7ZQ9

Dimeric PSI of Chlamydomonas reinhardtii at 2.74 A resolution (symmetry expanded)

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Chlamydomonas reinhardtii
  • Mutation(s): No 
  • Membrane Protein: Yes  OPM

  • Deposited: 2022-04-29 Released: 2022-11-23 
  • Deposition Author(s): Naschberger, A., Amunts, A.
  • Funding Organization(s): The Swedish Foundation for Strategic Research, Knut and Alice Wallenberg Foundation, German Federal Ministry for Education and Research, German-Israeli Foundation for Research and Development

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Algal photosystem I dimer and high-resolution model of PSI-plastocyanin complex.

Naschberger, A.Mosebach, L.Tobiasson, V.Kuhlgert, S.Scholz, M.Perez-Boerema, A.Ho, T.T.H.Vidal-Meireles, A.Takahashi, Y.Hippler, M.Amunts, A.

(2022) Nat Plants 8: 1191-1201

  • DOI: https://doi.org/10.1038/s41477-022-01253-4
  • Primary Citation of Related Structures:  
    7ZQ9, 7ZQC, 7ZQD, 7ZQE

  • PubMed Abstract: 

    Photosystem I (PSI) enables photo-electron transfer and regulates photosynthesis in the bioenergetic membranes of cyanobacteria and chloroplasts. Being a multi-subunit complex, its macromolecular organization affects the dynamics of photosynthetic membranes. Here we reveal a chloroplast PSI from the green alga Chlamydomonas reinhardtii that is organized as a homodimer, comprising 40 protein subunits with 118 transmembrane helices that provide scaffold for 568 pigments. Cryogenic electron microscopy identified that the absence of PsaH and Lhca2 gives rise to a head-to-head relative orientation of the PSI-light-harvesting complex I monomers in a way that is essentially different from the oligomer formation in cyanobacteria. The light-harvesting protein Lhca9 is the key element for mediating this dimerization. The interface between the monomers is lacking PsaH and thus partially overlaps with the surface area that would bind one of the light-harvesting complex II complexes in state transitions. We also define the most accurate available PSI-light-harvesting complex I model at 2.3 Å resolution, including a flexibly bound electron donor plastocyanin, and assign correct identities and orientations to all the pigments, as well as 621 water molecules that affect energy transfer pathways.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


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 
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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 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],
V [auth I2]
106Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]40Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VJ [auth L],
W [auth L2]
196Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplastic113Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticL [auth 1],
P [auth Z]
228Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic (Lhca4)Q [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 9],
X [auth 92]
213Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2U [auth B2]180Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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

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AL [auth 5]
AM [auth 6]
AN [auth 9]
BL [auth 5]
BM [auth 6]
AL [auth 5],
AM [auth 6],
AN [auth 9],
BL [auth 5],
BM [auth 6],
CK [auth 4],
DK [auth 4],
EJ [auth Z],
EK [auth 4],
II [auth 8],
IJ [auth Z],
IM [auth 6],
JH [auth 7],
JJ [auth Z],
KL [auth 5],
KM [auth 6],
MI [auth 8],
MK [auth 4],
NF [auth 1],
NH [auth 7],
NI [auth 8],
OH [auth 7],
QG [auth 3],
RF [auth 1],
SF [auth 1],
TO [auth 92],
UO [auth 92],
VL [auth 6],
YJ [auth 4],
ZK [auth 5],
ZL [auth 6],
ZM [auth 9]
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]
AD [auth B]
AG [auth 1]
AK [auth 4]
AA [auth A],
AB [auth A],
AD [auth B],
AG [auth 1],
AK [auth 4],
AO [auth B2],
AP [auth 92],
BA [auth A],
BB [auth A],
BD [auth B],
BK [auth 4],
BN [auth 9],
CA [auth A],
CB [auth A],
CD [auth B],
CF [auth L],
CL [auth 5],
CM [auth 6],
CN [auth 9],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth L],
DL [auth 5],
DM [auth 6],
DN [auth 9],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth B],
EL [auth 5],
EM [auth 6],
EN [auth 9],
FA [auth A],
FB [auth A],
FD [auth B],
FF [auth K],
FH [auth 3],
FI [auth 7],
FJ [auth Z],
FK [auth 4],
FL [auth 5],
FM [auth 6],
FN [auth 9],
GA [auth A],
GB [auth A],
GD [auth B],
GF [auth K],
GJ [auth Z],
GK [auth 4],
GL [auth 5],
GM [auth 6],
GN [auth 9],
GO [auth B2],
HA [auth A],
HB [auth A],
HD [auth B],
HF [auth K],
HJ [auth Z],
HK [auth 4],
HL [auth 5],
HM [auth 6],
HO [auth B2],
IA [auth A],
IB [auth A],
ID [auth B],
IF [auth K],
IK [auth 4],
IL [auth 5],
JA [auth A],
JB [auth A],
JD [auth B],
JI [auth 8],
JK [auth 4],
JL [auth 5],
JM [auth 6],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KH [auth 7],
KI [auth 8],
KJ [auth Z],
KK [auth 4],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LG [auth 3],
LH [auth 7],
LI [auth 8],
LJ [auth Z],
LK [auth 4],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MG [auth 3],
MH [auth 7],
MJ [auth Z],
ML [auth 5],
MO [auth L2],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth F],
NG [auth 3],
NJ [auth Z],
NM [auth 6],
NN [auth B2],
NO [auth L2],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth F],
OF [auth 1],
OG [auth 3],
OI [auth 8],
OJ [auth Z],
ON [auth B2],
PA [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PF [auth 1],
PG [auth 3],
PH [auth 7],
PI [auth 8],
PJ [auth Z],
PN [auth B2],
PO [auth 92],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QF [auth 1],
QH [auth 7],
QI [auth 8],
QJ [auth Z],
QN [auth B2],
QO [auth 92],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RG [auth 3],
RH [auth 7],
RI [auth 8],
RJ [auth Z],
RN [auth B2],
RO [auth 92],
SA [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SG [auth 3],
SH [auth 7],
SI [auth 8],
SN [auth B2],
SO [auth 92],
TA [auth A],
TC [auth B],
TD [auth B],
TF [auth 1],
TG [auth 3],
TH [auth 7],
TI [auth 8],
TN [auth B2],
UA [auth A],
UC [auth B],
UD [auth B],
UF [auth 1],
UG [auth 3],
UH [auth 7],
UI [auth 8],
UN [auth B2],
VA [auth A],
VC [auth B],
VD [auth B],
VF [auth 1],
VG [auth 3],
VH [auth 7],
VI [auth 8],
VK [auth 5],
VM [auth 9],
VN [auth B2],
VO [auth 92],
WA [auth A],
WC [auth B],
WD [auth B],
WE [auth J],
WF [auth 1],
WG [auth 3],
WH [auth 7],
WK [auth 5],
WL [auth 6],
WM [auth 9],
WN [auth B2],
WO [auth 92],
XA [auth A],
XC [auth B],
XD [auth B],
XF [auth 1],
XG [auth 3],
XK [auth 5],
XL [auth 6],
XM [auth 9],
XN [auth B2],
XO [auth 92],
YA [auth A],
YC [auth B],
YF [auth 1],
YK [auth 5],
YL [auth 6],
YM [auth 9],
YN [auth B2],
YO [auth 92],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZF [auth 1],
ZJ [auth 4],
ZN [auth B2],
ZO [auth 92]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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

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BC [auth A]
CJ [auth 8]
EH [auth 3]
FO [auth B2]
GE [auth B]
BC [auth A],
CJ [auth 8],
EH [auth 3],
FO [auth B2],
GE [auth B],
GI [auth 8],
IC [auth A],
IG [auth 1],
IH [auth 7],
IO [auth B2],
JE [auth B],
JN [auth 9],
LF [auth 1],
RK [auth 4],
UM [auth 6],
YE [auth J],
ZE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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AI [auth 7]
DH [auth 3]
DP [auth 92]
EG [auth 1]
FE [auth B]
AI [auth 7],
DH [auth 3],
DP [auth 92],
EG [auth 1],
FE [auth B],
GH [auth 3],
KN [auth 9],
LM [auth 6],
OL [auth 5],
QK [auth 4],
RB [auth A],
SB [auth A],
SM [auth 6],
UK [auth 4],
VJ [auth Z],
ZI [auth 8]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX (Subject of Investigation/LOI)
Query on NEX

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QL [auth 5],
QM [auth 6]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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CG [auth 1]
OK [auth 4]
PL [auth 5]
PM [auth 6]
TJ [auth Z]
CG [auth 1],
OK [auth 4],
PL [auth 5],
PM [auth 6],
TJ [auth Z],
XI [auth 8],
YH [auth 7]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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AH [auth 3]
BG [auth 1]
BP [auth 92]
CH [auth 3]
CP [auth 92]
AH [auth 3],
BG [auth 1],
BP [auth 92],
CH [auth 3],
CP [auth 92],
DG [auth 1],
DI [auth 7],
FC [auth A],
HN [auth 9],
IN [auth 9],
LL [auth 5],
MM [auth 6],
NK [auth 4],
QE [auth F],
RL [auth 5],
SJ [auth Z],
UJ [auth Z],
WI [auth 8],
XH [auth 7],
ZG [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AE [auth B]
AF [auth L]
BE [auth B]
BF [auth L]
BH [auth 3]
AE [auth B],
AF [auth L],
BE [auth B],
BF [auth L],
BH [auth 3],
BO [auth B2],
CE [auth B],
CO [auth B2],
DE [auth B],
DO [auth B2],
EF [auth K],
EO [auth B2],
EP [auth 92],
HH [auth 3],
IE [auth B],
JF [auth K],
JO [auth I2],
KE [auth B],
KO [auth L2],
LN [auth 9],
LO [auth L2],
NL [auth 5],
OM [auth 6],
PK [auth 4],
TB [auth A],
TE [auth G],
UB [auth A],
VB [auth A],
VE [auth I],
WB [auth A],
XB [auth A],
XE [auth J],
YG [auth 3],
YI [auth 8],
ZD [auth B],
ZH [auth 7]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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AC [auth A]
AJ [auth 8]
BI [auth 7]
BJ [auth 8]
CC [auth A]
AC [auth A],
AJ [auth 8],
BI [auth 7],
BJ [auth 8],
CC [auth A],
CI [auth 7],
DC [auth A],
DJ [auth 8],
EI [auth 7],
FG [auth 1],
GC [auth A],
GG [auth 1],
HC [auth A],
HE [auth B],
HG [auth 1],
HI [auth 8],
JC [auth A],
JG [auth 1],
KF [auth K],
KG [auth 1],
MF [auth 1],
MN [auth 9],
OO [auth 92],
RM [auth 6],
SK [auth 4],
SL [auth 5],
TK [auth 4],
TL [auth 6],
TM [auth 6],
UE [auth G],
UL [auth 6],
WJ [auth Z],
XJ [auth Z],
ZB [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
PB [auth A],
YD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
LE [auth C],
ME [auth C],
YB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Swedish Foundation for Strategic ResearchSwedenARC19-0051
Knut and Alice Wallenberg FoundationSweden2018.0080
German Federal Ministry for Education and ResearchGermanyNRW 28 313-WO44A
German-Israeli Foundation for Research and DevelopmentGermanyG-1483- 207/2018

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release