8WB4

Structure of PSII-ACPII supercomplex from cryptophyte algae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea.

Mao, Z.Li, X.Li, Z.Shen, L.Li, X.Yang, Y.Wang, W.Kuang, T.Shen, J.R.Han, G.

(2024) Nat Commun 15: 4535-4535

  • DOI: https://doi.org/10.1038/s41467-024-48878-x
  • Primary Citation of Related Structures:  
    8WB4, 8XKL

  • PubMed Abstract: 

    Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093, Beijing, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center MA [auth m],
B [auth M]
115Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-1C [auth 1],
SA [auth 7]
235Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-2D [auth 2],
TA [auth 8]
217Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-3E [auth 3],
UA [auth 9]
222Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-4F [auth 4],
RA [auth 0]
226Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-5BB [auth p],
G [auth 5]
218Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-6H [auth 6],
YA [auth P]
220Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1I [auth A],
ZA [auth a]
360Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Find proteins for A0A222AI41 (Chroomonas placoidea)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinCA [auth d],
J [auth D]
351Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaDA [auth e],
K [auth E]
84Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI74 (Chroomonas placoidea)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaEA [auth f],
L [auth F]
42Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAB [auth h],
M [auth H]
67Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AIE4 (Chroomonas placoidea)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IGA [auth i],
N [auth I]
38Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI80 (Chroomonas placoidea)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JHA [auth j],
O [auth J]
39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI54 (Chroomonas placoidea)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KIA [auth k],
P [auth K]
45Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein OKA [auth o],
Q [auth O]
330Chroomonas placoideaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein QCB [auth q],
R [auth Q]
21Chroomonas placoideaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein RLA [auth r],
S [auth R]
26Chroomonas placoideaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
CCPII-SDB [auth s],
T [auth S]
285Chroomonas placoideaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TEB [auth t],
U [auth T]
32Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AID2 (Chroomonas placoidea)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein UMA [auth u],
V [auth U]
150Chroomonas placoideaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II cytochrome c550NA [auth v],
W [auth V]
163Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI35 (Chroomonas placoidea)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinOA [auth x],
X
39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI61 (Chroomonas placoidea)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12PA [auth y],
Y
34Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI69 (Chroomonas placoidea)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
Z
62Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI96 (Chroomonas placoidea)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinAA [auth b],
FB [auth B]
509Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AIE3 (Chroomonas placoidea)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinBA [auth c],
VA [auth C]
461Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI36 (Chroomonas placoidea)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein GFA [auth g],
WA [auth G]
64Chroomonas placoideaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJA [auth l],
XA [auth L]
38Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein WGB [auth w],
HB [auth W]
114Chroomonas placoideaMutation(s): 0 
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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FI [auth c]
GI [auth c]
HI [auth c]
MG [auth H]
MM [auth C]
FI [auth c],
GI [auth c],
HI [auth c],
MG [auth H],
MM [auth C],
NM [auth C],
OM [auth C],
YN [auth a],
ZF [auth A],
ZN [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth 3]
AG [auth D]
AH [auth b]
AI [auth c]
AK [auth 7]
AD [auth 3],
AG [auth D],
AH [auth b],
AI [auth c],
AK [auth 7],
AM [auth C],
AN [auth P],
AP [auth B],
BD [auth 3],
BF [auth 6],
BH [auth b],
BI [auth c],
BK [auth 7],
BL [auth 8],
BM [auth C],
BN [auth P],
BP [auth B],
CC [auth 2],
CD [auth 3],
CF [auth 6],
CG [auth D],
CH [auth b],
CI [auth c],
CK [auth 7],
CL [auth 8],
CM [auth C],
CN [auth P],
CO [auth p],
CP [auth B],
DC [auth 2],
DD [auth 3],
DF [auth 6],
DG [auth D],
DH [auth b],
DI [auth c],
DK [auth 7],
DM [auth C],
DO [auth p],
DP [auth B],
EC [auth 2],
ED [auth 3],
EE [auth 5],
EH [auth b],
EI [auth c],
EJ [auth 0],
EK [auth 7],
EM [auth C],
EN [auth P],
EO [auth p],
EP [auth B],
FC [auth 2],
FD [auth 3],
FE [auth 5],
FF [auth 6],
FH [auth b],
FJ [auth 0],
FK [auth 7],
FM [auth C],
FN [auth P],
FO [auth p],
FP [auth B],
GC [auth 2],
GE [auth 5],
GF [auth 6],
GH [auth b],
GJ [auth 0],
GK [auth 7],
GM [auth C],
GO [auth p],
GP [auth B],
HC [auth 2],
HE [auth 5],
HH [auth b],
HJ [auth 0],
HM [auth C],
HO [auth p],
HP [auth B],
IC [auth 2],
IE [auth 5],
IH [auth b],
IJ [auth 0],
IK [auth 7],
IM [auth C],
IO [auth p],
IP [auth B],
JB [auth 1],
JC [auth 2],
JE [auth 5],
JH [auth b],
JJ [auth 0],
JK [auth 7],
JM [auth C],
JO [auth p],
JP [auth B],
KB [auth 1],
KC [auth 2],
KD [auth 4],
KE [auth 5],
KH [auth b],
KJ [auth 0],
KK [auth 7],
KL [auth 9],
KM [auth C],
KO [auth p],
KP [auth B],
LB [auth 1],
LD [auth 4],
LE [auth 5],
LH [auth b],
LI [auth d],
LJ [auth 0],
LL [auth 9],
LM [auth C],
LP [auth B],
MB [auth 1],
MC [auth 2],
MD [auth 4],
ME [auth 5],
MI [auth d],
MJ [auth 0],
ML [auth 9],
MO [auth p],
MP [auth B],
NB [auth 1],
NC [auth 2],
ND [auth 4],
NF [auth A],
NL [auth 9],
NO [auth p],
OB [auth 1],
OD [auth 4],
OE [auth 5],
OF [auth A],
OJ [auth 0],
OL [auth 9],
PB [auth 1],
PD [auth 4],
PE [auth 5],
PJ [auth 0],
PL [auth 9],
PN [auth a],
QB [auth 1],
QD [auth 4],
QF [auth A],
QJ [auth 0],
QL [auth 9],
QN [auth a],
RB [auth 1],
RD [auth 4],
RG [auth S],
RK [auth 8],
RL [auth 9],
RM [auth G],
SD [auth 4],
SG [auth S],
SH [auth c],
SI [auth d],
SK [auth 8],
SL [auth 9],
SN [auth a],
TB [auth 1],
TH [auth c],
TK [auth 8],
TL [auth 9],
UB [auth 1],
UD [auth 4],
UH [auth c],
UK [auth 8],
UL [auth 9],
UO [auth s],
VB [auth 1],
VC [auth 3],
VD [auth 4],
VH [auth c],
VK [auth 8],
VM [auth P],
VO [auth s],
WC [auth 3],
WD [auth 4],
WE [auth 6],
WG [auth b],
WH [auth c],
WK [auth 8],
WM [auth P],
XC [auth 3],
XE [auth 6],
XG [auth b],
XH [auth c],
XI [auth g],
XK [auth 8],
XM [auth P],
XO [auth B],
YC [auth 3],
YE [auth 6],
YG [auth b],
YH [auth c],
YJ [auth 7],
YK [auth 8],
YM [auth P],
YO [auth B],
ZC [auth 3],
ZE [auth 6],
ZG [auth b],
ZH [auth c],
ZJ [auth 7],
ZK [auth 8],
ZL [auth C],
ZO [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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BG [auth D],
PF [auth A],
RN [auth a],
TI [auth d]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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OH [auth b]
PP [auth B]
RF [auth A]
SO [auth p]
TN [auth a]
OH [auth b],
PP [auth B],
RF [auth A],
SO [auth p],
TN [auth a],
UE [auth 5],
VG [auth b],
WO [auth B]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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AJ [auth l]
BE [auth 4]
GG [auth D]
HL [auth 8]
II [auth c]
AJ [auth l],
BE [auth 4],
GG [auth D],
HL [auth 8],
II [auth c],
KG [auth D],
KI [auth d],
KN [auth P],
LF [auth 6],
MH [auth b],
NP [auth B],
PI [auth d],
PM [auth C],
SC [auth 2],
SF [auth A],
SM [auth G],
UM [auth L],
UN [auth a],
WI [auth g],
WJ [auth 0]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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EG [auth D],
NI [auth d],
UF [auth A],
WN [auth a]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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BJ [auth l]
FG [auth D]
IL [auth 8]
JG [auth D]
MN [auth a]
BJ [auth l],
FG [auth D],
IL [auth 8],
JG [auth D],
MN [auth a],
NH [auth b],
NN [auth a],
OI [auth d],
OP [auth B],
PH [auth b],
QG [auth S],
QP [auth B],
TC [auth 2],
TM [auth L],
TO [auth s],
UI [auth d],
XF [auth A],
YF [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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CJ [auth v],
LG [auth E],
TG [auth V],
VI [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC2 (Subject of Investigation/LOI)
Query on KC2

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AF [auth 6]
AL [auth 8]
DN [auth P]
EF [auth 6]
HK [auth 7]
AF [auth 6],
AL [auth 8],
DN [auth P],
EF [auth 6],
HK [auth 7],
LC [auth 2],
LO [auth p],
NE [auth 5],
NJ [auth 0],
SB [auth 1],
TD [auth 4],
ZM [auth P]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II3 (Subject of Investigation/LOI)
Query on II3

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HN [auth P],
IF [auth 6],
MK [auth 7],
XB [auth 1]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
VAGYSFRRYPPSFX-RLVOMNFVSA-N
II0 (Subject of Investigation/LOI)
Query on II0

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BC [auth 1]
BO [auth p]
CE [auth 4]
DE [auth 5]
DL [auth 8]
BC [auth 1],
BO [auth p],
CE [auth 4],
DE [auth 5],
DL [auth 8],
EL [auth 8],
FL [auth 8],
GD [auth 3],
GN [auth P],
HD [auth 3],
HF [auth 6],
ID [auth 3],
IN [auth P],
JF [auth 6],
JL [auth 8],
LK [auth 7],
NK [auth 7],
OC [auth 2],
OK [auth 7],
OO [auth p],
PC [auth 2],
PO [auth p],
QC [auth 2],
QE [auth 5],
QK [auth 7],
QO [auth p],
RE [auth 5],
SE [auth 5],
SJ [auth 0],
TJ [auth 0],
UC [auth 2],
UJ [auth 0],
VE [auth 5],
VL [auth 9],
WB [auth 1],
WL [auth 9],
XJ [auth 0],
XL [auth 9],
YB [auth 1],
YD [auth 4],
ZB [auth 1],
ZD [auth 4]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT (Subject of Investigation/LOI)
Query on IHT

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AC [auth 1]
AE [auth 4]
GL [auth 8]
PK [auth 7]
RC [auth 2]
AC [auth 1],
AE [auth 4],
GL [auth 8],
PK [auth 7],
RC [auth 2],
RJ [auth 0],
RO [auth p],
TE [auth 5],
VJ [auth 0],
XD [auth 4]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
8CT (Subject of Investigation/LOI)
Query on 8CT

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AO [auth h]
DJ [auth z]
IB [auth M]
IG [auth D]
JD [auth 3]
AO [auth h],
DJ [auth z],
IB [auth M],
IG [auth D],
JD [auth 3],
JI [auth c],
JN [auth P],
KF [auth 6],
NG [auth H],
OG [auth K],
PG [auth K],
QH [auth b],
QM [auth C],
RH [auth b],
RI [auth d],
RP [auth B],
SP [auth B],
TP [auth B],
UG [auth Z],
VF [auth A],
XN [auth a],
YI [auth k],
YL [auth 9],
ZI [auth k]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
OEX (Subject of Investigation/LOI)
Query on OEX

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MF [auth A],
ON [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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LN [auth a],
WF [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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HG [auth D],
QI [auth d]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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TF [auth A],
VN [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaYSBR-004

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release