9KQB | pdb_00009kqb

PSII-FCPII supercomplex from haptophyte Chrysotila roscoffensis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 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 a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization.

La Rocca, R.Kato, K.Tsai, P.C.Nakajima, Y.Akita, F.Shen, J.R.

(2025) Nat Commun 16: 4175-4175

  • DOI: https://doi.org/10.1038/s41467-025-59512-9
  • Primary Citation of Related Structures:  
    9KQB

  • PubMed Abstract: 

    Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO 3 production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein II (FCPII-1)A [auth 1],
C [auth 7],
NA [auth 5],
OA [auth g]
166Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein II (FCPII-5)B [auth 6],
J
167Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1D [auth A],
R [auth a]
360Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinE [auth B],
S [auth b]
509Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaF [auth E],
T [auth e]
82Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaG [auth F],
U [auth f]
42Chrysotila roscoffensisMutation(s): 0 
UniProt
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UniProt GroupQ4G381
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein H (psbH)H,
V [auth h]
65Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein I (psbI)I,
W [auth i]
38Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein K (psbK)K,
X [auth k]
40Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LL,
Y [auth l]
38Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein M (psbM)M,
Z [auth m]
130Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb36AA [auth n],
N
36Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBA [auth t],
O [auth T]
32Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein W (psbW)CA [auth w],
P [auth W]
53Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein X (psbX)DA [auth x],
Q [auth X]
36Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein II (FCPII-2)EA [auth 2],
FA [auth 8]
225Chrysotila roscoffensisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinGA [auth D],
HA [auth d]
351Chrysotila roscoffensisMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinIA [auth C],
JA [auth c]
445Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Light harvesting proteinKA [auth 9],
LA [auth 3]
216Chrysotila roscoffensisMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c binding protein II (FCPII-4)MA [auth 4],
PA [auth G]
167Chrysotila roscoffensisMutation(s): 0 
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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CJ [auth C]
DG [auth h]
DJ [auth C]
QD [auth B]
TJ [auth c]
CJ [auth C],
DG [auth h],
DJ [auth C],
QD [auth B],
TJ [auth c],
UJ [auth c],
WD [auth H],
ZE [auth b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AC [auth 7]
AD [auth B]
AE [auth J]
AH [auth 8]
AJ [auth C]
AC [auth 7],
AD [auth B],
AE [auth J],
AH [auth 8],
AJ [auth C],
AL [auth 5],
AM [auth G],
BC [auth 7],
BD [auth B],
BE [auth J],
BF [auth b],
BH [auth 8],
BL [auth 5],
BM [auth G],
CC [auth 7],
CD [auth B],
CE [auth J],
CF [auth b],
CH [auth 8],
CK [auth 3],
CM [auth G],
DC [auth 7],
DD [auth B],
DE [auth J],
DF [auth b],
DH [auth 8],
DK [auth 3],
DM [auth G],
EC [auth 7],
ED [auth B],
EE [auth J],
EF [auth b],
EH [auth 8],
EK [auth 3],
FD [auth B],
FE [auth J],
FF [auth b],
FI [auth d],
FJ [auth c],
FK [auth 3],
GD [auth B],
GF [auth b],
GG [auth 2],
GI [auth d],
GJ [auth c],
GK [auth 3],
HB [auth 6],
HD [auth B],
HF [auth b],
HG [auth 2],
HI [auth d],
HJ [auth c],
IB [auth 6],
ID [auth B],
IF [auth b],
IG [auth 2],
IJ [auth c],
JB [auth 6],
JF [auth b],
JG [auth 2],
JJ [auth c],
JK [auth 4],
KB [auth 6],
KF [auth b],
KG [auth 2],
KJ [auth c],
KK [auth 4],
KL [auth g],
LB [auth 6],
LC [auth A],
LF [auth b],
LG [auth 2],
LJ [auth c],
LK [auth 4],
LL [auth g],
MB [auth 6],
MC [auth A],
MF [auth b],
MJ [auth c],
MK [auth 4],
ML [auth g],
NB [auth 6],
ND [auth B],
NF [auth b],
NJ [auth c],
NK [auth 4],
NL [auth g],
OB [auth 6],
OC [auth A],
OF [auth b],
OI [auth C],
OJ [auth c],
OL [auth g],
PB [auth 6],
PF [auth b],
PI [auth C],
PJ [auth c],
PL [auth g],
QA [auth 1],
QI [auth C],
QJ [auth c],
QL [auth g],
RA [auth 1],
RI [auth C],
RJ [auth c],
RL [auth g],
SA [auth 1],
SE [auth a],
SI [auth C],
TA [auth 1],
TE [auth a],
TH [auth D],
TI [auth C],
UA [auth 1],
UC [auth B],
UI [auth C],
UK [auth 5],
VA [auth 1],
VB [auth 7],
VC [auth B],
VE [auth a],
VF [auth b],
VH [auth D],
VI [auth C],
VJ [auth 9],
VK [auth 5],
WA [auth 1],
WB [auth 7],
WC [auth B],
WH [auth D],
WI [auth C],
WJ [auth 9],
WK [auth 5],
XA [auth 1],
XB [auth 7],
XC [auth B],
XD [auth J],
XI [auth C],
XJ [auth 9],
XK [auth 5],
YA [auth 1],
YB [auth 7],
YC [auth B],
YD [auth J],
YI [auth C],
YJ [auth 9],
YK [auth 5],
ZA [auth 1],
ZB [auth 7],
ZC [auth B],
ZD [auth J],
ZG [auth 8],
ZI [auth C],
ZJ [auth 9],
ZK [auth 5],
ZL [auth G]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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EI [auth d],
NC [auth A],
QH [auth D],
UE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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AF [auth b],
NI [auth C],
QE [auth X],
RD [auth B],
SD [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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AG [auth f]
AI [auth D]
LD [auth B]
LE [auth L]
MD [auth B]
AG [auth f],
AI [auth D],
LD [auth B],
LE [auth L],
MD [auth B],
NE [auth M],
OD [auth B],
OE [auth N],
OH [auth 8],
PD [auth B],
RC [auth A],
SF [auth b],
TD [auth B],
TF [auth b],
UF [auth b],
WF [auth b],
XE [auth a],
XF [auth b],
XG [auth 2],
YF [auth b],
YG [auth 8]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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JI [auth d],
YH [auth D]
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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DI [auth d]
EG [auth l]
KI [auth d]
QC [auth A]
RE [auth a]
DI [auth d],
EG [auth l],
KI [auth d],
QC [auth A],
RE [auth a],
SH [auth D],
TC [auth B],
ZH [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86 (Subject of Investigation/LOI)
Query on A86

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BB [auth 1]
CB [auth 1]
DB [auth 1]
DL [auth 5]
EL [auth 5]
BB [auth 1],
CB [auth 1],
DB [auth 1],
DL [auth 5],
EL [auth 5],
EM [auth G],
FH [auth 8],
GC [auth 7],
GE [auth J],
GH [auth 8],
HC [auth 7],
HE [auth J],
HH [auth 8],
IC [auth 7],
IH [auth 8],
JH [auth 8],
MG [auth 2],
NG [auth 2],
OG [auth 2],
OK [auth 4],
PE [auth W],
PG [auth 2],
QB [auth 6],
QG [auth 2],
RB [auth 6],
RG [auth 2],
TL [auth g],
UL [auth g]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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UD [auth E],
ZF [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC1 (Subject of Investigation/LOI)
Query on KC1

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AK [auth 9]
BK [auth 9]
EB [auth 1]
FB [auth 1]
FL [auth 5]
AK [auth 9],
BK [auth 9],
EB [auth 1],
FB [auth 1],
FL [auth 5],
FM [auth G],
GL [auth 5],
GM [auth G],
HK [auth 3],
HL [auth 5],
HM [auth G],
IE [auth J],
IK [auth 3],
IM [auth G],
JC [auth 7],
JE [auth J],
KC [auth 7],
KE [auth J],
KH [auth 8],
LH [auth 8],
MH [auth 8],
NH [auth 8],
PK [auth 4],
QK [auth 4],
RK [auth 4],
SB [auth 6],
SG [auth 2],
SK [auth 4],
TB [auth 6],
TG [auth 2],
UB [auth 6],
UG [auth 2],
VG [auth 2],
VL [auth g],
WL [auth g],
XL [auth g]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

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AB [auth 1],
CL [auth 5],
FC [auth 7],
SL [auth g]
(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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BG [auth h]
BJ [auth C]
CG [auth h]
EJ [auth c]
FG [auth m]
BG [auth h],
BJ [auth C],
CG [auth h],
EJ [auth c],
FG [auth m],
GB [auth 1],
II [auth d],
JD [auth B],
KD [auth B],
ME [auth M],
MI [auth C],
PC [auth A],
QF [auth b],
RF [auth b],
SJ [auth c],
VD [auth H],
WE [auth a],
XH [auth D]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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BI [auth D]
IL [auth 5]
JL [auth g]
PH [auth 8]
SC [auth A]
BI [auth D],
IL [auth 5],
JL [auth g],
PH [auth 8],
SC [auth A],
TK [auth 5],
WG [auth 2],
YE [auth a],
YL [auth g]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

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CI [auth d],
RH [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2 (Subject of Investigation/LOI)
Query on FE2

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LI [auth d],
UH [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references