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Contents |
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740 a.a.
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739 a.a.
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80 a.a.
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138 a.a.
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69 a.a.
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141 a.a.
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38 a.a.
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41 a.a.
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46 a.a.
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151 a.a.
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31 a.a.
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29 a.a.
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* Residue conservation analysis
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PDB id:
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| Name: |
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Photosynthesis
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Title:
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Crystal structure of photosystem i: a photosynthetic reaction center and core antenna system from cyanobacteria
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Structure:
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Photosystem i p700 chlorophyll a apoprotein a1. Chain: a. Synonym: photosystem i subunit psaa. Photosystem i p700 chlorophyll a apoprotein a2. Chain: b. Synonym: photosystem i subunit psab. Photosystem i iron-sulfur center. Chain: c. Synonym: photosystem i subunit psac.
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Source:
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Synechococcus elongatus. Organism_taxid: 32046. Organism_taxid: 32046
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Biol. unit:
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Dodecamer (from
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Resolution:
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2.50Å
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R-factor:
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0.199
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R-free:
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0.217
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Authors:
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P.Jordan,P.Fromme,H.T.Witt,O.Klukas,W.Saenger,N.Krauss
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Key ref:
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P.Jordan
et al.
(2001).
Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.
Nature,
411,
909-917.
PubMed id:
DOI:
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Date:
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01-Jun-01
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Release date:
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01-Aug-01
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PROCHECK
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Headers
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References
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P0A405
(PSAA_THEEB) -
Photosystem I P700 chlorophyll a apoprotein A1 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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755 a.a.
740 a.a.
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P0A407
(PSAB_THEEB) -
Photosystem I P700 chlorophyll a apoprotein A2 from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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741 a.a.
739 a.a.
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P0A415
(PSAC_THEEB) -
Photosystem I iron-sulfur center from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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81 a.a.
80 a.a.
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P0A420
(PSAD_THEEB) -
Photosystem I reaction center subunit II from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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139 a.a.
138 a.a.
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P0A423
(PSAE_THEEB) -
Photosystem I reaction center subunit IV from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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76 a.a.
69 a.a.
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P0A401
(PSAF_THEEB) -
Photosystem I reaction center subunit III from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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164 a.a.
141 a.a.
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P0A427
(PSAI_THEEB) -
Photosystem I reaction center subunit VIII from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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38 a.a.
38 a.a.
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P0A429
(PSAJ_THEEB) -
Photosystem I reaction center subunit IX from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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41 a.a.
41 a.a.
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P0A425
(PSAK_THEEB) -
Photosystem I reaction center subunit PsaK from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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83 a.a.
46 a.a.
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Q8DGB4
(PSAL_THEEB) -
Photosystem I reaction center subunit XI from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)
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Seq:
Struc:
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155 a.a.
151 a.a.*
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Enzyme class:
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Chains A, B, C:
E.C.1.97.1.12
- photosystem I.
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Reaction:
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reduced [plastocyanin] + hnu + oxidized [2Fe-2S]-[ferredoxin] = oxidized [plastocyanin] + reduced [2Fe-2S]-[ferredoxin]
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DOI no:
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Nature
411:909-917
(2001)
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PubMed id:
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| |
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Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution.
|
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P.Jordan,
P.Fromme,
H.T.Witt,
O.Klukas,
W.Saenger,
N.Krauss.
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ABSTRACT
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Life on Earth depends on photosynthesis, the conversion of light energy from the
Sun to chemical energy. In plants, green algae and cyanobacteria, this process
is driven by the cooperation of two large protein-cofactor complexes,
photosystems I and II, which are located in the thylakoid photosynthetic
membranes. The crystal structure of photosystem I from the thermophilic
cyanobacterium Synechococcus elongatus described here provides a picture at
atomic detail of 12 protein subunits and 127 cofactors comprising 96
chlorophylls, 2 phylloquinones, 3 Fe4S4 clusters, 22 carotenoids, 4 lipids, a
putative Ca2+ ion and 201 water molecules. The structural information on the
proteins and cofactors and their interactions provides a basis for understanding
how the high efficiency of photosystem I in light capturing and electron
transfer is achieved.
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Selected figure(s)
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Figure 1.
Figure 1: Structural model of PS I trimer at 2.5 Å resolution.
a, View along the membrane normal from the stromal side. For
clarity, stromal subunits have been omitted. Different
structural elements are shown in each of the three monomers (I,
II and III). I, arrangement of the transmembrane  -helices
(cylinders). Subunits are labelled. The transmembrane -helices
of PsaA (blue) and PsaB (red) are named A-a to A-k (B-a to B-k)
from the N to the C terminus (capital letters omitted). All loop
regions of PsaA and PsaB are named according to the
transmembrane helices which they connect. For all other subunits
the -helices
and  -sheets
are numbered in alphabetical order from the N to the C terminus.
Six helices in extra-membranous loop regions are drawn as
spirals. II, membrane-intrinsic subunits. In addition to the
transmembrane -helices
of the stromal and lumenal loop regions are shown in ribbon
representation. III, complete set of cofactors shown with the
transmembrane -helices
(the side chains of the antenna Chla molecules have been
omitted). Electron transfer chain: quinones and chlorophylls in blue, iron and
sulphur atoms of the three Fe[4]S[4] clusters as orange and
yellow spheres, respectively. Antenna system: chlorophylls in
yellow, carotenoids in black, lipids in turquoise. b, Side view
of the arrangement of all proteins in one monomer of PSI
(colours as in a), including the stromal subunits PsaC (pink),
PsaD (turquoise), PsaE (green) and the Fe[4]S[4] clusters. View
direction indicated by arrow at monomer II in a. The vertical
line (right) shows the crystallographic C[3] axis. c, View as in
a showing stromal subunits PsaC, PsaD and PsaE. They cover some
of the loop regions and helices of PsaA and PsaB (light grey).
Dashed ellipse: putative docking site of ferredoxin, covering
loops of PsaA.
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Figure 2.
Figure 2: Cofactors of the electron transfer chain (ETC) and of
PsaC. View parallel to the membrane plane. The pairs of
chlorophylls of the ETC are arranged in two branches A and B.
They are labelled eC, followed by the letter A or B indicating
whether PsaA or PsaB, respectively, coordinates Mg2+, and by
numbers 1 to 3 starting from the lumenal side. Phylloquinones
are Q[K]-A and Q[K]-B. The Fe[4]S[4] clusters are labelled F[X],
F[A] and F[B] according to their spectroscopic terms. The
centre-to-centre distances between the cofactors (black lines)
are given in Å. In PsaC, parts analogous to 2[Fe[4]S[4]]
bacterial ferredoxins are pink, an insertion and extensions at
C and N termini are green.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2001,
411,
909-917)
copyright 2001.
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Figures were
selected
by the author.
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Literature references that cite this PDB file's key reference
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PubMed id
|
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Reference
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E.R.Moellering,
and
C.Benning
(2011).
Galactoglycerolipid metabolism under stress: a time for remodeling.
|
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Trends Plant Sci,
16,
98.
|
|
|
|
|
|
|
E.Wientjes,
and
R.Croce
(2011).
The light-harvesting complexes of higher-plant Photosystem I: Lhca1/4 and Lhca2/3 form two red-emitting heterodimers.
|
| |
Biochem J,
433,
477-485.
|
|
|
|
|
|
|
H.N.Chapman,
P.Fromme,
A.Barty,
T.A.White,
R.A.Kirian,
A.Aquila,
M.S.Hunter,
J.Schulz,
D.P.Deponte,
U.Weierstall,
R.B.Doak,
F.R.Maia,
A.V.Martin,
I.Schlichting,
L.Lomb,
N.Coppola,
R.L.Shoeman,
S.W.Epp,
R.Hartmann,
D.Rolles,
A.Rudenko,
L.Foucar,
N.Kimmel,
G.Weidenspointner,
P.Holl,
M.Liang,
M.Barthelmess,
C.Caleman,
S.Boutet,
M.J.Bogan,
J.Krzywinski,
C.Bostedt,
S.Bajt,
L.Gumprecht,
B.Rudek,
B.Erk,
C.Schmidt,
A.Hömke,
C.Reich,
D.Pietschner,
L.Strüder,
G.Hauser,
H.Gorke,
J.Ullrich,
S.Herrmann,
G.Schaller,
F.Schopper,
H.Soltau,
K.U.Kühnel,
M.Messerschmidt,
J.D.Bozek,
S.P.Hau-Riege,
M.Frank,
C.Y.Hampton,
R.G.Sierra,
D.Starodub,
G.J.Williams,
J.Hajdu,
N.Timneanu,
M.M.Seibert,
J.Andreasson,
A.Rocker,
O.Jönsson,
M.Svenda,
S.Stern,
K.Nass,
R.Andritschke,
C.D.Schröter,
F.Krasniqi,
M.Bott,
K.E.Schmidt,
X.Wang,
I.Grotjohann,
J.M.Holton,
T.R.Barends,
R.Neutze,
S.Marchesini,
R.Fromme,
S.Schorb,
D.Rupp,
M.Adolph,
T.Gorkhover,
I.Andersson,
H.Hirsemann,
G.Potdevin,
H.Graafsma,
B.Nilsson,
and
J.C.Spence
(2011).
Femtosecond X-ray protein nanocrystallography.
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Nature,
470,
73-77.
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PDB code:
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H.W.Wang,
C.H.Chen,
T.S.Lim,
S.L.Huang,
and
T.Y.Luh
(2011).
Supramolecular Porphyrin-DABCO Array in Single- and Double-Stranded Polynorbornenes.
|
| |
Chem Asian J,
6,
524-533.
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|
|
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|
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K.Illergård,
A.Kauko,
and
A.Elofsson
(2011).
Why are polar residues within the membrane core evolutionary conserved?
|
| |
Proteins,
79,
79-91.
|
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|
|
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|
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M.Sener,
J.Strümpfer,
J.Hsin,
D.Chandler,
S.Scheuring,
C.N.Hunter,
and
K.Schulten
(2011).
Förster energy transfer theory as reflected in the structures of photosynthetic light-harvesting systems.
|
| |
Chemphyschem,
12,
518-531.
|
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|
|
|
|
|
M.Watanabe,
H.Kubota,
H.Wada,
R.Narikawa,
and
M.Ikeuchi
(2011).
Novel Supercomplex Organization of Photosystem I in Anabaena and Cyanophora paradoxa.
|
| |
Plant Cell Physiol,
52,
162-168.
|
|
|
|
|
|
|
R.A.Kirian,
T.A.White,
J.M.Holton,
H.N.Chapman,
P.Fromme,
A.Barty,
L.Lomb,
A.Aquila,
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A.V.Martin,
R.Fromme,
X.Wang,
M.S.Hunter,
K.E.Schmidt,
and
J.C.Spence
(2011).
Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals.
|
| |
Acta Crystallogr A,
67,
131-140.
|
|
|
|
|
|
|
X.Qin,
W.Wang,
K.Wang,
Y.Xin,
and
T.Kuang
(2011).
Isolation and Characteristics of the PSI-LHCI-LHCII Supercomplex Under High Light.
|
| |
Photochem Photobiol,
87,
143-150.
|
|
|
|
|
|
|
Z.Gardian,
J.Tichý,
and
F.Vácha
(2011).
Structure of PSI, PSII and antennae complexes from yellow-green alga Xanthonema debile.
|
| |
Photosynth Res,
108,
25-32.
|
|
|
|
|
|
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A.Amunts,
H.Toporik,
A.Borovikova,
and
N.Nelson
(2010).
Structure determination and improved model of plant photosystem I.
|
| |
J Biol Chem,
285,
3478-3486.
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PDB codes:
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A.Schwarze,
M.J.Kopczak,
M.Rögner,
and
O.Lenz
(2010).
Requirements for construction of a functional hybrid complex of photosystem I and [NiFe]-hydrogenase.
|
| |
Appl Environ Microbiol,
76,
2641-2651.
|
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|
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H.N.Su,
B.B.Xie,
X.Y.Zhang,
B.C.Zhou,
and
Y.Z.Zhang
(2010).
The supramolecular architecture, function, and regulation of thylakoid membranes in red algae: an overview.
|
| |
Photosynth Res,
106,
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|
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I.J.Iwuchukwu,
M.Vaughn,
N.Myers,
H.O'Neill,
P.Frymier,
and
B.D.Bruce
(2010).
Self-organized photosynthetic nanoparticle for cell-free hydrogen production.
|
| |
Nat Nanotechnol,
5,
73-79.
|
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J.L.Klassen
(2010).
Phylogenetic and evolutionary patterns in microbial carotenoid biosynthesis are revealed by comparative genomics.
|
| |
PLoS One,
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|
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J.Niklas,
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B.Epel,
W.Lubitz,
and
M.L.Antonkine
(2010).
Investigation of the Stationary and Transient A(1) Radical in Trp --> Phe Mutants of Photosystem I.
|
| |
Appl Magn Reson,
38,
187-203.
|
|
|
|
|
|
|
K.McLuskey,
A.W.Roszak,
Y.Zhu,
and
N.W.Isaacs
(2010).
Crystal structures of all-alpha type membrane proteins.
|
| |
Eur Biophys J,
39,
723-755.
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K.R.Vinothkumar,
and
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(2010).
Structures of membrane proteins.
|
| |
Q Rev Biophys,
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|
M.G.Müller,
C.Slavov,
R.Luthra,
K.E.Redding,
and
A.R.Holzwarth
(2010).
Independent initiation of primary electron transfer in the two branches of the photosystem I reaction center.
|
| |
Proc Natl Acad Sci U S A,
107,
4123-4128.
|
|
|
|
|
|
|
M.Miyachi,
Y.Yamanoi,
Y.Shibata,
H.Matsumoto,
K.Nakazato,
M.Konno,
K.Ito,
Y.Inoue,
and
H.Nishihara
(2010).
A photosensing system composed of photosystem I, molecular wire, gold nanoparticle, and double surfactants in water.
|
| |
Chem Commun (Camb),
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2557-2559.
|
|
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|
|
O.Sozer,
J.Komenda,
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H.Laczkó-Dobos,
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and
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(2010).
Involvement of carotenoids in the synthesis and assembly of protein subunits of photosynthetic reaction centers of Synechocystis sp. PCC 6803.
|
| |
Plant Cell Physiol,
51,
823-835.
|
|
|
|
|
|
|
R.A.Kirian,
X.Wang,
U.Weierstall,
K.E.Schmidt,
J.C.Spence,
M.Hunter,
P.Fromme,
T.White,
H.N.Chapman,
and
J.Holton
(2010).
Femtosecond protein nanocrystallography-data analysis methods.
|
| |
Opt Express,
18,
5713-5723.
|
|
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|
|
|
R.R.Ramiscal,
S.S.Tang,
H.Korres,
and
N.K.Verma
(2010).
Structural and functional divergence of the newly identified GtrIc from its Gtr family of conserved Shigella flexneri serotype-converting glucosyltransferases.
|
| |
Mol Membr Biol,
27,
114-122.
|
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|
|
|
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R.Sakamoto,
M.Nishikawa,
T.Yamamura,
S.Kume,
and
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(2010).
A new special pair model comprising meso-di-p-anisylaminoporphyrin: enhancement of visible-light absorptivities and quantification of electronic communication in mixed-valent cation radical.
|
| |
Chem Commun (Camb),
46,
2028-2030.
|
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|
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|
R.Subramanyam,
C.Jolley,
B.Thangaraj,
S.Nellaepalli,
A.N.Webber,
and
P.Fromme
(2010).
Structural and functional changes of PSI-LHCI supercomplexes of Chlamydomonas reinhardtii cells grown under high salt conditions.
|
| |
Planta,
231,
913-922.
|
|
|
|
|
|
|
S.Ohashi,
T.Iemura,
N.Okada,
S.Itoh,
H.Furukawa,
M.Okuda,
M.Ohnishi-Kameyama,
T.Ogawa,
H.Miyashita,
T.Watanabe,
S.Itoh,
H.Oh-oka,
K.Inoue,
and
M.Kobayashi
(2010).
An overview on chlorophylls and quinones in the photosystem I-type reaction centers.
|
| |
Photosynth Res,
104,
305-319.
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