6JLU | pdb_00006jlu

Structure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis at 3.02 angstrom resolution

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 3.0 of the entry. See complete history. 


Literature

The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex.

Pi, X., Zhao, S., Wang, W., Liu, D., Xu, C., Han, G., Kuang, T., Sui, S.F., Shen, J.R.

(2019) Science 365

  • DOI: https://doi.org/10.1126/science.aax4406
  • Primary Citation of Related Structures:  
    6JLU

  • PubMed Abstract: 

    Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II (PSII)-fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom Chaetoceros gracilis The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.

    • Organizational Affiliation: 
    • State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PsbAA,
Z [auth a]		359Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PsbBAA [auth b],
B		509Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PsbCBA [auth c],
C		450Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsbDCA [auth d],
D		341Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsbEDA [auth e],
E		79Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsbFEA [auth f],
F		32Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Psb31FA [auth g],
G		179Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HGA [auth h],
H		65Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsbIHA [auth i],
I		34Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsbJIA [auth j],
J		34Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsbKJA [auth k],
K		37Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsbLKA [auth l],
L		38Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsbMLA [auth m],
M		41Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Psb34MA [auth n],
N		30Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IINA [auth o],
O		249Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
FCP-DOA [auth p],
P		226Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIPA [auth q],
Q		211Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsbGQA [auth r],
R		73Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PsbTRA [auth t],
S [auth T]		31Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IISA [auth u],
T [auth U]		93Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550TA [auth v],
U [auth V]		137Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsbWUA [auth w],
V [auth W]		51Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinVA [auth x],
W [auth X]		35Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
PsbYWA [auth y],
X [auth Y]		33Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
PsbZXA [auth z],
Y [auth Z]		61Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
FCP-EIB [auth 10],
YA [auth 0]		178Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
FCP-A172Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
FCP-FHB [auth 9],
RB [auth 19]		166Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
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EI [auth h]
GJ [auth w]
HR [auth 11]
JE [auth H]
JF [auth W]
EI [auth h],
GJ [auth w],
HR [auth 11],
JE [auth H],
JF [auth W],
MH [auth c],
NH [auth c],
OH [auth c],
RD [auth C],
SD [auth C],
TD [auth C],
TG [auth b],
TK [auth 1],
XC [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
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AE [auth D]
AG [auth b]
AH [auth c]
AK [auth 0]
AM [auth 3]
AE [auth D],
AG [auth b],
AH [auth c],
AK [auth 0],
AM [auth 3],
AO [auth 6],
AT [auth 14],
AW [auth 19],
BD [auth C],
BE [auth D],
BG [auth b],
BH [auth c],
BJ [auth r],
BM [auth 3],
BN [auth 5],
BP [auth 8],
BR [auth 11],
BT [auth 14],
BV [auth 17],
CD [auth C],
CG [auth b],
CH [auth c],
CL [auth 2],
CP [auth 8],
CQ [auth 10],
CR [auth 11],
CW [auth 19],
DC [auth B],
DD [auth C],
DG [auth b],
DH [auth c],
DL [auth 2],
DN [auth 5],
DQ [auth 10],
DT [auth 14],
DW [auth 19],
EC [auth B],
ED [auth C],
EG [auth b],
EH [auth c],
EN [auth 5],
EP [auth 8],
EQ [auth 10],
ER [auth 11],
ET [auth 14],
EU [auth 16],
EW [auth 19],
FC [auth B],
FD [auth C],
FF [auth R],
FG [auth b],
FH [auth c],
FJ [auth w],
FL [auth 2],
FR [auth 11],
FU [auth 16],
FW [auth 19],
GC [auth B],
GD [auth C],
GG [auth b],
GH [auth c],
GN [auth 5],
GQ [auth 10],
GS [auth 13],
HC [auth B],
HD [auth C],
HG [auth b],
HH [auth c],
HL [auth 2],
HO [auth 7],
HQ [auth 10],
HS [auth 13],
HU [auth 16],
HW [auth 19],
IC [auth B],
ID [auth C],
IF [auth W],
IG [auth b],
IH [auth c],
IJ [auth z],
IK [auth 1],
IL [auth 2],
IM [auth 4],
IO [auth 7],
IQ [auth 10],
IV [auth 18],
JC [auth B],
JD [auth C],
JG [auth b],
JK [auth 1],
JQ [auth 10],
JS [auth 13],
JU [auth 16],
JV [auth 18],
KC [auth B],
KD [auth C],
KG [auth b],
KJ [auth z],
KL [auth 2],
KM [auth 4],
KO [auth 7],
KU [auth 16],
LC [auth B],
LD [auth C],
LF [auth Z],
LG [auth b],
LK [auth 1],
LL [auth 2],
LQ [auth 10],
LS [auth 13],
LV [auth 18],
MC [auth B],
MD [auth C],
MG [auth b],
MI [auth p],
MM [auth 4],
MO [auth 7],
MQ [auth 10],
MS [auth 13],
MT [auth 15],
MU [auth 16],
NC [auth B],
ND [auth C],
NG [auth b],
NI [auth p],
NK [auth 1],
NM [auth 4],
NO [auth 7],
NP [auth 9],
NT [auth 15],
NV [auth 18],
OC [auth B],
OG [auth b],
OI [auth p],
OK [auth 1],
OP [auth 9],
OS [auth 13],
OV [auth 18],
PC [auth B],
PI [auth p],
PM [auth 4],
PO [auth 7],
PS [auth 13],
PT [auth 15],
QC [auth B],
QE [auth P],
QF [auth a],
QI [auth p],
QK [auth 1],
QM [auth 4],
QP [auth 9],
QR [auth 12],
QV [auth 18],
RC [auth B],
RE [auth P],
RF [auth a],
RI [auth p],
RJ [auth 0],
RK [auth 1],
RP [auth 9],
RR [auth 12],
RT [auth 15],
SC [auth B],
SE [auth P],
SH [auth d],
SI [auth p],
SJ [auth 0],
SL [auth 3],
SN [auth 6],
SP [auth 9],
ST [auth 15],
TE [auth P],
TF [auth a],
TI [auth p],
TJ [auth 0],
TL [auth 3],
TN [auth 6],
TP [auth 9],
TR [auth 12],
TT [auth 15],
TU [auth 17],
UB [auth A],
UE [auth P],
UU [auth 17],
VB [auth A],
VE [auth P],
VH [auth d],
VI [auth p],
VJ [auth 0],
VL [auth 3],
VN [auth 6],
VP [auth 9],
VR [auth 12],
VS [auth 14],
WE [auth P],
WG [auth c],
WH [auth d],
WJ [auth 0],
WK [auth 1],
WO [auth 8],
WQ [auth 11],
WR [auth 12],
WS [auth 14],
WU [auth 17],
XB [auth A],
XD [auth D],
XE [auth P],
XG [auth c],
XJ [auth 0],
XL [auth 3],
XN [auth 6],
XO [auth 8],
XQ [auth 11],
YG [auth c],
YJ [auth 0],
YL [auth 3],
YM [auth 5],
YN [auth 6],
YR [auth 12],
YS [auth 14],
YU [auth 17],
ZE [auth P],
ZF [auth b],
ZG [auth c],
ZM [auth 5],
ZO [auth 8],
ZQ [auth 11],
ZR [auth 12],
ZU [auth 17],
ZV [auth 19]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
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SF [auth a],
TH [auth d],
WB [auth A],
YD [auth D]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
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CC [auth A]
FI [auth i]
II [auth l]
NE [auth L]
PQ [auth 10]
CC [auth A],
FI [auth i],
II [auth l],
NE [auth L],
PQ [auth 10],
QO [auth 8],
VF [auth a],
YF [auth b],
ZB [auth A],
ZC [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
Query on LMG
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BK [auth 0]
CI [auth f]
CK [auth 1]
DF [auth P]
DJ [auth w]
BK [auth 0],
CI [auth f],
CK [auth 1],
DF [auth P],
DJ [auth w],
EE [auth D],
FT [auth 14],
GI [auth j],
GR [auth 11],
HE [auth F],
HF [auth W],
HI [auth k],
HN [auth 5],
IN [auth 5],
KE [auth J],
KI [auth m],
LE [auth K],
LI [auth n],
MF [auth Z],
OE [auth M],
OQ [auth 10],
PE [auth N],
PH [auth c],
QH [auth c],
QQ [auth 11],
RM [auth 4],
SG [auth b],
SK [auth 1],
UH [auth d],
UT [auth 15],
VD [auth C],
VT [auth 15],
WC [auth B],
ZD [auth D],
ZH [auth d],
ZI [auth p]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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AC [auth A],
CE [auth D],
WF [auth a],
XH [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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AJ [auth p]
BC [auth A]
DE [auth D]
EF [auth P]
EJ [auth w]
AJ [auth p],
BC [auth A],
DE [auth D],
EF [auth P],
EJ [auth w],
FP [auth 8],
GP [auth 8],
GT [auth 14],
JI [auth l],
JJ [auth z],
JN [auth 5],
ME [auth L],
NF [auth Z],
RV [auth 18],
SM [auth 4],
SV [auth 18],
UD [auth C],
UG [auth b],
WT [auth 15],
XF [auth a],
YC [auth B],
YH [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86
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AF [auth P]
AL [auth 2]
AQ [auth 10]
AS [auth 13]
AU [auth 16]
AF [auth P],
AL [auth 2],
AQ [auth 10],
AS [auth 13],
AU [auth 16],
BL [auth 2],
BO [auth 7],
BQ [auth 10],
BS [auth 13],
BU [auth 16],
CF [auth P],
CM [auth 4],
CO [auth 7],
CS [auth 13],
CU [auth 16],
CV [auth 17],
DK [auth 1],
DM [auth 4],
DO [auth 7],
DS [auth 13],
DU [auth 16],
DV [auth 18],
EK [auth 1],
EM [auth 4],
EO [auth 7],
ES [auth 13],
EV [auth 18],
FK [auth 1],
FM [auth 4],
FO [auth 7],
FS [auth 13],
FV [auth 18],
GK [auth 1],
GM [auth 4],
GO [auth 7],
GV [auth 18],
HK [auth 1],
HM [auth 4],
HP [auth 9],
HT [auth 15],
HV [auth 18],
IP [auth 9],
IR [auth 11],
IT [auth 15],
JP [auth 9],
JR [auth 11],
JT [auth 15],
KN [auth 5],
KP [auth 9],
KR [auth 12],
KT [auth 15],
LJ [auth 0],
LN [auth 6],
LP [auth 9],
LR [auth 12],
LT [auth 15],
MJ [auth 0],
ML [auth 3],
MN [auth 6],
MP [auth 9],
MR [auth 12],
NJ [auth 0],
NL [auth 3],
NN [auth 6],
NQ [auth 10],
NR [auth 12],
NU [auth 17],
OJ [auth 0],
OL [auth 3],
ON [auth 6],
OR [auth 12],
OU [auth 17],
PJ [auth 0],
PL [auth 3],
PN [auth 6],
PR [auth 12],
PU [auth 17],
QJ [auth 0],
QL [auth 3],
QN [auth 6],
QS [auth 14],
QU [auth 17],
RL [auth 3],
RN [auth 6],
RO [auth 8],
RQ [auth 11],
RS [auth 14],
RU [auth 17],
SO [auth 8],
SQ [auth 11],
SS [auth 14],
SU [auth 17],
TM [auth 5],
TO [auth 8],
TQ [auth 11],
TS [auth 14],
TV [auth 19],
UK [auth 1],
UM [auth 5],
UO [auth 8],
UQ [auth 11],
US [auth 14],
UV [auth 19],
VK [auth 1],
VM [auth 5],
VO [auth 8],
VQ [auth 11],
VV [auth 19],
WI [auth p],
WM [auth 5],
WP [auth 10],
WV [auth 19],
XK [auth 2],
XM [auth 5],
XP [auth 10],
XV [auth 19],
YI [auth p],
YK [auth 2],
YP [auth 10],
YT [auth 16],
YV [auth 19],
ZK [auth 2],
ZP [auth 10],
ZT [auth 16]
(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
Download Ideal Coordinates CCD File 
AI [auth e],
CJ [auth v],
FE [auth E],
GF [auth V]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC1
Query on KC1
Download Ideal Coordinates CCD File 
AV [auth 17]
CT [auth 14]
DP [auth 8]
DR [auth 11]
FN [auth 5]
AV [auth 17],
CT [auth 14],
DP [auth 8],
DR [auth 11],
FN [auth 5],
GW [auth 19],
JL [auth 2],
KQ [auth 10],
LU [auth 16],
NS [auth 13],
OM [auth 4],
OO [auth 7],
PK [auth 1],
PV [auth 18],
UI [auth p],
UP [auth 9],
XR [auth 12],
XT [auth 15],
YE [auth P],
ZJ [auth 0],
ZL [auth 3],
ZN [auth 6]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2
Query on KC2
Download Ideal Coordinates CCD File 
AN [auth 5]
AP [auth 8]
AR [auth 11]
BW [auth 19]
CN [auth 5]
AN [auth 5],
AP [auth 8],
AR [auth 11],
BW [auth 19],
CN [auth 5],
EL [auth 2],
FQ [auth 10],
GL [auth 2],
GU [auth 16],
IS [auth 13],
IU [auth 16],
JM [auth 4],
JO [auth 7],
KK [auth 1],
KS [auth 13],
KV [auth 18],
LM [auth 4],
LO [auth 7],
MK [auth 1],
MV [auth 18],
OT [auth 15],
PP [auth 9],
QT [auth 15],
SR [auth 12],
UJ [auth 0],
UL [auth 3],
UN [auth 6],
UR [auth 12],
VU [auth 17],
WL [auth 3],
WN [auth 6],
XS [auth 14],
XU [auth 17],
YO [auth 8],
YQ [auth 11],
ZS [auth 14]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6
Query on DD6
Download Ideal Coordinates CCD File 
BF [auth P],
XI [auth p]		(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
Query on BCR
Download Ideal Coordinates CCD File 
BI [auth f]
DI [auth h]
GE [auth F]
HJ [auth y]
IE [auth H]
BI [auth f],
DI [auth h],
GE [auth F],
HJ [auth y],
IE [auth H],
JH [auth c],
KF [auth Y],
KH [auth c],
LH [auth c],
OD [auth C],
PD [auth C],
PG [auth b],
QD [auth C],
QG [auth b],
RG [auth b],
TC [auth B],
UC [auth B],
UF [auth a],
VC [auth B],
YB [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
Query on OEX
Download Ideal Coordinates CCD File 
OF [auth a],
SB [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
RH [auth d],
WD [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
PF [auth a],
TB [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
AD [auth C],
VG [auth c]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2025-09-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary