7WYI

Native Photosystem I of Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Three structures of PSI-LHCI from Chlamydomonas reinhardtii suggest a resting state re-activated by ferredoxin.

Gerle, C.Misumi, Y.Kawamoto, A.Tanaka, H.Kubota-Kawai, H.Tokutsu, R.Kim, E.Chorev, D.Abe, K.Robinson, C.V.Mitsuoka, K.Minagawa, J.Kurisu, G.

(2023) Biochim Biophys Acta Bioenerg 1864: 148986-148986

  • DOI: https://doi.org/10.1016/j.bbabio.2023.148986
  • Primary Citation of Related Structures:  
    7WYI, 7WZN, 8H2U

  • PubMed Abstract: 

    Photosystem I (PSI) from the green alga Chlamydomonas reinhardtii, with various numbers of membrane bound antenna complexes (LHCI), has been described in great detail. In contrast, structural characterization of soluble binding partners is less advanced. Here, we used X-ray crystallography and single particle cryo-EM to investigate three structures of the PSI-LHCI supercomplex from Chlamydomonas reinhardtii. An X-ray structure demonstrates the absence of six chlorophylls from the luminal side of the LHCI belts, suggesting these pigments were either physically absent or less stably associated with the complex, potentially influencing excitation transfer significantly. CryoEM revealed extra densities on luminal and stromal sides of the supercomplex, situated in the vicinity of the electron transfer sites. These densities disappeared after the binding of oxidized ferredoxin to PSI-LHCI. Based on these structures, we propose the existence of a PSI-LHCI resting state with a reduced active chlorophyll content, electron donors docked in waiting positions and regulatory binding partners positioned at the electron acceptor site. The resting state PSI-LHCI supercomplex would be recruited to its active form by the availability of oxidized ferredoxin.


  • Organizational Affiliation

    Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Hyogo, Japan; Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan. Electronic address: christoph.gerle@riken.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2735Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic196Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplastic97Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplastic227Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXG [auth J]41Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticH [auth 1]224Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticI [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticJ [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticK [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticL [auth Z]228Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL (Subject of Investigation/LOI)
Query on CHL

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AD [auth 1]
AG [auth 6]
CE [auth 7]
JF [auth 5]
QD [auth 3]
AD [auth 1],
AG [auth 6],
CE [auth 7],
JF [auth 5],
QD [auth 3],
QE [auth 8],
RF [auth 5],
YF [auth 6],
ZE [auth Z],
ZF [auth 6]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AE [auth 7]
AF [auth 4]
AA [auth A],
AB [auth A],
AC [auth B],
AE [auth 7],
AF [auth 4],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth 1],
BE [auth 7],
BF [auth 4],
BG [auth 6],
CA [auth A],
CC [auth B],
CD [auth 1],
CF [auth 4],
CG [auth 6],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth 1],
DE [auth 7],
DF [auth 4],
DG [auth 6],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth 1],
EE [auth 7],
EF [auth 4],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth 1],
FE [auth 7],
FF [auth 5],
GA [auth A],
GB [auth B],
GC [auth B],
GD [auth 1],
GE [auth 7],
GF [auth 5],
HA [auth A],
HB [auth B],
HC [auth B],
HD [auth 1],
HE [auth 7],
HF [auth 5],
IA [auth A],
IC [auth B],
ID [auth 1],
IE [auth 7],
IF [auth 5],
JA [auth A],
JB [auth B],
JC [auth B],
JD [auth 1],
JE [auth 7],
KA [auth A],
KB [auth B],
KC [auth B],
KD [auth 3],
KE [auth 7],
KF [auth 5],
LA [auth A],
LB [auth B],
LC [auth B],
LD [auth 3],
LE [auth 8],
LF [auth 5],
MA [auth A],
MB [auth B],
MC [auth B],
MD [auth 3],
ME [auth 8],
MF [auth 5],
NA [auth A],
NB [auth B],
NC [auth B],
ND [auth 3],
NE [auth 8],
NF [auth 5],
OA [auth A],
OB [auth B],
OC [auth B],
OD [auth 3],
OE [auth 8],
OF [auth 5],
PA [auth A],
PB [auth B],
PC [auth B],
PD [auth 3],
PE [auth 8],
PF [auth 5],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
QF [auth 5],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth 3],
RE [auth 8],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
SD [auth 3],
SE [auth 8],
SF [auth 5],
T [auth A],
TA [auth A],
TB [auth B],
TD [auth 3],
TE [auth 8],
TF [auth 5],
U [auth A],
UA [auth A],
UB [auth B],
UD [auth 3],
UE [auth 8],
UF [auth 6],
V [auth A],
VA [auth A],
VB [auth B],
VD [auth 3],
VE [auth 8],
VF [auth 6],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth F],
WD [auth 3],
WE [auth 8],
WF [auth 6],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth F],
XD [auth 7],
XE [auth 8],
XF [auth 6],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth J],
YD [auth 7],
YE [auth 8],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth J],
ZD [auth 7]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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P [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
PQN (Subject of Investigation/LOI)
Query on PQN

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CB [auth A],
TC [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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IB [auth B],
UC [auth C],
VC [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapanJPMJCR13M4
Ministry of Education, Culture, Sports, Science and Technology (Japan)JapanNanotechnology Platform

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2023-07-05
    Changes: Database references, Structure summary
  • Version 1.3: 2023-07-12
    Changes: Database references
  • Version 1.4: 2024-06-26
    Changes: Data collection, Refinement description