],
MB [auth 2],
MD [auth A],
ME [auth A],
MG [auth B],
MH [auth B],
MI [auth H],
NA [auth 1],
NB [auth 2],
ND [auth A],
NE [auth A],
NG [auth B],
NH [auth B],
OA [auth 1],
OD [auth A],
OE [auth A],
OG [auth B],
OI [auth I],
PA [auth 1],
PC [auth 4],
PD [auth A],
PE [auth A],
PG [auth B],
QA [auth 1],
QC [auth 4],
QD [auth A],
QE [auth A],
QG [auth B],
QI [auth J],
RC [auth 4],
RD [auth A],
RE [auth A],
RF [auth B],
RG [auth B],
RJ [auth R],
SA [auth 1],
SB [auth 2],
SC [auth 4],
SD [auth A],
SE [auth A],
SF [auth B],
SG [auth B],
SI [auth J],
SJ [auth R],
TA [auth 1],
TB [auth 3],
TC [auth 4],
TD [auth A],
TE [auth A],
TF [auth B],
TG [auth B],
TI [auth K],
UA [auth 1],
UB [auth 3],
UC [auth 4],
UD [auth A],
UE [auth A],
UF [auth B],
UG [auth B],
UI [auth K],
VB [auth 3],
VC [auth 4],
VD [auth A],
VE [auth A],
VF [auth B],
VG [auth B],
VI [auth K],
WB [auth 3],
WC [auth 4],
WD [auth A],
WE [auth A],
WF [auth B],
WG [auth B],
XB [auth 3],
XC [auth 4],
XD [auth A],
XE [auth A],
XF [auth B],
XG [auth B],
XH [auth F],
YB [auth 3],
YC [auth 4],
YD [auth A],
YE [auth A],
YF [auth B],
YG [auth B],
YH [auth F],
ZA [auth 2],
ZB [auth 3],
ZC [auth 4],
ZD [auth A],
ZF [auth B],
ZG [auth B],
ZH [auth F],
ZI [auth K]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG


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

Query on BCR


Download:Ideal Coordinates CCD File
AF [auth A]
BF [auth A]
CF [auth A]
DF [auth A]
EF [auth A]
AF [auth A],
BF [auth A],
CF [auth A],
DF [auth A],
EF [auth A],
EH [auth B],
FH [auth B],
GC [auth 3],
GH [auth B],
HH [auth B],
IH [auth B],
IJ [auth L],
NI [auth I],
OH [auth B],
PI [auth I],
RI [auth J],
VH [auth F],
WH [auth F]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU


Download:Ideal Coordinates CCD File
AI [auth G]
AJ [auth K]
ED [auth 4]
EJ [auth L]
FF [auth A]
AI [auth G],
AJ [auth K],
ED [auth 4],
EJ [auth L],
FF [auth A],
FI [auth H],
FJ [auth L],
GF [auth A],
GI [auth H],
HD [auth 4],
HI [auth H],
ID [auth 4],
II [auth H],
JD [auth 4],
JH [auth B],
JI [auth H],
JJ [auth L],
KF [auth A],
KJ [auth N],
LB [auth 2],
LF [auth A],
LJ [auth R],
MC [auth 3],
MF [auth A],
MJ [auth R],
NC [auth 3],
NF [auth A],
NJ [auth R],
OB [auth 2],
OC [auth 4],
OJ [auth R],
PB [auth 2],
PF [auth B],
PH [auth C],
PJ [auth R],
QB [auth 2],
QF [auth B],
QJ [auth R],
RA [auth 1],
RB [auth 2],
SH [auth D],
TH [auth E],
TJ [auth R],
UH [auth F],
VA [auth 1],
WA [auth 1],
WI [auth K],
XA [auth 1],
XI [auth K],
YA [auth 1],
YI [auth K]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN


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

Query on SF4


Download:Ideal Coordinates CCD File
OF [auth A],
QH [auth C],
RH [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL

Query on UNL


Download:Ideal Coordinates CCD File
LI [auth H]Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free:  0.375 (Depositor), 0.408 (DCC) 
  • R-Value Work:  0.369 (Depositor), 0.387 (DCC) 
  • R-Value Observed: 0.369 (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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2012-08-08
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2018-06-27
    Changes: Advisory, Data collection, Derived calculations
  • Version 2.0: 2018-10-03
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2018-12-19
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 2.2: 2019-01-23
    Changes: Data collection, Database references
  • Version 2.3: 2019-05-15
    Changes: Data collection
  • Version 3.0: 2019-09-18
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 4.0: 2019-10-30
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Other
  • Version 5.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 6.0: 2025-04-09
    Changes: Data collection, Database references, Non-polymer description, Structure summary
  • Version 7.0: 2025-10-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary