8JJR

Cryo-EM structure of Symbiodinium photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 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

Architecture of symbiotic dinoflagellate photosystem I-light-harvesting supercomplex in Symbiodinium.

Zhao, L.S.Wang, N.Li, K.Li, C.Y.Guo, J.P.He, F.Y.Liu, G.M.Chen, X.L.Gao, J.Liu, L.N.Zhang, Y.Z.

(2024) Nat Commun 15: 2392-2392

  • DOI: https://doi.org/10.1038/s41467-024-46791-x
  • Primary Citation of Related Structures:  
    8JJR

  • PubMed Abstract: 

    Symbiodinium are the photosynthetic endosymbionts for corals and play a vital role in supplying their coral hosts with photosynthetic products, forming the nutritional foundation for high-yield coral reef ecosystems. Here, we determine the cryo-electron microscopy structure of Symbiodinium photosystem I (PSI) supercomplex with a PSI core composed of 13 subunits including 2 previously unidentified subunits, PsaT and PsaU, as well as 13 peridinin-Chl a/c-binding light-harvesting antenna proteins (AcpPCIs). The PSI-AcpPCI supercomplex exhibits distinctive structural features compared to their red lineage counterparts, including extended termini of PsaD/E/I/J/L/M/R and AcpPCI-1/3/5/7/8/11 subunits, conformational changes in the surface loops of PsaA and PsaB subunits, facilitating the association between the PSI core and peripheral antennae. Structural analysis and computational calculation of excitation energy transfer rates unravel specific pigment networks in Symbiodinium PSI-AcpPCI for efficient excitation energy transfer. Overall, this study provides a structural basis for deciphering the mechanisms governing light harvesting and energy transfer in Symbiodinium PSI-AcpPCI supercomplexes adapted to their symbiotic ecosystem, as well as insights into the evolutionary diversity of PSI-LHCI among various photosynthetic organisms.


  • Organizational Affiliation

    MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-7256Symbiodinium sp.Mutation(s): 0 
UniProt
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UniProt GroupA0AA36I308
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-1269Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA36MZ23 (Effrenium voratum)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PCP-11193Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-6177Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-5253Symbiodinium sp.Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-8286Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-4228Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-10271Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-3246Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-9203Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-13226Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-12L [auth T]206Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PCPI-2M [auth U]137Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaAN [auth a]687Symbiodinium sp.Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaBO [auth b]669Symbiodinium sp.Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PsaCP [auth c]161Symbiodinium sp.Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDQ [auth d]295Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsaER [auth e]121Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PsaFS [auth f]279Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
PsaIT [auth i]179Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsaJU [auth j]141Symbiodinium sp.Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsaLV [auth l]361Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMW [auth m]142Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRX [auth r]152Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
PsaTY [auth x]121Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
PsaUZ [auth y]223Symbiodinium sp.Mutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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BM [auth l],
EL [auth f],
HL [auth j],
IH [auth K]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth A]
AB [auth B]
AC [auth D]
AD [auth E]
AF [auth H]
AA [auth A],
AB [auth B],
AC [auth D],
AD [auth E],
AF [auth H],
AH [auth K],
AI [auth U],
AJ [auth a],
AK [auth b],
BA [auth A],
BB [auth B],
BC [auth D],
BD [auth E],
BE [auth F],
BF [auth H],
BI [auth U],
BJ [auth a],
BK [auth b],
BL [auth f],
CA [auth A],
CC [auth D],
CD [auth E],
CF [auth H],
CH [auth K],
CJ [auth a],
CK [auth b],
CL [auth f],
DA [auth A],
DC [auth D],
DE [auth F],
DF [auth H],
DJ [auth a],
DK [auth b],
EA [auth A],
EC [auth D],
ED [auth E],
EF [auth H],
EG [auth I],
EI [auth a],
EJ [auth a],
EK [auth b],
FA [auth A],
FC [auth D],
FD [auth E],
FE [auth G],
FG [auth J],
FI [auth a],
FJ [auth a],
FK [auth b],
GA [auth A],
GC [auth D],
GE [auth G],
GF [auth H],
GI [auth a],
GJ [auth a],
GK [auth b],
GM [auth r],
HC [auth D],
HE [auth G],
HF [auth H],
HG [auth J],
HI [auth a],
HJ [auth a],
HK [auth b],
HM [auth r],
IA [auth A],
IB [auth C],
IC [auth D],
IE [auth G],
II [auth a],
IJ [auth a],
IK [auth b],
IL [auth j],
JA [auth A],
JB [auth C],
JC [auth D],
JE [auth G],
JG [auth J],
JH [auth T],
JI [auth a],
JK [auth b],
KA [auth A],
KB [auth C],
KC [auth D],
KE [auth G],
KH [auth T],
KI [auth a],
KK [auth b],
LA [auth A],
LB [auth C],
LD [auth F],
LE [auth G],
LG [auth J],
LH [auth T],
LI [auth a],
LK [auth b],
MB [auth C],
MD [auth F],
ME [auth G],
MH [auth T],
MI [auth a],
MK [auth b],
NB [auth C],
ND [auth F],
NE [auth G],
NF [auth H],
NG [auth J],
NH [auth T],
NI [auth a],
NK [auth b],
NL [auth l],
OB [auth C],
OD [auth F],
OE [auth G],
OH [auth T],
OI [auth a],
OJ [auth a],
OK [auth b],
OL [auth l],
PB [auth C],
PD [auth F],
PF [auth I],
PH [auth T],
PI [auth a],
PK [auth b],
PL [auth l],
QB [auth C],
QD [auth F],
QF [auth I],
QI [auth a],
QJ [auth a],
QK [auth b],
QL [auth l],
RD [auth F],
RF [auth I],
RH [auth T],
RI [auth a],
RJ [auth b],
RK [auth b],
RL [auth l],
SA [auth B],
SB [auth C],
SD [auth F],
SI [auth a],
SJ [auth b],
SK [auth b],
SL [auth l],
TB [auth C],
TF [auth I],
TI [auth a],
TJ [auth b],
TL [auth l],
UA [auth B],
UD [auth F],
UF [auth I],
UI [auth a],
UJ [auth b],
UL [auth l],
VA [auth B],
VC [auth E],
VF [auth I],
VG [auth K],
VI [auth a],
VJ [auth b],
VL [auth l],
WA [auth B],
WC [auth E],
WF [auth I],
WG [auth K],
WH [auth U],
WI [auth a],
WJ [auth b],
WL [auth l],
XA [auth B],
XC [auth E],
XE [auth H],
XF [auth I],
XG [auth K],
XI [auth a],
XJ [auth b],
XL [auth l],
YA [auth B],
YC [auth E],
YE [auth H],
YF [auth I],
YG [auth K],
YH [auth U],
YI [auth a],
YJ [auth b],
ZB [auth D],
ZC [auth E],
ZE [auth H],
ZF [auth I],
ZG [auth K],
ZI [auth a],
ZJ [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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KM [auth y],
OF [auth H],
RA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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AE [auth F]
CM [auth l]
HH [auth K]
QC [auth D]
RC [auth D]
AE [auth F],
CM [auth l],
HH [auth K],
QC [auth D],
RC [auth D],
XK [auth b],
YB [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CE [auth F]
FM [auth r]
LL [auth j]
MJ [auth a]
ML [auth l]
CE [auth F],
FM [auth r],
LL [auth j],
MJ [auth a],
ML [auth l],
SC [auth D],
UE [auth G]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
UIX (Subject of Investigation/LOI)
Query on UIX

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AG [auth I]
CB [auth B]
GB [auth B]
IF [auth H]
JD [auth E]
AG [auth I],
CB [auth B],
GB [auth B],
IF [auth H],
JD [auth E],
KL [auth j],
LF [auth H],
MA [auth A],
OC [auth D],
PA [auth A],
SE [auth G],
UB [auth C],
UG [auth J],
UH [auth T],
WB [auth C],
XD [auth F]
[(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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CG [auth I]
DI [auth U]
EB [auth B]
FH [auth K]
PG [auth J]
CG [auth I],
DI [auth U],
EB [auth B],
FH [auth K],
PG [auth J],
RG [auth J],
SG [auth J],
TG [auth J],
YD [auth F],
ZD [auth F]
PERIDININ
C39 H50 O7
UYRDHEJRPVSJFM-FROCQLDGSA-N
KC2 (Subject of Investigation/LOI)
Query on KC2

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BH [auth K]
DD [auth E]
EE [auth G]
FF [auth H]
GG [auth J]
BH [auth K],
DD [auth E],
EE [auth G],
FF [auth H],
GG [auth J],
HA [auth A],
IG [auth J],
KG [auth J],
MG [auth J],
OG [auth J],
QH [auth T],
RB [auth C],
SF [auth I],
TA [auth B],
TD [auth F],
UC [auth E],
WE [auth H],
XH [auth U],
ZA [auth B],
ZH [auth U]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

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BG [auth I]
CI [auth U]
DB [auth B]
DG [auth I]
DH [auth K]
BG [auth I],
CI [auth U],
DB [auth B],
DG [auth I],
DH [auth K],
EH [auth K],
EM [auth r],
FB [auth B],
GD [auth E],
GH [auth K],
GL [auth i],
HB [auth B],
HD [auth E],
ID [auth E],
IM [auth r],
JF [auth H],
JM [auth r],
KD [auth E],
KF [auth H],
LC [auth D],
MC [auth D],
MF [auth H],
NA [auth A],
NC [auth D],
OA [auth A],
PC [auth D],
PE [auth G],
QA [auth A],
QE [auth G],
QG [auth J],
RE [auth G],
SH [auth T],
TC [auth D],
TE [auth G],
TH [auth T],
UK [auth b],
VB [auth C],
VD [auth F],
VE [auth H],
WD [auth F],
XB [auth C]
(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

Download Ideal Coordinates CCD File 
AL [auth f]
AM [auth l]
DL [auth f]
DM [auth m]
FL [auth i]
AL [auth f],
AM [auth l],
DL [auth f],
DM [auth m],
FL [auth i],
JL [auth j],
KJ [auth a],
LJ [auth a],
NJ [auth a],
VK [auth b],
WK [auth b],
YL [auth l],
ZL [auth l]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

Download Ideal Coordinates CCD File 
VH [auth T]DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
JJ [auth a],
TK [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
PJ [auth a],
YK [auth c],
ZK [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Structure summary