8XR6 | pdb_00008xr6

Cryo-EM structure of cryptophyte photosystem II

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex.

Zhang, Y.Z., Li, K., Qin, B.Y., Guo, J.P., Zhang, Q.B., Zhao, D.L., Chen, X.L., Gao, J., Liu, L.N., Zhao, L.S.

(2024) Nat Commun 15: 4999-4999

  • DOI: https://doi.org/10.1038/s41467-024-49453-0
  • Primary Citation of Related Structures:  
    8XR6

  • PubMed Abstract: 

    Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs.

    • Organizational Affiliation: 
    • Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China. zhangyz@sdu.edu.cn.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A [auth a],
B [auth A]		360Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI41 (Chroomonas placoidea)
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UniProt GroupA0A222AI41
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-4C [auth 0],
G [auth 4]		219Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-1D [auth 1],
J [auth 7]		218Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-2E [auth 2],
K [auth 8]		200Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-3F [auth 3],
L [auth 9]		229Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-5H [auth 5],
MA [auth g]		216Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-6I [auth 6],
VA [auth p]		234Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinHA [auth b],
M [auth B]		509Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsbC_CP43IA [auth c],
N [auth C]		473Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinJA [auth d],
O [auth D]		351Chroomonas placoideaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaKA [auth e],
P [auth E]		84Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaLA [auth f],
Q [auth F]		42Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HNA [auth h],
R [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: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IOA [auth i],
S [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: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JPA [auth j],
T [auth J]		39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KQA [auth k],
U [auth K]		45Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LRA [auth l],
V [auth L]		38Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsbMSA [auth m],
W [auth M]		37Chroomonas placoideaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Psb-gama_linkerTA [auth n],
X [auth N]		297Chroomonas placoideaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
PsbOUA [auth o],
Y [auth O]		300Chroomonas placoideaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsbQWA [auth q],
Z [auth Q]		144Chroomonas placoideaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TAA [auth T],
XA [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: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PsbUBA [auth U],
YA [auth u]		121Chroomonas placoideaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II cytochrome c550CA [auth V],
ZA [auth v]		163Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI35 (Chroomonas placoidea)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
PsbWAB [auth w],
DA [auth W]		130Chroomonas placoideaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XBB [auth x],
EA [auth X]		39Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI61 (Chroomonas placoidea)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30CB [auth y],
FA [auth Y]		34Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI69 (Chroomonas placoidea)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZDB [auth z],
GA [auth Z]		62Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A222AI96 (Chroomonas placoidea)
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
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BL [auth H]
FN [auth c]
GN [auth c]
IN [auth c]
LO [auth h]
BL [auth H],
FN [auth c],
GN [auth c],
IN [auth c],
LO [auth h],
MK [auth C],
NK [auth C],
PK [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
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AD [auth 1]
AF [auth 4]
AH [auth 7]
AJ [auth B]
AK [auth C]
AD [auth 1],
AF [auth 4],
AH [auth 7],
AJ [auth B],
AK [auth C],
AM [auth b],
AN [auth c],
AO [auth g],
AP [auth p],
BC [auth A],
BD [auth 1],
BE [auth 3],
BF [auth 4],
BG [auth 5],
BH [auth 7],
BJ [auth B],
BK [auth C],
BM [auth b],
BN [auth c],
BO [auth g],
BP [auth p],
CC [auth 0],
CE [auth 3],
CF [auth 4],
CH [auth 7],
CJ [auth B],
CK [auth C],
CM [auth b],
CP [auth p],
DC [auth 0],
DE [auth 3],
DF [auth 4],
DG [auth 6],
DH [auth 7],
DI [auth 9],
DJ [auth B],
DK [auth C],
DM [auth b],
DO [auth g],
DP [auth p],
EC [auth 0],
EE [auth 3],
EF [auth 4],
EG [auth 6],
EI [auth 9],
EJ [auth B],
EK [auth C],
EM [auth b],
EO [auth g],
EP [auth p],
FC [auth 0],
FE [auth 3],
FG [auth 6],
FI [auth 9],
FJ [auth B],
FK [auth C],
FL [auth N],
FM [auth b],
FP [auth p],
GE [auth 3],
GG [auth 6],
GI [auth 9],
GJ [auth B],
GK [auth C],
GL [auth N],
GM [auth b],
GP [auth p],
HC [auth 0],
HE [auth 3],
HG [auth 6],
HI [auth 9],
HJ [auth B],
HK [auth C],
HL [auth N],
HM [auth b],
IB [auth a],
IC [auth 0],
IE [auth 3],
IG [auth 6],
II [auth 9],
IJ [auth B],
IK [auth C],
IL [auth N],
IP [auth p],
JB [auth a],
JC [auth 0],
JG [auth 6],
JI [auth 9],
JJ [auth B],
JL [auth N],
JP [auth p],
KC [auth 0],
KD [auth 2],
KE [auth 3],
KG [auth 6],
KI [auth 9],
KJ [auth B],
KL [auth N],
KO [auth g],
LB [auth a],
LC [auth 0],
LD [auth 2],
LE [auth 3],
LF [auth 5],
LG [auth 6],
LJ [auth B],
LL [auth N],
MC [auth 0],
MD [auth 2],
ME [auth 3],
MF [auth 5],
MH [auth 8],
MI [auth 9],
MJ [auth B],
MN [auth d],
ND [auth 2],
NE [auth 3],
NF [auth 5],
NG [auth 6],
NH [auth 8],
NI [auth 9],
NJ [auth B],
NN [auth d],
OD [auth 2],
OF [auth 5],
OG [auth 6],
OH [auth 8],
OI [auth 9],
OJ [auth B],
PB [auth a],
PD [auth 2],
PF [auth 5],
PH [auth 8],
PI [auth 9],
PM [auth c],
PP [auth p],
QD [auth 2],
QF [auth 5],
QH [auth 8],
QM [auth c],
RD [auth 2],
RF [auth 5],
RH [auth 8],
RL [auth b],
RM [auth c],
RO [auth n],
SF [auth 5],
SH [auth 8],
SL [auth b],
SM [auth c],
SO [auth n],
TC [auth 1],
TD [auth 2],
TH [auth 8],
TK [auth D],
TL [auth b],
TM [auth c],
TO [auth n],
UB [auth A],
UC [auth 1],
UF [auth 5],
UG [auth 6],
UK [auth D],
UL [auth b],
UM [auth c],
UN [auth g],
UO [auth n],
VB [auth A],
VC [auth 1],
VE [auth 4],
VF [auth 5],
VG [auth 7],
VH [auth 8],
VL [auth b],
VM [auth c],
VN [auth g],
VO [auth n],
WC [auth 1],
WE [auth 4],
WG [auth 7],
WJ [auth C],
WL [auth b],
WM [auth c],
WN [auth g],
WO [auth n],
XB [auth A],
XC [auth 1],
XE [auth 4],
XG [auth 7],
XJ [auth C],
XL [auth b],
XM [auth c],
XN [auth g],
YC [auth 1],
YE [auth 4],
YG [auth 7],
YI [auth B],
YJ [auth C],
YL [auth b],
YM [auth c],
YN [auth g],
YO [auth p],
ZC [auth 1],
ZG [auth 7],
ZI [auth B],
ZJ [auth C],
ZL [auth b],
ZM [auth c],
ZN [auth g],
ZO [auth p]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
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KB [auth a],
LN [auth d],
SK [auth D],
WB [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
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DL [auth J]
EL [auth L]
NO [auth j]
OM [auth c]
OO [auth l]
DL [auth J],
EL [auth L],
NO [auth j],
OM [auth c],
OO [auth l],
QL [auth b],
VJ [auth C],
XI [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
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HN [auth c]
LM [auth b]
ML [auth T]
NM [auth b]
OK [auth C]
HN [auth c],
LM [auth b],
ML [auth T],
NM [auth b],
OK [auth C],
OL [auth W],
PO [auth l],
QO [auth m],
QP [auth t],
RN [auth d],
SJ [auth B],
SN [auth d],
SP [auth w],
UJ [auth B],
YK [auth D],
ZK [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
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NB [auth a],
PN [auth d],
WK [auth D],
ZB [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
Query on LHG
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AC [auth A]
AE [auth 3]
AG [auth 5]
AI [auth 8]
CI [auth 9]
AC [auth A],
AE [auth 3],
AG [auth 5],
AI [auth 8],
CI [auth 9],
JD [auth 1],
JN [auth d],
JO [auth g],
KF [auth 4],
KN [auth d],
LH [auth 7],
MM [auth b],
OB [auth a],
QK [auth D],
QN [auth d],
RK [auth D],
SC [auth 0],
TE [auth 3],
TJ [auth B],
UE [auth 3],
VI [auth 9],
WI [auth 9],
XK [auth D],
YD [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
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AL [auth F],
NL [auth V],
RP [auth v],
TN [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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CD [auth 1]
CO [auth g]
DD [auth 1]
EH [auth 7]
FH [auth 7]
CD [auth 1],
CO [auth g],
DD [auth 1],
EH [auth 7],
FH [auth 7],
GC [auth 0],
HP [auth p],
JE [auth 3],
LI [auth 9],
MG [auth 6],
SD [auth 2],
TF [auth 5],
UH [auth 8],
ZE [auth 4]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0
Query on II0
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BI [auth 9]
CG [auth 6]
FD [auth 1]
FO [auth g]
GD [auth 1]
BI [auth 9],
CG [auth 6],
FD [auth 1],
FO [auth g],
GD [auth 1],
GF [auth 4],
GO [auth g],
HD [auth 1],
HF [auth 4],
HH [auth 7],
HO [auth g],
ID [auth 1],
IF [auth 4],
IH [auth 7],
JF [auth 4],
JH [auth 7],
KH [auth 7],
KP [auth p],
LP [auth p],
MP [auth p],
NP [auth p],
OC [auth 0],
OE [auth 3],
PC [auth 0],
PE [auth 3],
PG [auth 6],
QC [auth 0],
QE [auth 3],
QG [auth 6],
QI [auth 9],
RC [auth 0],
RE [auth 3],
RG [auth 6],
RI [auth 9],
SG [auth 6],
SI [auth 9],
TI [auth 9],
UD [auth 2],
VD [auth 2],
WD [auth 2],
WF [auth 5],
WH [auth 8],
XF [auth 5],
XH [auth 8],
XO [auth p],
YF [auth 5],
YH [auth 8],
ZD [auth 3]
(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
Query on IHT
Download Ideal Coordinates CCD File 
IO [auth g]
OP [auth p]
SE [auth 3]
TG [auth 6]
UI [auth 9]
IO [auth g],
OP [auth p],
SE [auth 3],
TG [auth 6],
UI [auth 9],
XD [auth 2],
ZF [auth 5],
ZH [auth 8]
(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
Query on 8CT
Download Ideal Coordinates CCD File 
CL [auth H]
CN [auth c]
DN [auth c]
ED [auth 1]
EN [auth c]
CL [auth H],
CN [auth c],
DN [auth c],
ED [auth 1],
EN [auth c],
FF [auth 4],
GH [auth 7],
IM [auth b],
JK [auth C],
JM [auth b],
KK [auth C],
KM [auth b],
LK [auth C],
MB [auth a],
MO [auth h],
NC [auth 0],
ON [auth d],
PJ [auth B],
PL [auth Y],
QJ [auth B],
RJ [auth B],
TP [auth y],
VK [auth D],
YB [auth A]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
OEX
Query on OEX
Download Ideal Coordinates CCD File 
EB [auth a],
QB [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
GB [auth a],
SB [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
FB [auth a],
RB [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
HB [auth a],
TB [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2025-01-01
    Changes: Data collection, Database references, Structure summary