6FOS

Cyanidioschyzon merolae photosystem I


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.430 
  • R-Value Work: 0.378 
  • R-Value Observed: 0.379 

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Ligand Structure Quality Assessment 


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Literature

Structure and function of photosystem I in Cyanidioschyzon merolae.

Antoshvili, M.Caspy, I.Hippler, M.Nelson, N.

(2019) Photosynth Res 139: 499-508

  • DOI: https://doi.org/10.1007/s11120-018-0501-4
  • Primary Citation of Related Structures:  
    6FOS

  • PubMed Abstract: 

    The evolution of photosynthesis from primitive photosynthetic bacteria to higher plants has been driven by the need to adapt to a wide range of environmental conditions. The red alga Cyanidioschyzon merolae is a primitive organism, which is capable of performing photosynthesis in extreme acidic and hot environments. The study of its photosynthetic machinery may provide new insight on the evolutionary path of photosynthesis and on light harvesting and its regulation in eukaryotes. With that aim, the structural and functional properties of the PSI complex were investigated by biochemical characterization, mass spectrometry, and X-ray crystallography. PSI was purified from cells grown at 25 and 42 °C, crystallized and its crystal structure was solved at 4 Å resolution. The structure of C. merolae reveals a core complex with a crescent-shaped structure, formed by antenna proteins. In addition, the structural model shows the position of PsaO and PsaM. PsaG and PsaH are present in plant complex and are missing from the C. merolae model as expected. This paper sheds new light onto the evolution of photosynthesis, which gives a strong indication for the chimerical properties of red algae PSI. The subunit composition of the PSI core from C. merolae and its associated light-harvesting antennae suggests that it is an evolutionary and functional intermediate between cyanobacteria and plants.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978, Tel Aviv, Israel.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Similar to chlorophyll a/b-binding protein, CP24A [auth 2],
B [auth 3]
222Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for M1UU36 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Similar to light harvesting proteinC [auth 4]214Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for M1VKK5 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1D [auth A]740Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85FY7 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2E [auth B]725Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85FY6 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerF [auth C]80Cyanidioschyzon merolae strain 10DMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q85G47 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I p700 chlorophyll A apoprotein A2G [auth D]124Cyanidioschyzon merolae strain 10DMutation(s): 0 
UniProt
Find proteins for Q85FY0 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center subunit VIIH [auth E]69Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FZ1 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III [auth F]155Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FS9 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIJ [auth I]32Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FQ6 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]38Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85FS8 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XL [auth K]47Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85G51 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIM [auth L]140Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIN [auth M]29Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q85G73 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaM98Cyanidioschyzon merolae strain 10DMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for M1VFJ4 (Cyanidioschyzon merolae (strain NIES-3377 / 10D))
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AA [auth 2]
AB [auth 4]
AC [auth A]
AE [auth B]
AF [auth L]
AA [auth 2],
AB [auth 4],
AC [auth A],
AE [auth B],
AF [auth L],
BA [auth 2],
BB [auth 4],
BC [auth A],
BD [auth B],
BE [auth B],
BF [auth L],
CA [auth 2],
CB [auth A],
CC [auth A],
CD [auth B],
CE [auth B],
CF [auth L],
DA [auth 2],
DB [auth A],
DC [auth A],
DD [auth B],
DE [auth B],
DF [auth O],
EA [auth 3],
EB [auth A],
EC [auth A],
ED [auth B],
EE [auth B],
EF [auth O],
FA [auth 3],
FB [auth A],
FC [auth A],
FD [auth B],
FE [auth B],
FF [auth O],
GA [auth 3],
GB [auth A],
GC [auth A],
GD [auth B],
GE [auth B],
HA [auth 3],
HB [auth A],
HC [auth A],
HD [auth B],
HE [auth B],
IA [auth 3],
IB [auth A],
IC [auth A],
ID [auth B],
IE [auth B],
JA [auth 3],
JB [auth A],
JC [auth A],
JD [auth B],
JE [auth B],
KA [auth 3],
KB [auth A],
KC [auth A],
KD [auth B],
KE [auth B],
LA [auth 3],
LB [auth A],
LC [auth A],
LD [auth B],
LE [auth B],
MA [auth 3],
MB [auth A],
MC [auth A],
MD [auth B],
ME [auth B],
NA [auth 3],
NB [auth A],
NC [auth A],
ND [auth B],
NE [auth B],
OA [auth 3],
OB [auth A],
OC [auth A],
OD [auth B],
OE [auth B],
P [auth 2],
PA [auth 4],
PB [auth A],
PC [auth A],
PD [auth B],
Q [auth 2],
QA [auth 4],
QB [auth A],
QC [auth A],
QD [auth B],
R [auth 2],
RA [auth 4],
RB [auth A],
RC [auth A],
RD [auth B],
S [auth 2],
SA [auth 4],
SB [auth A],
SC [auth A],
SD [auth B],
T [auth 2],
TA [auth 4],
TB [auth A],
TC [auth A],
TD [auth B],
U [auth 2],
UA [auth 4],
UB [auth A],
UD [auth B],
UE [auth F],
V [auth 2],
VA [auth 4],
VB [auth A],
VD [auth B],
VE [auth F],
W [auth 2],
WA [auth 4],
WB [auth A],
WD [auth B],
X [auth 2],
XA [auth 4],
XB [auth A],
XD [auth B],
XE [auth J],
Y [auth 2],
YA [auth 4],
YB [auth A],
YD [auth B],
YE [auth K],
Z [auth 2],
ZA [auth 4],
ZB [auth A],
ZD [auth B],
ZE [auth K]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
BCR
Query on BCR

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AD [auth A]
QE [auth B]
RE [auth B]
WC [auth A]
WE [auth I]
AD [auth A],
QE [auth B],
RE [auth B],
WC [auth A],
WE [auth I],
XC [auth A],
YC [auth A],
ZC [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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PE [auth B],
UC [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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SE [auth C],
TE [auth C],
VC [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.430 
  • R-Value Work: 0.378 
  • R-Value Observed: 0.379 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 163.13α = 90
b = 213.52β = 90
c = 349.58γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
MOLREPphasing
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium293579
israel science foundationIsrael569/17

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references