6IJO | pdb_00006ijo

Photosystem I of Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6IJO

This is version 3.0 of the entry. See complete history

Literature

Antenna arrangement and energy transfer pathways of a green algal photosystem-I-LHCI supercomplex.

Su, X.Ma, J.Pan, X.Zhao, X.Chang, W.Liu, Z.Zhang, X.Li, M.

(2019) Nat Plants 5: 273-281

  • DOI: https://doi.org/10.1038/s41477-019-0380-5
  • Primary Citation Related Structures: 
    6IJJ, 6IJO

  • PubMed Abstract: 

    During oxygenic photosynthesis, photosystems I and II (PSI and PSII) are essential for light-driven electron transport. Excitation energy transfer in PSI occurs extremely quickly, making it an efficient energy converter. In the alga Chlamydomonas reinhardtii (Cr), multiple units of light-harvesting complex I (LHCI) bind to the PSI core and function as peripheral antennae, forming a PSI-LHCI supercomplex. CrPSI-LHCI shows significantly larger antennae compared with plant PSI-LHCI while maintaining highly efficient energy transfer from LHCI to PSI. Here, we report structures of CrPSI-LHCI, solved by cryo-electron microscopy, revealing that up to ten LHCIs are associated with the PSI core. The structures provide detailed information about antenna organization and pigment arrangement within the supercomplexes. Highly populated and closely associated chlorophylls in the antennae explain the high efficiency of light harvesting and excitation energy transfer in CrPSI-LHCI.


  • Organizational Affiliation
    • National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 892.59 kDa 
  • Atom Count: 49,685 
  • Modeled Residue Count: 4,382 
  • Deposited Residue Count: 5,718 
  • Unique protein chains: 22

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaA751Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaB735Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P09144 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaC81Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaD247Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q39615 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaE143Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaF227Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaG159Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaH155Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaI106Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaJ41Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59777 (Chlamydomonas reinhardtii)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaK160Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P14225 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaL258Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8IL32 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca1M [auth 1],
N [auth a]
248Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q05093 (Chlamydomonas reinhardtii)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca3O [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca4P [auth 4]290Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca5Q [auth 5]274Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca6R [auth 6]318Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca7S [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca8T [auth 8]272Chlamydomonas reinhardtiiMutation(s): 0 
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca2U [auth 2]227Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Lhca9V [auth 9]213Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
ChainXW [auth X]26Chlamydomonas reinhardtiiMutation(s): 0 

Small Molecules

Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
AE [auth B],
NE [auth J]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AG [auth a]
AK [auth 7]
AA [auth A],
AB [auth A],
AD [auth B],
AG [auth a],
AK [auth 7],
AL [auth 8],
BA [auth A],
BB [auth A],
BD [auth B],
BF [auth 1],
BG [auth a],
BI [auth 5],
BJ [auth 6],
BK [auth 7],
BL [auth 8],
CA [auth A],
CB [auth A],
CD [auth B],
CF [auth 1],
CG [auth a],
CI [auth 5],
CJ [auth 6],
CK [auth 7],
CL [auth 8],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth 1],
DG [auth a],
DI [auth 5],
DJ [auth 6],
DK [auth 7],
DL [auth 8],
DM [auth 9],
EA [auth A],
EB [auth A],
ED [auth B],
EE [auth F],
EF [auth 1],
EG [auth a],
EI [auth 5],
EJ [auth 6],
EK [auth 7],
EL [auth 8],
EM [auth 9],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth F],
FF [auth 1],
FG [auth a],
FI [auth 5],
FJ [auth 6],
FK [auth 7],
FL [auth 8],
FM [auth 9],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GE [auth F],
GF [auth 1],
GG [auth a],
GH [auth 4],
GI [auth 5],
GJ [auth 6],
GK [auth 7],
GM [auth 9],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HH [auth 4],
HI [auth 5],
HJ [auth 6],
HK [auth 7],
HM [auth 9],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth G],
IF [auth 1],
IH [auth 4],
II [auth 5],
IJ [auth 6],
IK [auth 7],
IM [auth 9],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth G],
JF [auth 1],
JH [auth 4],
JI [auth 5],
JJ [auth 6],
JK [auth 7],
JM [auth 9],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth 1],
KH [auth 4],
KI [auth 5],
KJ [auth 6],
KK [auth 7],
KM [auth 9],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth J],
LF [auth 1],
LG [auth 3],
LH [auth 4],
LI [auth 5],
LJ [auth 6],
LK [auth 7],
LM [auth 9],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth 1],
MG [auth 3],
MH [auth 4],
MI [auth 5],
MJ [auth 6],
MM [auth 9],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth 1],
NG [auth 3],
NH [auth 4],
NI [auth 5],
NJ [auth 6],
NL [auth 2],
NM [auth 9],
OA [auth A],
OC [auth B],
OD [auth B],
OF [auth 1],
OG [auth 3],
OH [auth 4],
OI [auth 5],
OJ [auth 6],
OL [auth 2],
OM [auth 9],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth K],
PG [auth 3],
PH [auth 4],
PI [auth 5],
PJ [auth 6],
PL [auth 2],
QA [auth A],
QC [auth B],
QD [auth B],
QG [auth 3],
QH [auth 4],
QI [auth 5],
QJ [auth 6],
QL [auth 2],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth K],
RG [auth 3],
RH [auth 4],
RI [auth 5],
RL [auth 2],
SA [auth A],
SC [auth B],
SD [auth B],
SE [auth K],
SG [auth 3],
SH [auth 4],
SJ [auth 6],
SK [auth 8],
SL [auth 2],
TA [auth A],
TC [auth B],
TE [auth K],
TF [auth a],
TG [auth 3],
TH [auth 4],
TK [auth 8],
TL [auth 2],
UA [auth A],
UC [auth B],
UF [auth a],
UG [auth 3],
UH [auth 4],
UK [auth 8],
UL [auth 2],
VA [auth A],
VC [auth B],
VF [auth a],
VG [auth 3],
VK [auth 8],
VL [auth 2],
WA [auth A],
WC [auth B],
WF [auth a],
WG [auth 3],
WK [auth 8],
WL [auth 2],
X [auth A],
XA [auth A],
XC [auth B],
XE [auth L],
XF [auth a],
XG [auth 3],
XJ [auth 7],
XK [auth 8],
XL [auth 2],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YE [auth L],
YF [auth a],
YG [auth 3],
YJ [auth 7],
YK [auth 8],
YL [auth 2],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZE [auth L],
ZF [auth a],
ZJ [auth 7],
ZK [auth 8],
ZL [auth 2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
AI [auth 4]
DC [auth A]
OE [auth J]
RK [auth 7]
YI [auth 5]
AI [auth 4],
DC [auth A],
OE [auth J],
RK [auth 7],
YI [auth 5],
ZH [auth 4],
ZI [auth 5]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



Download:Ideal Coordinates CCD File
BE [auth B]
CM [auth 2]
EH [auth 3]
FH [auth 3]
JL [auth 8]
BE [auth B],
CM [auth 2],
EH [auth 3],
FH [auth 3],
JL [auth 8],
KG [auth a],
KL [auth 8],
PK [auth 7],
QB [auth A],
RB [auth A],
RM [auth 9],
SF [auth 1],
VI [auth 5],
VJ [auth 6],
XI [auth 5],
YH [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT

Query on XAT



Download:Ideal Coordinates CCD File
AH [auth 3]
BM [auth 2]
HL [auth 8]
IG [auth a]
NK [auth 7]
AH [auth 3],
BM [auth 2],
HL [auth 8],
IG [auth a],
NK [auth 7],
QF [auth 1],
QM [auth 9],
TI [auth 5],
TJ [auth 6],
WH [auth 4]
(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
NEX

Query on NEX



Download:Ideal Coordinates CCD File
WI [auth 5],
WJ [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
LUT

Query on LUT



Download:Ideal Coordinates CCD File
AM [auth 2]
GL [auth 8]
HG [auth a]
MK [auth 7]
PF [auth 1]
AM [auth 2],
GL [auth 8],
HG [auth a],
MK [auth 7],
PF [auth 1],
PM [auth 9],
RJ [auth 6],
SI [auth 5],
VH [auth 4],
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

Query on BCR



Download:Ideal Coordinates CCD File
AF [auth L]
BH [auth 3]
CH [auth 3]
DH [auth 3]
EC [auth B]
AF [auth L],
BH [auth 3],
CH [auth 3],
DH [auth 3],
EC [auth B],
HE [auth F],
IL [auth 8],
JG [auth a],
KE [auth G],
ME [auth J],
OK [auth 7],
QE [auth K],
QK [auth 7],
RF [auth 1],
SB [auth A],
TB [auth A],
UB [auth A],
UD [auth B],
UE [auth K],
UI [auth 5],
UJ [auth 6],
VB [auth A],
VD [auth B],
WB [auth A],
WD [auth B],
WE [auth L],
XD [auth B],
XH [auth 4],
YD [auth B],
ZB [auth A],
ZD [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU



Download:Ideal Coordinates CCD File
AC [auth A]
AJ [auth 5]
BC [auth A]
CC [auth A]
LL [auth 8]
AC [auth A],
AJ [auth 5],
BC [auth A],
CC [auth A],
LL [auth 8],
ML [auth 8],
VE [auth K]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
OB [auth A],
TD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
CE [auth C],
DE [auth C],
XB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Ministry of Science and Technology (China)China2017YFA0504700
Ministry of Science and Technology (China)China2016YFA0502900
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaXDB08030204
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31770778
National Natural Science Foundation of ChinaChina31700649
National Natural Science Foundation of ChinaChina31600609

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references, Structure summary
  • Version 2.0: 2019-05-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.0: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary