7R3K

Chlamydomonas reinhardtii TSP9 mutant small Photosystem I complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Photosystem I Supercomplex Isolated from a Chlamydomonas reinhardtii Cytochrome b6f Temperature-Sensitive Mutant.

Schwartz, T.Fadeeva, M.Klaiman, D.Nelson, N.

(2023) Biomolecules 13

  • DOI: https://doi.org/10.3390/biom13030537
  • Primary Citation of Related Structures:  
    7R3K

  • PubMed Abstract: 

    The unicellular green alga, Chlamydomonas reinhardtii , has been widely used as a model system to study photosynthesis. Its possibility to generate and analyze specific mutants has made it an excellent tool for mechanistic and biogenesis studies. Using negative selection of ultraviolet (UV) irradiation-mutated cells, we isolated a mutant (TSP9) with a single amino acid mutation in the Rieske protein of the cytochrome b6f complex. The W143R mutation in the petC gene resulted in total loss of cytochrome b6f complex function at the non-permissive temperature of 37 °C and recovery at the permissive temperature of 25 °C. We then isolated photosystem I (PSI) and photosystem II (PSII) supercomplexes from cells grown at the non-permissive temperature and determined the PSI structure with high-resolution cryogenic electron microscopy. There were several structural alterations compared with the structures obtained from wild-type cells. Our structural data suggest that the mutant responded by excluding the Lhca2, Lhca9, PsaL, and PsaH subunits. This structural alteration prevents state two transition, where LHCII migrates from PSII to bind to the PSI complex. We propose this as a possible response mechanism triggered by the TSP9 phenotype at the non-permissive temperature.


  • Organizational Affiliation

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


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 
UniProt
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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 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic126Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth I]106Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]41Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticJ [auth K]113Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticK [auth 1],
L [auth Z]
228Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic (Lhca4)P [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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UD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AI [auth 8]
BF [auth 1]
GF [auth 1]
IL [auth 6]
JF [auth 1]
AI [auth 8],
BF [auth 1],
GF [auth 1],
IL [auth 6],
JF [auth 1],
JK [auth 5],
JL [auth 6],
KK [auth 5],
KL [auth 6],
MJ [auth 4],
MK [auth 5],
ML [auth 6],
NF [auth Z],
NJ [auth 4],
OI [auth 8],
OK [auth 5],
OL [auth 6],
PH [auth 7],
PI [auth 8],
PJ [auth 4],
QH [auth 7],
QI [auth 8],
RJ [auth 4],
SI [auth 8],
UF [auth Z],
VF [auth Z],
VG [auth 3],
YF [auth Z]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AF [auth 1]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AF [auth 1],
AG [auth Z],
AK [auth 5],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
BE [auth F],
BK [auth 5],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth 1],
CK [auth 5],
CL [auth 6],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DF [auth 1],
DK [auth 5],
DL [auth 6],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth G],
EF [auth 1],
EJ [auth 4],
EK [auth 5],
EL [auth 6],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth G],
FF [auth 1],
FJ [auth 4],
FK [auth 5],
FL [auth 6],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GI [auth 8],
GJ [auth 4],
GK [auth 5],
GL [auth 6],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HH [auth 7],
HI [auth 8],
HJ [auth 4],
HK [auth 5],
HL [auth 6],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth I],
IF [auth 1],
IH [auth 7],
II [auth 8],
IJ [auth 4],
IK [auth 5],
JA [auth A],
JC [auth B],
JD [auth B],
JE [auth J],
JH [auth 7],
JI [auth 8],
JJ [auth 4],
KA [auth A],
KC [auth B],
KD [auth B],
KF [auth 1],
KH [auth 7],
KI [auth 8],
KJ [auth 4],
LA [auth A],
LC [auth B],
LD [auth B],
LH [auth 7],
LI [auth 8],
LJ [auth 4],
LK [auth 5],
LL [auth 6],
MA [auth A],
MC [auth B],
MD [auth B],
MG [auth 3],
MH [auth 7],
MI [auth 8],
NA [auth A],
NC [auth B],
NG [auth 3],
NH [auth 7],
NI [auth 8],
NK [auth 5],
NL [auth 6],
OA [auth A],
OC [auth B],
OE [auth K],
OF [auth Z],
OG [auth 3],
OH [auth 7],
OJ [auth 4],
PA [auth A],
PC [auth B],
PE [auth K],
PF [auth Z],
PG [auth 3],
PK [auth 5],
PL [auth 6],
QA [auth A],
QC [auth B],
QE [auth K],
QF [auth Z],
QG [auth 3],
QJ [auth 4],
QK [auth 5],
QL [auth 6],
RA [auth A],
RC [auth B],
RE [auth K],
RF [auth Z],
RG [auth 3],
RH [auth 7],
RI [auth 8],
SA [auth A],
SC [auth B],
SF [auth Z],
SG [auth 3],
SH [auth 7],
T [auth A],
TA [auth A],
TC [auth B],
TF [auth Z],
TG [auth 3],
TH [auth 7],
TI [auth 8],
TK [auth 5],
U [auth A],
UA [auth A],
UC [auth B],
UG [auth 3],
UH [auth 7],
UK [auth 6],
V [auth A],
VA [auth A],
VC [auth B],
VJ [auth 5],
VK [auth 6],
W [auth A],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth Z],
WG [auth 3],
X [auth A],
XA [auth A],
XC [auth B],
XF [auth Z],
XG [auth 3],
Y [auth A],
YA [auth A],
YC [auth B],
YE [auth 1],
YG [auth 3],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B],
ZD [auth F],
ZE [auth 1],
ZF [auth Z],
ZH [auth 7]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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S [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD
Query on SQD

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BI [auth 8]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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CH [auth 7],
LE [auth J],
ME [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BG [auth Z]
LF [auth 1]
QB [auth A]
RB [auth A]
RK [auth 5]
BG [auth Z],
LF [auth 1],
QB [auth A],
RB [auth A],
RK [auth 5],
RL [auth 6],
SJ [auth 4],
TE [auth 1],
UI [auth 8],
VH [auth 7],
WK [auth 6],
ZG [auth 3]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH

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AH [auth 3],
SK [auth 5],
SL [auth 6],
VI [auth 8]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA
Query on DGA

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DH [auth 7]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
LUT
Query on LUT

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CG [auth Z]
CJ [auth 4]
DG [auth Z]
DI [auth 8]
EH [auth 7]
CG [auth Z],
CJ [auth 4],
DG [auth Z],
DI [auth 8],
EH [auth 7],
EI [auth 8],
FH [auth 7],
GG [auth 3],
HG [auth 3],
VE [auth 1],
WE [auth 1],
XJ [auth 5],
YK [auth 6],
ZK [auth 6]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
C7Z
Query on C7Z

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KE [auth J],
XE [auth 1],
XK [auth 6]
(1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
RRX
Query on RRX

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BJ [auth 4],
CE [auth F],
WJ [auth 5]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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AE [auth F]
AL [auth 6]
BL [auth 6]
CI [auth 8]
DJ [auth 4]
AE [auth F],
AL [auth 6],
BL [auth 6],
CI [auth 8],
DJ [auth 4],
FI [auth 8],
GE [auth G],
GH [auth 7],
IG [auth 3],
JG [auth 3],
KG [auth 3],
LB [auth A],
LG [auth 3],
MB [auth A],
NB [auth A],
OB [auth A],
OD [auth B],
PB [auth A],
PD [auth B],
QD [auth B],
RD [auth B],
SD [auth B],
SE [auth K],
TD [auth B],
XB [auth A],
YB [auth A],
YJ [auth 5],
ZJ [auth 5]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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AJ [auth 4]
BH [auth 3]
DE [auth F]
EG [auth Z]
HE [auth G]
AJ [auth 4],
BH [auth 3],
DE [auth F],
EG [auth Z],
HE [auth G],
MF [auth Z],
SB [auth A],
TB [auth A],
TJ [auth 4],
UB [auth A],
UE [auth 1],
UJ [auth 4],
VB [auth A],
WI [auth 8],
XI [auth 8],
YH [auth 7]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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JB [auth A],
ND [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
ERG
Query on ERG

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TL [auth 6],
YI [auth 8]
ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
SF4
Query on SF4

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KB [auth A],
XD [auth C],
YD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SPH
Query on SPH

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FG [auth 3],
WH [auth 7],
ZI [auth 4]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
PLM
Query on PLM

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XH [auth 7]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
DAO
Query on DAO

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NE [auth K]LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
CA
Query on CA

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VD [auth B]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNC
Query on SNC
D
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.52 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-22
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-04-12
    Changes: Database references
  • Version 1.3: 2024-11-13
    Changes: Data collection, Refinement description, Structure summary