7ZQ9

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

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Chlamydomonas reinhardtii
  • Mutation(s): No 

  • 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: 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 ...

    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. amunts@scilifelab.se.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A751Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaAps1a1
EC: 1.97.1.12
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B735Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaBps1a2
EC: 1.97.1.12
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC81Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticD196Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaD
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, chloroplasticE97Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAE
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticF227Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAF
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG126Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAG
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth I],
V [auth I2]
106Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAICHLRE_03g165100v5CHLREDRAFT_144056
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]40Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: psaJ
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
PSI subunit VJ [auth L],
W [auth L2]
196Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSALCHLRE_12g486300v5CHLREDRAFT_205935
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticK113Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: PSAK
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticL [auth 1],
P [auth Z]
228Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: Lhca1LhcI-6CHLRE_06g283050v5
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LHCA3CHLREDRAFT_153678
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcaCHLRE_16g687900v5
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-4LHCA8CHLRE_06g272650v5CHLREDRAFT_187025
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic (Lhca4)Q [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-1CHLRE_10g452050v5
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-3LHCA5CHLRE_10g425900v5CHLREDRAFT_186299
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LhcI-5LHCA6CHLRE_06g278213v5CHLREDRAFT_192961
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 9],
X [auth 92]
213Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LHCA9CHLRE_07g344950v5CHLREDRAFT_136294
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2U [auth B2]180Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 13 Unique
IDChainsName / 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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
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
 Ligand Interaction
LMU (Subject of Investigation/LOI)
Query on LMU

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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
 Ligand Interaction
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-VKOJMFJBAC
 Ligand Interaction
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