8C29

Cryo-EM structure of photosystem II C2S2 supercomplex from Norway spruce (Picea abies) at 2.8 Angstrom resolution

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Picea abies
  • Mutation(s): No 
  • Membrane Protein: Yes  PDBTMMemProtMD

  • Deposited: 2022-12-21 Released: 2023-07-26 
  • Deposition Author(s): Kopecny, D., Semchonok, D.A., Kouril, R.
  • Funding Organization(s): Grant Agency of the Czech Republic, Ministry of Education, Youth and Sports of the Czech Republic, German Federal Ministry for Education and Research, German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of a plant photosystem II supercomplex with light-harvesting protein Lhcb8 and alpha-tocopherol.

Opatikova, M.Semchonok, D.A.Kopecny, D.Ilik, P.Pospisil, P.Ilikova, I.Roudnicky, P.Zeljkovic, S.C.Tarkowski, P.Kyrilis, F.L.Hamdi, F.Kastritis, P.L.Kouril, R.

(2023) Nat Plants 9: 1359-1369

  • DOI: https://doi.org/10.1038/s41477-023-01483-0
  • Primary Citation of Related Structures:  
    8C29

  • PubMed Abstract: 

    The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure-functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution.


  • Organizational Affiliation

    Department of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
X [auth a]
353Picea abiesMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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UniProt GroupP50155
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
Y [auth b]
508Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGX1 (Picea abies)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
Z [auth c]
473Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinAA [auth d],
D
353Picea abiesMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaBA [auth e],
E
83Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaCA [auth f],
F
39Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic275Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEA [auth h],
H
75Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IFA [auth i],
I
36Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KGA [auth k],
J [auth K]
59Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LHA [auth l],
K [auth L]
38Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MIA [auth m],
L [auth M]
37Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1, chloroplasticKA [auth o],
N [auth O]
341Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticLA [auth r],
O [auth R]
300Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticMA [auth s],
P [auth S]
303Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TNA [auth t],
Q [auth T]
35Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticOA [auth u],
R [auth U]
133Picea abiesMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12PA [auth v],
S [auth V]
33Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PSII 6.1 kDa proteinQA [auth w],
T [auth W]
146Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II PsbXRA [auth x],
U [auth X]
129Picea abiesMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZTA [auth z],
W [auth Z]
62Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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OE [auth H],
QK [auth d],
WC [auth C],
XJ [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AE [auth G]
AF [auth N]
AL [auth g]
BE [auth G]
BF [auth N]
AE [auth G],
AF [auth N],
AL [auth g],
BE [auth G],
BF [auth N],
BO [auth y],
CF [auth N],
CH [auth Y],
CO [auth y],
DF [auth N],
DN [auth s],
DO [auth y],
EN [auth s],
EO [auth y],
FN [auth s],
GG [auth S],
GH [auth Y],
HH [auth Y],
IH [auth Y],
JH [auth Y],
KG [auth S],
KL [auth g],
LG [auth S],
ME [auth G],
MG [auth S],
MM [auth r],
NM [auth r],
OL [auth n],
OM [auth r],
SF [auth R],
SK [auth g],
SL [auth n],
TD [auth G],
TF [auth R],
TL [auth n],
UF [auth R],
UL [auth n],
VE [auth N],
VL [auth n],
WK [auth g],
WL [auth n],
XD [auth G],
XK [auth g],
XN [auth y],
YD [auth G],
YK [auth g],
ZD [auth G],
ZE [auth N],
ZK [auth g],
ZM [auth s]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AI [auth a]
AM [auth n]
AN [auth s]
AO [auth y]
BL [auth g]
AI [auth a],
AM [auth n],
AN [auth s],
AO [auth y],
BL [auth g],
BM [auth n],
BN [auth s],
CE [auth G],
CL [auth g],
CN [auth s],
DE [auth G],
DH [auth Y],
DL [auth g],
EE [auth G],
EF [auth N],
EH [auth Y],
EL [auth g],
FE [auth G],
FF [auth N],
FH [auth Y],
FL [auth g],
FO [auth y],
GE [auth G],
GF [auth N],
GN [auth s],
GO [auth y],
HF [auth N],
HG [auth S],
HI [auth b],
HN [auth s],
HO [auth y],
IB [auth B],
IC [auth C],
IF [auth N],
IG [auth S],
II [auth b],
IM [auth r],
IN [auth s],
IO [auth y],
JB [auth B],
JC [auth C],
JG [auth S],
JI [auth b],
JJ [auth c],
JM [auth r],
JN [auth s],
JO [auth y],
KB [auth B],
KC [auth C],
KH [auth Y],
KI [auth b],
KJ [auth c],
KK [auth d],
KM [auth r],
KN [auth s],
LB [auth B],
LC [auth C],
LD [auth D],
LH [auth Y],
LI [auth b],
LJ [auth c],
LK [auth d],
LM [auth r],
LN [auth s],
MB [auth B],
MC [auth C],
MD [auth D],
MH [auth Y],
MI [auth b],
MJ [auth c],
NB [auth B],
NC [auth C],
NG [auth S],
NH [auth Y],
NI [auth b],
NJ [auth c],
OB [auth B],
OC [auth C],
OF [auth R],
OG [auth S],
OH [auth Y],
OI [auth b],
OJ [auth c],
PB [auth B],
PC [auth C],
PF [auth R],
PG [auth S],
PI [auth b],
PJ [auth c],
PL [auth n],
PM [auth r],
QB [auth B],
QC [auth C],
QF [auth R],
QG [auth S],
QI [auth b],
QJ [auth c],
QL [auth n],
QM [auth r],
RB [auth B],
RC [auth C],
RF [auth R],
RG [auth S],
RI [auth b],
RJ [auth c],
RL [auth n],
RM [auth r],
SB [auth B],
SC [auth C],
SG [auth S],
SI [auth b],
SJ [auth c],
SM [auth r],
TB [auth B],
TC [auth C],
TI [auth b],
TJ [auth c],
TK [auth g],
TM [auth r],
UB [auth B],
UC [auth C],
UD [auth G],
UI [auth b],
UJ [auth c],
UK [auth g],
VA [auth A],
VB [auth B],
VD [auth G],
VF [auth R],
VI [auth b],
VJ [auth c],
VK [auth g],
WA [auth A],
WB [auth B],
WD [auth G],
WE [auth N],
WF [auth R],
WH [auth a],
WI [auth b],
XA [auth A],
XB [auth B],
XE [auth N],
XF [auth R],
XH [auth a],
XL [auth n],
YE [auth N],
YF [auth R],
YH [auth a],
YL [auth n],
YN [auth y],
ZA [auth A],
ZF [auth R],
ZL [auth n],
ZN [auth y]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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HK [auth d],
ID [auth D],
YA [auth A],
ZH [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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BB [auth A],
CI [auth a],
RE [auth L],
UE [auth M]
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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AJ [auth b]
BC [auth B]
CB [auth A]
EG [auth R]
FK [auth c]
AJ [auth b],
BC [auth B],
CB [auth A],
EG [auth R],
FK [auth c],
GD [auth C],
HC [auth B],
IJ [auth b],
OK [auth d],
PD [auth D],
SN [auth w],
YM [auth r]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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EB [auth A],
EI [auth a],
MK [auth d],
ND [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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DG [auth R]
FB [auth A]
FI [auth a]
GM [auth n]
HJ [auth b]
DG [auth R],
FB [auth A],
FI [auth a],
GM [auth n],
HJ [auth b],
JK [auth d],
JL [auth g],
KD [auth D],
KE [auth G],
MF [auth N],
MO [auth y],
NK [auth d],
OD [auth D],
ON [auth s],
SH [auth Y],
TE [auth L],
VG [auth S],
XM [auth r]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH

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AH [auth X]
DB [auth A]
DI [auth a]
FD [auth C]
IK [auth d]
AH [auth X],
DB [auth A],
DI [auth a],
FD [auth C],
IK [auth d],
JD [auth D],
QN [auth s],
SE [auth L],
TN [auth w],
UN [auth x],
XG [auth T],
ZG [auth W]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA
Query on DGA

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GJ [auth b],
QD [auth D]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
HEM
Query on HEM

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RK [auth f],
SD [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XAT
Query on XAT

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BH [auth Y]
CG [auth R]
EM [auth n]
HM [auth n]
LE [auth G]
BH [auth Y],
CG [auth R],
EM [auth n],
HM [auth n],
LE [auth G],
NF [auth N],
WM [auth r],
WN [auth y]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
NEX
Query on NEX

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BG [auth R]
FG [auth R]
FM [auth n]
IL [auth g]
JE [auth G]
BG [auth R],
FG [auth R],
FM [auth n],
IL [auth g],
JE [auth G],
LF [auth N],
PN [auth s],
RH [auth Y],
VM [auth r],
WG [auth S]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
LUT
Query on LUT

Download Ideal Coordinates CCD File 
AG [auth R]
CM [auth n]
DM [auth n]
GL [auth g]
HE [auth G]
AG [auth R],
CM [auth n],
DM [auth n],
GL [auth g],
HE [auth G],
HL [auth g],
IE [auth G],
JF [auth N],
KF [auth N],
KO [auth y],
LO [auth y],
MN [auth s],
NN [auth s],
PH [auth Y],
QH [auth Y],
TG [auth S],
UG [auth S],
UM [auth r]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth B]
BI [auth a]
LL [auth h]
NE [auth H]
AB [auth A],
AC [auth B],
BI [auth a],
LL [auth h],
NE [auth H],
NL [auth k],
NO [auth z],
PK [auth d],
QE [auth K],
RD [auth D],
RN [auth v],
TH [auth Z],
VC [auth C],
WJ [auth c],
XI [auth b],
YB [auth B],
YG [auth V],
YI [auth b],
ZB [auth B],
ZI [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
VIV
Query on VIV

Download Ideal Coordinates CCD File 
ED [auth C],
VN [auth y]
(2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL
C29 H50 O2
GVJHHUAWPYXKBD-IEOSBIPESA-N
LNL
Query on LNL

Download Ideal Coordinates CCD File 
AD [auth C]
AK [auth c]
BD [auth C]
BK [auth c]
CD [auth C]
AD [auth C],
AK [auth c],
BD [auth C],
BK [auth c],
CD [auth C],
CJ [auth b],
CK [auth c],
DC [auth B],
DD [auth C],
DJ [auth b],
DK [auth c],
EC [auth B],
EJ [auth b],
EK [auth c],
FC [auth B],
FJ [auth b],
GB [auth A],
GC [auth B],
GI [auth a],
HB [auth A],
ML [auth i],
PE [auth I],
UH [auth a],
YC [auth C],
ZC [auth C],
ZJ [auth c]
ALPHA-LINOLENIC ACID
C18 H30 O2
DTOSIQBPPRVQHS-PDBXOOCHSA-N
PAM
Query on PAM

Download Ideal Coordinates CCD File 
BJ [auth b],
CC [auth B]
PALMITOLEIC ACID
C16 H30 O2
SECPZKHBENQXJG-FPLPWBNLSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
GK [auth d],
HD [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
UA [auth A],
VH [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
XC [auth C],
YJ [auth c]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.0
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant Agency of the Czech RepublicCzech Republic21-05497S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/0.0/16_019/0000827
German Federal Ministry for Education and ResearchGermany03Z22HN23
German Federal Ministry for Education and ResearchGermany03Z22HI2
German Federal Ministry for Education and ResearchGermany03COV04
German Research Foundation (DFG)Germany391498659
German Research Foundation (DFG)GermanyRTG 2467
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicNo. CZ.02.1.01/0.0/0.0/18_046/0015974
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2018127

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references
  • Version 1.2: 2023-08-30
    Changes: Database references