8JW0 | pdb_00008jw0

PSI-AcpPCI supercomplex from Amphidinium carterae

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history. 

Literature

Structures and organizations of PSI-AcpPCI supercomplexes from red tidal and coral symbiotic photosynthetic dinoflagellates.

Li, X., Li, Z., Wang, F., Zhao, S., Xu, C., Mao, Z., Duan, J., Feng, Y., Yang, Y., Shen, L., Wang, G., Yang, Y., Yu, L.J., Sang, M., Han, G., Wang, X., Kuang, T., Shen, J.R., Wang, W.

(2024) Proc Natl Acad Sci U S A 121: e2315476121-e2315476121

  • DOI: https://doi.org/10.1073/pnas.2315476121
  • Primary Citation Related Structures: 
    8JW0, 8JZE, 8JZF

  • PubMed Abstract: 

    Marine photosynthetic dinoflagellates are a group of successful phytoplankton that can form red tides in the ocean and also symbiosis with corals. These features are closely related to the photosynthetic properties of dinoflagellates. We report here three structures of photosystem I (PSI)-chlorophylls (Chls) a / c -peridinin protein complex (PSI-AcpPCI) from two species of dinoflagellates by single-particle cryoelectron microscopy. The crucial PsaA/B subunits of a red tidal dinoflagellate Amphidinium carterae are remarkably smaller and hence losing over 20 pigment-binding sites, whereas its PsaD/F/I/J/L/M/R subunits are larger and coordinate some additional pigment sites compared to other eukaryotic photosynthetic organisms, which may compensate for the smaller PsaA/B subunits. Similar modifications are observed in a coral symbiotic dinoflagellate Symbiodinium species, where two additional core proteins and fewer AcpPCIs are identified in the PSI-AcpPCI supercomplex. The antenna proteins AcpPCIs in dinoflagellates developed some loops and pigment sites as a result to accommodate the changed PSI core, therefore the structures of PSI-AcpPCI supercomplex of dinoflagellates reveal an unusual protein assembly pattern. A huge pigment network comprising Chls a and c and various carotenoids is revealed from the structural analysis, which provides the basis for our deeper understanding of the energy transfer and dissipation within the PSI-AcpPCI supercomplex, as well as the evolution of photosynthetic organisms.

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

Macromolecule Content 

  • Total Structure Weight: 931.23 kDa 
  • Atom Count: 63,119 
  • Modeled Residue Count: 5,585 
  • Deposited Residue Count: 5,586 
  • Unique protein chains: 28

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaAA [auth a]645Amphidinium carteraeMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58309 (Amphidinium carterae)
Explore P58309 
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Entity Groups
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UniProt GroupP58309
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaBB [auth b]617Amphidinium carteraeMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P58383 (Amphidinium carterae)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaCC [auth c]86Amphidinium carteraeMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaDD [auth d]257Amphidinium carteraeMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaEE [auth e]74Amphidinium carteraeMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaFF [auth f]185Amphidinium carteraeMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaRG [auth h]132Amphidinium carteraeMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaIH [auth i]126Amphidinium carteraeMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaJI [auth j]70Amphidinium carteraeMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaLJ [auth l]253Amphidinium carteraeMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I PsaMK [auth m]89Amphidinium carteraeMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-10, acpPCI-10L [auth A]180Amphidinium carteraeMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-8, acpPCI-8M [auth G]215Amphidinium carteraeMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-7, acpPCI-7N [auth I]194Amphidinium carteraeMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-6, acpPCI-6O [auth K]172Amphidinium carteraeMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-2, acpPCI-2P [auth F]176Amphidinium carteraeMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-3, acpPCI-3Q [auth J]165Amphidinium carteraeMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-4, acpPCI-4R [auth M]168Amphidinium carteraeMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-5, acpPCI-5S [auth L]185Amphidinium carteraeMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-9, acpPCI-9T [auth D]160Amphidinium carteraeMutation(s): 0 
UniProt
Find proteins for Q38689 (Amphidinium carterae)
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Entity Groups
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UniProt GroupQ38689
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-11, acpPCI-11U [auth B]172Amphidinium carteraeMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-12, acpPCI-12V [auth H]160Amphidinium carteraeMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-13, acpPCI-13W [auth N]160Amphidinium carteraeMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-15, acpPCI-15X [auth O]161Amphidinium carteraeMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-16, acpPCI-16AA [auth C],
Y [auth T]		160Amphidinium carteraeMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-17, acpPCI-17Z [auth Q]162Amphidinium carteraeMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-14, acpPCI-14BA [auth P]160Amphidinium carteraeMutation(s): 0 
UniProt
Find proteins for Q38688 (Amphidinium carterae)
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UniProt GroupQ38688
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Reference Sequence
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-chlorophyll c-peridinin-protein-complex I-1, acpPCI-1CA [auth E]142Amphidinium carteraeMutation(s): 0 

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD


Download:Ideal Coordinates CCD File
GE [auth m]
ID [auth h]
RD [auth j]
TD [auth j]
UD [auth j]
GE [auth m],
ID [auth h],
RD [auth j],
TD [auth j],
UD [auth j],
UF [auth G],
VC [auth b],
YK [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
(Subject of Investigation/LOI)

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth a]
AC [auth b]
AO [auth Q]
AP [auth P]
BB [auth a]
AB [auth a],
AC [auth b],
AO [auth Q],
AP [auth P],
BB [auth a],
BC [auth b],
BF [auth G],
BG [auth I],
BH [auth K],
BI [auth J],
BK [auth D],
BM [auth N],
CB [auth a],
CC [auth b],
CD [auth f],
CE [auth l],
CF [auth G],
CG [auth I],
CH [auth K],
CI [auth J],
CK [auth D],
CM [auth N],
CN [auth T],
CP [auth P],
DA [auth a],
DB [auth a],
DC [auth b],
DD [auth f],
DE [auth l],
DG [auth I],
DH [auth K],
DI [auth J],
DK [auth D],
DN [auth T],
EA [auth a],
EB [auth a],
EC [auth b],
EE [auth l],
EF [auth G],
EG [auth I],
EI [auth J],
EK [auth D],
EM [auth N],
EP [auth P],
FA [auth a],
FB [auth a],
FC [auth b],
FD [auth f],
FG [auth I],
FI [auth J],
FN [auth T],
FP [auth P],
GA [auth a],
GB [auth a],
GC [auth b],
GD [auth h],
GG [auth I],
GI [auth J],
GJ [auth L],
GK [auth D],
GL [auth H],
HA [auth a],
HB [auth a],
HC [auth b],
HG [auth I],
HI [auth J],
HJ [auth L],
HL [auth H],
HN [auth T],
HP [auth P],
IA [auth a],
IC [auth b],
IG [auth I],
IJ [auth L],
IN [auth T],
IO [auth C],
JA [auth a],
JC [auth b],
JI [auth J],
JJ [auth L],
JL [auth H],
JO [auth C],
KA [auth a],
KC [auth b],
KG [auth I],
KJ [auth L],
KN [auth T],
LA [auth a],
LC [auth b],
LD [auth i],
LF [auth G],
LG [auth I],
LJ [auth L],
LL [auth H],
LO [auth C],
MA [auth a],
MC [auth b],
MD [auth i],
MF [auth G],
MJ [auth L],
MK [auth B],
ML [auth H],
MM [auth O],
MP [auth E],
NA [auth a],
NB [auth a],
NC [auth b],
ND [auth i],
NE [auth A],
NF [auth G],
NH [auth F],
NK [auth B],
NM [auth O],
NO [auth C],
NP [auth E],
OA [auth a],
OC [auth b],
OE [auth A],
OF [auth G],
OH [auth F],
OJ [auth L],
OK [auth B],
OL [auth H],
OO [auth C],
PA [auth a],
PB [auth b],
PE [auth A],
PJ [auth L],
PK [auth B],
PM [auth O],
PP [auth E],
QA [auth a],
QB [auth b],
QE [auth A],
QF [auth G],
QH [auth F],
QI [auth M],
QJ [auth L],
QK [auth B],
QO [auth C],
QP [auth E],
RA [auth a],
RB [auth b],
RE [auth A],
RF [auth G],
RH [auth F],
RI [auth M],
RK [auth B],
RM [auth O],
RP [auth E],
SA [auth a],
SB [auth b],
SD [auth j],
SE [auth A],
SG [auth K],
SH [auth F],
SI [auth M],
SK [auth B],
SM [auth O],
SN [auth Q],
SP [auth E],
TA [auth a],
TB [auth b],
TC [auth b],
TE [auth A],
TF [auth G],
TG [auth K],
TH [auth F],
TI [auth M],
TN [auth Q],
UA [auth a],
UB [auth b],
UG [auth K],
UI [auth M],
UK [auth B],
UM [auth O],
UP [auth E],
VA [auth a],
VB [auth b],
VD [auth l],
VE [auth A],
VF [auth I],
VG [auth K],
VH [auth F],
VI [auth M],
VK [auth B],
VN [auth Q],
VP [auth E],
WA [auth a],
WB [auth b],
WD [auth l],
WE [auth A],
WG [auth K],
WH [auth F],
WK [auth B],
WL [auth N],
WP [auth E],
XA [auth a],
XB [auth b],
XD [auth l],
XE [auth A],
XG [auth K],
XI [auth M],
XL [auth N],
XN [auth Q],
YA [auth a],
YB [auth b],
YC [auth b],
YD [auth l],
YE [auth A],
YG [auth K],
YI [auth M],
YJ [auth D],
YN [auth Q],
ZA [auth a],
ZB [auth b],
ZD [auth l],
ZE [auth A],
ZG [auth K],
ZI [auth M],
ZJ [auth D],
ZL [auth N],
ZO [auth P]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD


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KI [auth J],
XK [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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AF [auth A]
EH [auth K]
FH [auth K]
KD [auth h]
MG [auth K]
AF [auth A],
EH [auth K],
FH [auth K],
KD [auth h],
MG [auth K],
QD [auth j],
RO [auth P],
SC [auth b],
UC [auth b],
WC [auth b],
XP [auth E]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG


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JB [auth a]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
UIX
(Subject of Investigation/LOI)

Query on UIX


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AI [auth J]
AN [auth T]
BJ [auth L]
GO [auth C]
KE [auth A]
AI [auth J],
AN [auth T],
BJ [auth L],
GO [auth C],
KE [auth A],
KK [auth B],
KM [auth O],
LH [auth F],
LP [auth E],
QN [auth Q],
UL [auth N],
XO [auth P]
[(1~{S},5~{R})-3,3,5-trimethyl-5-oxidanyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]cyclohexyl] ethanoate
C42 H58 O5
PVNVIBOWBAPFOE-GYMZYDTCSA-N
PID
(Subject of Investigation/LOI)

Query on PID


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AL [auth H]
BL [auth H]
BN [auth T]
BO [auth C]
CO [auth C]
AL [auth H],
BL [auth H],
BN [auth T],
BO [auth C],
CO [auth C],
DF [auth G],
DL [auth H],
EL [auth H],
EO [auth C],
FL [auth H],
FM [auth O],
FO [auth C],
GM [auth O],
HO [auth C],
IH [auth F],
IM [auth O],
IP [auth E],
JD [auth h],
JF [auth G],
JM [auth O],
KF [auth G],
KH [auth F],
LM [auth O],
LN [auth T],
MH [auth F],
MN [auth Q],
ON [auth Q],
PD [auth j],
PL [auth N],
PN [auth Q],
QL [auth N],
RN [auth Q],
SJ [auth D],
SL [auth N],
SO [auth P],
TJ [auth D],
TL [auth N],
TO [auth P],
VJ [auth D],
VL [auth N],
VM [auth T],
VO [auth P],
WJ [auth D],
WM [auth T],
WO [auth P],
XJ [auth D],
YM [auth T],
YO [auth P],
ZM [auth T]
PERIDININ
C39 H50 O7
UYRDHEJRPVSJFM-FROCQLDGSA-N
KC1
(Subject of Investigation/LOI)

Query on KC1


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AH [auth K]
AK [auth D]
AM [auth N]
BP [auth P]
DM [auth N]
AH [auth K],
AK [auth D],
AM [auth N],
BP [auth P],
DM [auth N],
DP [auth P],
EN [auth T],
FJ [auth L],
FK [auth D],
GN [auth T],
GP [auth P],
II [auth J],
IL [auth H],
JG [auth I],
JN [auth T],
KL [auth H],
KO [auth C],
ME [auth A],
MO [auth C],
NJ [auth L],
NL [auth H],
OM [auth O],
OP [auth E],
PF [auth G],
PH [auth F],
PI [auth M],
PO [auth C],
QM [auth O],
SF [auth G],
TK [auth B],
TM [auth O],
TP [auth E],
UE [auth A],
UH [auth F],
UN [auth Q],
WI [auth M],
WN [auth Q],
YL [auth N],
ZN [auth Q]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6
(Subject of Investigation/LOI)

Query on DD6


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AG [auth I]
AJ [auth L]
CJ [auth L]
CL [auth H]
DJ [auth L]
AG [auth I],
AJ [auth L],
CJ [auth L],
CL [auth H],
DJ [auth L],
DO [auth C],
EJ [auth L],
FE [auth m],
FF [auth G],
GF [auth G],
GH [auth K],
HD [auth h],
HF [auth G],
HH [auth F],
HK [auth B],
HM [auth O],
IE [auth A],
IF [auth G],
IK [auth B],
JE [auth A],
JH [auth F],
JK [auth B],
JP [auth E],
KP [auth E],
LE [auth A],
LI [auth M],
LK [auth B],
MI [auth M],
NG [auth K],
NI [auth M],
NN [auth Q],
OG [auth K],
OI [auth M],
PG [auth K],
QG [auth K],
RG [auth K],
RJ [auth D],
RL [auth N],
UJ [auth D],
UO [auth P],
WF [auth I],
XF [auth I],
XH [auth J],
XM [auth T],
YF [auth I],
YH [auth J],
ZF [auth I],
ZH [auth J],
ZK [auth B]
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR


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AE [auth l]
BD [auth f]
BE [auth l]
ED [auth f]
HE [auth m]
AE [auth l],
BD [auth f],
BE [auth l],
ED [auth f],
HE [auth m],
KB [auth a],
LB [auth a],
OB [auth a],
OD [auth i],
QC [auth b],
RC [auth b],
XC [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN

Query on PQN


Download:Ideal Coordinates CCD File
IB [auth a],
PC [auth b]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4


Download:Ideal Coordinates CCD File
AD [auth c],
MB [auth a],
ZC [auth c]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2021YFA1300403
Chinese Academy of SciencesChina2019YFA0906300
Chinese Academy of SciencesChinaXDA26050402
Chinese Academy of SciencesChinaXDB17000000
Chinese Academy of SciencesChina2020081
Chinese Academy of SciencesChinaJCTD-2020-06
Chinese Academy of SciencesChina31970260
Chinese Academy of SciencesChina32222007

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-07-23
    Changes: Data collection