7DZ7

State transition supercomplex PSI-LHCI-LHCII from double phosphatase mutant pph1;pbcp of green alga Chlamydomonas reinhardtii


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis of LhcbM5-mediated state transitions in green algae.

Pan, X.Tokutsu, R.Li, A.Takizawa, K.Song, C.Murata, K.Yamasaki, T.Liu, Z.Minagawa, J.Li, M.

(2021) Nat Plants 7: 1119-1131

  • DOI: https://doi.org/10.1038/s41477-021-00960-8
  • Primary Citation of Related Structures:  
    7DZ7, 7DZ8, 7E0H, 7E0I, 7E0J, 7E0K

  • PubMed Abstract: 

    In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). During the process, a portion of light-harvesting complex II (LHCII) is phosphorylated, dissociated from PSII and binds with PSI to form the supercomplex PSI-LHCI-LHCII. Here, we report high-resolution structures of PSI-LHCI-LHCII from Chlamydomonas reinhardtii, revealing the mechanism of assembly between the PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM protein. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in supercomplex formation. The results unravel the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


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 
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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 VI, chloroplastic130Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII106Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Chlamydomonas 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
PSI subunit V196Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit OM [auth O]126Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth a],
O [auth 1]
228Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 2]246Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 3]298Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 4]264Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 5]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 6]257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticU [auth 7]241Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticV [auth 8]243Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth 9]213Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticCA [auth W],
X
249Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticAA [auth U],
Y
257Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic256Chlamydomonas reinhardtiiMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticBA [auth V]268Chlamydomonas reinhardtiiMutation(s): 0 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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GE [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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AO [auth X]
AQ [auth U]
AR [auth V]
BO [auth X]
BR [auth V]
AO [auth X],
AQ [auth U],
AR [auth V],
BO [auth X],
BR [auth V],
CO [auth X],
DO [auth X],
EQ [auth U],
FQ [auth U],
GQ [auth U],
HP [auth Z],
HQ [auth U],
IQ [auth U],
LP [auth Z],
MP [auth Z],
NP [auth Z],
NR [auth W],
OO [auth Y],
OP [auth Z],
PP [auth Z],
RR [auth W],
SO [auth Y],
SR [auth W],
TO [auth Y],
TQ [auth V],
TR [auth W],
UO [auth Y],
UR [auth W],
VN [auth X],
VO [auth Y],
VR [auth W],
WO [auth Y],
XQ [auth V],
YQ [auth V],
ZN [auth X],
ZQ [auth V]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
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AB [auth A]
AD [auth B]
AG [auth a]
AH [auth 1]
AJ [auth 4]
AB [auth A],
AD [auth B],
AG [auth a],
AH [auth 1],
AJ [auth 4],
AK [auth 5],
AL [auth 6],
AM [auth 7],
AP [auth Y],
AS [auth W],
BB [auth A],
BD [auth B],
BG [auth a],
BH [auth 1],
BI [auth 3],
BJ [auth 4],
BK [auth 5],
BL [auth 6],
BM [auth 7],
BP [auth Y],
BQ [auth U],
CB [auth A],
CD [auth B],
CF [auth K],
CG [auth a],
CH [auth 1],
CI [auth 3],
CJ [auth 4],
CK [auth 5],
CL [auth 6],
CN [auth 9],
CQ [auth U],
CR [auth V],
DA [auth A],
DB [auth A],
DD [auth B],
DG [auth a],
DH [auth 1],
DI [auth 3],
DJ [auth 4],
DK [auth 5],
DL [auth 6],
DN [auth 9],
DQ [auth U],
DR [auth V],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth B],
EF [auth K],
EG [auth a],
EH [auth 1],
EI [auth 3],
EJ [auth 4],
EK [auth 5],
EL [auth 6],
EN [auth 9],
EO [auth X],
ER [auth V],
FA [auth A],
FB [auth A],
FD [auth B],
FF [auth K],
FG [auth a],
FI [auth 3],
FJ [auth 4],
FK [auth 5],
FL [auth 6],
FN [auth 9],
FO [auth X],
FR [auth V],
GA [auth A],
GB [auth A],
GD [auth B],
GF [auth K],
GG [auth a],
GI [auth 3],
GJ [auth 4],
GK [auth 5],
GL [auth 6],
GN [auth 9],
GO [auth X],
GR [auth V],
HA [auth A],
HB [auth A],
HD [auth B],
HG [auth a],
HI [auth 3],
HJ [auth 4],
HK [auth 5],
HM [auth 8],
HN [auth 9],
HO [auth X],
IA [auth A],
IB [auth A],
ID [auth B],
IG [auth a],
II [auth 3],
IJ [auth 4],
IL [auth 6],
IM [auth 8],
IN [auth 9],
IO [auth X],
IP [auth Z],
JA [auth A],
JB [auth A],
JD [auth B],
JG [auth a],
JI [auth 3],
JJ [auth 4],
JM [auth 8],
JN [auth 9],
JP [auth Z],
JQ [auth U],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth L],
KG [auth a],
KH [auth 2],
KI [auth 3],
KJ [auth 4],
KM [auth 8],
KN [auth 9],
KP [auth Z],
KQ [auth U],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth L],
LG [auth a],
LH [auth 2],
LI [auth 3],
LM [auth 8],
LN [auth 9],
LQ [auth U],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth L],
MG [auth a],
MH [auth 2],
MI [auth 3],
MM [auth 8],
MN [auth 9],
MQ [auth U],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth F],
NH [auth 2],
NI [auth 3],
NL [auth 7],
NM [auth 8],
NN [auth 9],
NQ [auth U],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth F],
OF [auth L],
OH [auth 2],
OI [auth 3],
OL [auth 7],
OM [auth 8],
OR [auth W],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PF [auth L],
PH [auth 2],
PL [auth 7],
PM [auth 8],
PO [auth Y],
PR [auth W],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QH [auth 2],
QL [auth 7],
QM [auth 8],
QO [auth Y],
QP [auth Z],
QR [auth W],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RG [auth 1],
RH [auth 2],
RJ [auth 5],
RK [auth 6],
RL [auth 7],
RM [auth 8],
RO [auth Y],
RP [auth Z],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SG [auth 1],
SH [auth 2],
SJ [auth 5],
SK [auth 6],
SL [auth 7],
SM [auth 8],
SP [auth Z],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TF [auth O],
TG [auth 1],
TH [auth 2],
TJ [auth 5],
TK [auth 6],
TL [auth 7],
TM [auth 8],
TP [auth Z],
UA [auth A],
UC [auth B],
UD [auth B],
UE [auth H],
UF [auth O],
UG [auth 1],
UH [auth 2],
UJ [auth 5],
UK [auth 6],
UL [auth 7],
UM [auth 8],
UP [auth Z],
UQ [auth V],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth H],
VF [auth O],
VG [auth 1],
VH [auth 2],
VJ [auth 5],
VK [auth 6],
VL [auth 7],
VQ [auth V],
WA [auth A],
WC [auth B],
WD [auth B],
WG [auth 1],
WH [auth 2],
WI [auth 4],
WJ [auth 5],
WK [auth 6],
WL [auth 7],
WN [auth X],
WQ [auth V],
WR [auth W],
XA [auth A],
XC [auth B],
XD [auth B],
XG [auth 1],
XI [auth 4],
XJ [auth 5],
XK [auth 6],
XL [auth 7],
XN [auth X],
XO [auth Y],
XR [auth W],
YA [auth A],
YC [auth B],
YE [auth J],
YG [auth 1],
YI [auth 4],
YJ [auth 5],
YK [auth 6],
YL [auth 7],
YN [auth X],
YO [auth Y],
YR [auth W],
ZA [auth A],
ZC [auth B],
ZF [auth a],
ZG [auth 1],
ZI [auth 4],
ZJ [auth 5],
ZK [auth 6],
ZL [auth 7],
ZO [auth Y],
ZR [auth W]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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AF [auth J]
BF [auth J]
BN [auth 8]
IC [auth A]
MR [auth V]
AF [auth J],
BF [auth J],
BN [auth 8],
IC [auth A],
MR [auth V],
OK [auth 5],
PJ [auth 4],
QJ [auth 4],
SF [auth L],
UN [auth 9],
XE [auth H]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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FM [auth 7]
FS [auth W]
GP [auth Y]
HE [auth B]
IH [auth 1]
FM [auth 7],
FS [auth W],
GP [auth Y],
HE [auth B],
IH [auth 1],
KE [auth B],
LK [auth 5],
LL [auth 6],
LR [auth V],
NK [auth 5],
NO [auth X],
OJ [auth 4],
QG [auth a],
RN [auth 9],
SN [auth 9],
SQ [auth U],
TN [auth 9],
UI [auth 3],
VI [auth 3],
WB [auth A],
WE [auth H],
XB [auth A],
YF [auth O],
YM [auth 8],
ZH [auth 2],
ZM [auth 8],
ZP [auth Z]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

Download Ideal Coordinates CCD File 
ES [auth W]
FP [auth Y]
KR [auth V]
MK [auth 5]
ML [auth 6]
ES [auth W],
FP [auth Y],
KR [auth V],
MK [auth 5],
ML [auth 6],
MO [auth X],
RQ [auth U],
YP [auth Z]
(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
Query on XAT

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DM [auth 7]
DS [auth W]
EP [auth Y]
GH [auth 1]
JK [auth 5]
DM [auth 7],
DS [auth W],
EP [auth Y],
GH [auth 1],
JK [auth 5],
JL [auth 6],
JR [auth V],
LO [auth X],
MJ [auth 4],
OG [auth a],
PN [auth 9],
QI [auth 3],
QQ [auth U],
WM [auth 8],
XP [auth Z],
YH [auth 2]
(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
Query on LUT

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BS [auth W]
CM [auth 7]
CP [auth Y]
CS [auth W]
DP [auth Y]
BS [auth W],
CM [auth 7],
CP [auth Y],
CS [auth W],
DP [auth Y],
FH [auth 1],
HL [auth 6],
HR [auth V],
IK [auth 5],
IR [auth V],
JO [auth X],
KO [auth X],
LJ [auth 4],
NG [auth a],
ON [auth 9],
OQ [auth U],
PI [auth 3],
PQ [auth U],
VM [auth 8],
VP [auth Z],
WP [auth Z],
XH [auth 2]
(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

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AC [auth A]
AE [auth B]
AI [auth 2]
BC [auth A]
BE [auth B]
AC [auth A],
AE [auth B],
AI [auth 2],
BC [auth A],
BE [auth B],
CC [auth A],
CE [auth B],
DE [auth B],
DF [auth K],
EE [auth B],
EM [auth 7],
FC [auth A],
FE [auth B],
GM [auth 7],
HF [auth K],
HH [auth 1],
IE [auth B],
JC [auth B],
JE [auth B],
JF [auth L],
KK [auth 5],
KL [auth 6],
NF [auth L],
NJ [auth 4],
PG [auth a],
QE [auth F],
QF [auth L],
QN [auth 9],
RF [auth L],
RI [auth 3],
SI [auth 3],
TE [auth G],
TI [auth 3],
WF [auth O],
XF [auth O],
XM [auth 8],
YB [auth A],
ZB [auth A],
ZD [auth B],
ZE [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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AN [auth 8]
GC [auth A]
HC [auth A]
IF [auth K]
JH [auth 1]
AN [auth 8],
GC [auth A],
HC [auth A],
IF [auth K],
JH [auth 1],
PK [auth 5],
QK [auth 5]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

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UB [auth A],
YD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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DC [auth A],
LE [auth C],
ME [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
Z
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 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 (MoST, China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaXDB37020101
National Natural Science Foundation of China (NSFC)China31925024
National Natural Science Foundation of China (NSFC)China31930064
Chinese Academy of SciencesChinaZDBS-LY-SM003
Japan Society for the Promotion of Science (JSPS)Japan16H06553
Japan Society for the Promotion of Science (JSPS)JapanJP15H05599

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 2.0: 2021-07-21
    Changes: Data collection, Database references, Non-polymer description
  • Version 2.1: 2021-09-01
    Changes: Database references