6J3Y

Structure of C2S2-type PSII-FCPII supercomplex from diatom


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.

Nagao, R.Kato, K.Suzuki, T.Ifuku, K.Uchiyama, I.Kashino, Y.Dohmae, N.Akimoto, S.Shen, J.R.Miyazaki, N.Akita, F.

(2019) Nat Plants 5: 890-901

  • DOI: https://doi.org/10.1038/s41477-019-0477-x
  • Primary Citation of Related Structures:  
    6J3Y, 6J3Z, 6J40

  • PubMed Abstract: 

    Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D1A,
Y [auth a]
344Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP47B,
Z [auth b]
509Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP43AA [auth c],
C
471Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D2BA [auth d],
D
351Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaCA [auth e],
E
84Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaDA [auth f],
F
43Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEA [auth h],
G [auth H]
67Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B7XBY7 (Chaetoceros neogracilis)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IFA [auth i],
H [auth I]
38Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JGA [auth j],
I [auth J]
39Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KHA [auth k],
J [auth K]
44Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LIA [auth l],
K [auth L]
38Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MJA [auth m],
L [auth M]
131Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIKA [auth o],
M [auth O]
248Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B6ZHE8 (Chaetoceros neogracilis)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TLA [auth t],
N [auth T]
31Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIMA [auth u],
O [auth U]
93Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B6ZHF0 (Chaetoceros neogracilis)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550NA [auth v],
P [auth V]
137Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12OA [auth y],
Q [auth Y]
34Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinPA [auth x],
R [auth X]
38Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
S [auth Z]
61Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIRA [auth q],
T [auth Q]
155Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein WSA [auth w],
U [auth W]
72Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 0TA [auth 5],
V [auth 0]
31Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 1UA [auth 6],
W [auth 1]
30Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 2VA [auth 7],
X [auth 2]
10Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1207Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AD [auth C]
AG [auth c]
BD [auth C]
NG [auth h]
OG [auth j]
AD [auth C],
AG [auth c],
BD [auth C],
NG [auth h],
OG [auth j],
PD [auth H],
QD [auth J],
ZF [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AC [auth B]
AF [auth b]
AH [auth w]
AI [auth 12]
AL [auth 33]
AC [auth B],
AF [auth b],
AH [auth w],
AI [auth 12],
AL [auth 33],
BC [auth B],
BE [auth W],
BH [auth w],
BI [auth 12],
BJ [auth 14],
BL [auth 33],
CE [auth W],
CG [auth d],
CH [auth 11],
CI [auth 12],
CJ [auth 14],
CL [auth 33],
DG [auth d],
DH [auth 11],
DI [auth 12],
DJ [auth 14],
DL [auth 33],
ED [auth D],
EE [auth a],
EH [auth 11],
EI [auth 12],
EJ [auth 14],
EK [auth 31],
EL [auth 33],
FB [auth A],
FD [auth D],
FH [auth 11],
FJ [auth 14],
FL [auth 33],
GE [auth a],
GG [auth d],
GH [auth 11],
GJ [auth 14],
GL [auth 33],
HB [auth A],
HF [auth b],
HG [auth d],
HH [auth 11],
HJ [auth 14],
HL [auth 33],
IC [auth B],
ID [auth D],
IH [auth 11],
IJ [auth 14],
IK [auth 32],
IL [auth 33],
JD [auth D],
JH [auth 11],
JI [auth 13],
JJ [auth 14],
KF [auth c],
KH [auth 11],
KJ [auth 14],
KK [auth 32],
LC [auth C],
LF [auth c],
LI [auth 13],
LK [auth 32],
MC [auth C],
ME [auth b],
MF [auth c],
MI [auth 13],
MK [auth 32],
NB [auth B],
NC [auth C],
NE [auth b],
NF [auth c],
NI [auth 13],
NK [auth 32],
OB [auth B],
OC [auth C],
OE [auth b],
OF [auth c],
OI [auth 13],
OK [auth 32],
PB [auth B],
PC [auth C],
PE [auth b],
PF [auth c],
PI [auth 13],
PK [auth 32],
PL [auth 34],
QB [auth B],
QC [auth C],
QE [auth b],
QF [auth c],
QH [auth 11],
QI [auth 13],
QJ [auth 31],
QK [auth 32],
RB [auth B],
RC [auth C],
RE [auth b],
RF [auth c],
RI [auth 13],
RJ [auth 31],
RK [auth 32],
RL [auth 34],
SB [auth B],
SC [auth C],
SE [auth b],
SF [auth c],
SG [auth m],
SI [auth 13],
SJ [auth 31],
SK [auth 32],
SL [auth 34],
TB [auth B],
TC [auth C],
TE [auth b],
TF [auth c],
TI [auth 13],
TJ [auth 31],
TL [auth 34],
UB [auth B],
UC [auth C],
UE [auth b],
UF [auth c],
UH [auth 12],
UJ [auth 31],
UL [auth 34],
VB [auth B],
VC [auth C],
VD [auth M],
VE [auth b],
VF [auth c],
VJ [auth 31],
VL [auth 34],
WB [auth B],
WC [auth C],
WE [auth b],
WF [auth c],
WH [auth 12],
WJ [auth 31],
WL [auth 34],
XB [auth B],
XC [auth C],
XE [auth b],
XG [auth z],
XH [auth 12],
XJ [auth 31],
XL [auth 34],
YB [auth B],
YE [auth b],
YH [auth 12],
YJ [auth 31],
YK [auth 33],
YL [auth 34],
ZB [auth B],
ZD [auth Z],
ZE [auth b],
ZH [auth 12],
ZL [auth 34]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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EG [auth d],
FE [auth a],
GB [auth A],
GD [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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FF [auth b]
GC [auth B]
IE [auth a]
JB [auth A]
PG [auth l]
FF [auth b],
GC [auth B],
IE [auth a],
JB [auth A],
PG [auth l],
TD [auth L]
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 W]
CD [auth C]
DF [auth b]
EC [auth B]
EF [auth b]
AE [auth W],
CD [auth C],
DF [auth b],
EC [auth B],
EF [auth b],
FC [auth B],
GK [auth 32],
JG [auth d],
LD [auth D],
SH [auth 12],
TG [auth m],
WD [auth M],
YG [auth q],
ZG [auth w]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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FG [auth d],
HD [auth D],
IG [auth d],
KD [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
Query on LHG

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GF [auth b]
HC [auth B]
KE [auth a]
LB [auth A]
QG [auth l]
GF [auth b],
HC [auth B],
KE [auth a],
LB [auth A],
QG [auth l],
RD [auth L],
RG [auth l],
SD [auth L]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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AJ [auth 14]
AK [auth 31]
AM [auth 34]
BK [auth 31]
BM [auth 34]
AJ [auth 14],
AK [auth 31],
AM [auth 34],
BK [auth 31],
BM [auth 34],
CK [auth 31],
CM [auth 34],
DK [auth 31],
DM [auth 34],
FI [auth 12],
FK [auth 31],
GI [auth 12],
HI [auth 12],
II [auth 12],
JK [auth 32],
JL [auth 33],
KI [auth 13],
KL [auth 33],
LH [auth 11],
LJ [auth 14],
LL [auth 33],
MH [auth 11],
MJ [auth 14],
ML [auth 33],
NH [auth 11],
NJ [auth 14],
NL [auth 33],
OH [auth 11],
OJ [auth 14],
OL [auth 34],
PH [auth 11],
PJ [auth 14],
QL [auth 34],
RH [auth 11],
TK [auth 32],
UI [auth 13],
UK [auth 32],
VH [auth 12],
VI [auth 13],
VK [auth 32],
WI [auth 13],
WK [auth 32],
XI [auth 13],
XK [auth 32],
YI [auth 13],
ZI [auth 13],
ZJ [auth 31],
ZK [auth 33]
(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
Query on HEM

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LG [auth f],
MD [auth E],
VG [auth v],
XD [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR

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BF [auth b]
BG [auth c]
CC [auth B]
CF [auth b]
DC [auth B]
BF [auth b],
BG [auth c],
CC [auth B],
CF [auth b],
DC [auth B],
DD [auth C],
HE [auth a],
IB [auth A],
IF [auth b],
JC [auth B],
KG [auth f],
LE [auth a],
MB [auth A],
MG [auth h],
ND [auth F],
OD [auth H],
UD [auth M],
UG [auth m],
WG [auth z],
XF [auth c],
YC [auth C],
YD [auth Z],
YF [auth c],
ZC [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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HK [auth 32],
TH [auth 12]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX
Query on OEX

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JF [auth c],
KC [auth C]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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JE [auth a],
KB [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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DE [auth a],
EB [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.13_2998
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other