8XKL

Structure of ACPII-CCPII from cryptophyte algae


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


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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
ACPII-4A [auth 0]226Chroomonas placoideaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-1B [auth 7]235Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-2C [auth 8]217Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-3D [auth 9]222Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein GE [auth G]64Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-6F [auth P]220Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-5G [auth p]218Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CCPII-SH [auth s]285Chroomonas placoideaMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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AB [auth 8]
AD [auth p]
BA [auth 7]
BB [auth 8]
BD [auth p]
AB [auth 8],
AD [auth p],
BA [auth 7],
BB [auth 8],
BD [auth p],
CA [auth 7],
CB [auth 8],
CC [auth G],
CD [auth p],
DA [auth 7],
DD [auth p],
EA [auth 7],
EB [auth 8],
ED [auth p],
FA [auth 7],
FB [auth 8],
FC [auth P],
GA [auth 7],
GC [auth P],
GD [auth p],
HA [auth 7],
HC [auth P],
HD [auth p],
I [auth 0],
IA [auth 7],
IC [auth P],
J [auth 0],
JA [auth 7],
K [auth 0],
KC [auth P],
L [auth 0],
LA [auth 7],
LC [auth P],
M [auth 0],
MA [auth 7],
MC [auth P],
N [auth 0],
NA [auth 7],
NB [auth 9],
O [auth 0],
OB [auth 9],
OC [auth P],
OD [auth s],
P [auth 0],
PB [auth 9],
PC [auth P],
PD [auth s],
Q [auth 0],
QB [auth 9],
RB [auth 9],
S [auth 0],
SB [auth 9],
T [auth 0],
TB [auth 9],
U [auth 0],
UA [auth 8],
UB [auth 9],
VA [auth 8],
VB [auth 9],
WA [auth 8],
WB [auth 9],
WC [auth p],
XA [auth 8],
XB [auth 9],
XC [auth p],
YA [auth 8],
YC [auth p],
ZA [auth 8],
ZC [auth p]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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MD [auth p]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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DC [auth G],
EC [auth G],
KB [auth 8],
Z [auth 0]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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LB [auth 8],
ND [auth s]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2 (Subject of Investigation/LOI)
Query on KC2

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DB [auth 8]
FD [auth p]
JC [auth P]
KA [auth 7]
NC [auth P]
DB [auth 8],
FD [auth p],
JC [auth P],
KA [auth 7],
NC [auth P],
R [auth 0]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II3
Query on II3

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PA [auth 7],
RC [auth P]
(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
Query on II0

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AA [auth 0]
AC [auth 9]
GB [auth 8]
HB [auth 8]
IB [auth 8]
AA [auth 0],
AC [auth 9],
GB [auth 8],
HB [auth 8],
IB [auth 8],
ID [auth p],
JD [auth p],
KD [auth p],
MB [auth 8],
OA [auth 7],
QA [auth 7],
QC [auth P],
RA [auth 7],
SC [auth P],
TA [auth 7],
UC [auth p],
VC [auth p],
W [auth 0],
X [auth 0],
YB [auth 9],
ZB [auth 9]
(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

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JB [auth 8],
LD [auth p],
SA [auth 7],
V [auth 0],
Y [auth 0]
(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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BC [auth 9],
TC [auth P]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
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
Chinese Academy of SciencesChinaYSBR-004

Revision History  (Full details and data files)

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