2O01

The Structure of a plant photosystem I supercomplex at 3.4 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.409 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.351 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The structure of a plant photosystem I supercomplex at 3.4 A resolution.

Amunts, A.Drory, O.Nelson, N.

(2007) Nature 447: 58-63

  • DOI: 10.1038/nature05687
  • Primary Citation of Related Structures:  
    2O01

  • PubMed Abstract: 
  • All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems ...

    All higher organisms on Earth receive energy directly or indirectly from oxygenic photosynthesis performed by plants, green algae and cyanobacteria. Photosystem I (PSI) is a supercomplex of a reaction centre and light-harvesting complexes. It generates the most negative redox potential in nature, and thus largely determines the global amount of enthalpy in living systems. We report the structure of plant PSI at 3.4 A resolution, revealing 17 protein subunits. PsaN was identified in the luminal side of the supercomplex, and most of the amino acids in the reaction centre were traced. The crystal structure of PSI provides a picture at near atomic detail of 11 out of 12 protein subunits of the reaction centre. At this level, 168 chlorophylls (65 assigned with orientations for Q(x) and Q(y) transition dipole moments), 2 phylloquinones, 3 Fe(4)S(4) clusters and 5 carotenoids are described. This structural information extends the understanding of the most efficient nano-photochemical machine in nature.


    Organizational Affiliation

    Department of Biochemistry, The George S. Wise Faculty of Life Sciences, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Tel Aviv, 69978, Israel.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A754Pisum sativumMutation(s): 0 
Gene Names: psaApsaA1
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P05310 (Pisum sativum)
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UniProt GroupP05310
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B732Pisum sativumMutation(s): 0 
Gene Names: psaBpsaA2
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC80Pisum sativumMutation(s): 0 
Gene Names: psaCfrxA
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastD138Spinacia oleraceaMutation(s): 0 
Gene Names: psaD
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplastE62Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAE1At4g28750F16A16.140
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastF154Spinacia oleraceaMutation(s): 0 
Gene Names: PSAF
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastG95Spinacia oleraceaMutation(s): 0 
Gene Names: PSAG
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI, chloroplastH75Spinacia oleraceaMutation(s): 0 
Gene Names: PSAH
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIII30Pisum sativumMutation(s): 0 
Gene Names: psaI
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJ42Spinacia oleraceaMutation(s): 0 
Gene Names: psaJ
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplastK38Arabidopsis thalianaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplastL164Spinacia oleraceaMutation(s): 0 
Gene Names: PSAL
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I-N subunitM [auth N]85Phaseolus vulgarisMutation(s): 0 
Gene Names: PSI-NPHAVU_002G269400g
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
AT3g54890N [auth 1]187Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA1CAB6At3g54890F28P10.130
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Type II chlorophyll a/b binding protein from photosystem IO [auth 2]186Pisum sativumMutation(s): 0 
Gene Names: lhaB
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
PSI type III chlorophyll a/b-binding proteinP [auth 3]165Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA3At1g61520T25B24.12
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
PSI light-harvesting antenna chlorophyll a/b-binding proteinQ [auth 4]165Pisum sativumMutation(s): 0 
Gene Names: lhcA-P4
Membrane Entity: Yes 
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Find proteins for Q9SQL2 (Pisum sativum)
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth K],
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth K],
AF [auth 2],
AG [auth 4],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth K],
BF [auth 2],
BG [auth 4],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth K],
CF [auth 2],
CG [auth 4],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth L],
DF [auth 2],
DG [auth 4],
EA [auth A],
EB [auth A],
EC [auth B],
EE [auth L],
EF [auth 2],
EG [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FE [auth L],
FF [auth 2],
FG [auth 4],
GA [auth A],
GB [auth A],
GC [auth B],
GE [auth L],
GF [auth 2],
GG [auth 4],
HA [auth A],
HB [auth A],
HC [auth B],
HE [auth L],
HF [auth 2],
HG [auth 4],
IA [auth A],
IB [auth A],
IC [auth B],
IF [auth 2],
IG [auth 4],
JA [auth A],
JC [auth B],
JD [auth F],
JE [auth 1],
JF [auth 3],
JG [auth 4],
KA [auth A],
KC [auth B],
KD [auth F],
KE [auth 1],
KF [auth 3],
KG [auth 4],
LA [auth A],
LB [auth B],
LC [auth B],
LD [auth F],
LE [auth 1],
LF [auth 3],
LG [auth 4],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth F],
ME [auth 1],
MF [auth 3],
MG [auth 4],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth F],
NE [auth 1],
NF [auth 3],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth F],
OE [auth 1],
OF [auth 3],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth F],
PE [auth 1],
PF [auth 3],
QA [auth A],
QB [auth B],
QC [auth B],
QE [auth 1],
QF [auth 3],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth G],
RE [auth 1],
RF [auth 3],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SD [auth G],
SE [auth 1],
SF [auth 3],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
TD [auth H],
TE [auth 1],
TF [auth 3],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth H],
UE [auth 1],
UF [auth 3],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth I],
VE [auth 1],
VF [auth 3],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WE [auth 2],
WF [auth 3],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
XD [auth J],
XE [auth 2],
XF [auth 3],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
YD [auth J],
YE [auth 2],
YF [auth 4],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth J],
ZE [auth 2],
ZF [auth 4]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
 Ligand Interaction
BCR
Query on BCR

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GD [auth B],
IE [auth L],
KB [auth A],
QD [auth F],
WD [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
PQN
Query on PQN

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FD [auth B],
JB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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ED [auth B],
HD [auth C],
ID [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.409 
  • R-Value Work: 0.348 
  • R-Value Observed: 0.351 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.054α = 90
b = 188.784β = 95.19
c = 127.518γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2007-11-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description