7OUI | pdb_00007oui

Structure of C2S2M2-type Photosystem supercomplex from Arabidopsis thaliana (digitonin-extracted)

Experimental Data Snapshot

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

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This is version 2.0 of the entry. See complete history. 

Literature

High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction.

Graca, A.T., Hall, M., Persson, K., Schroder, W.P.

(2021) Sci Rep 11: 15534-15534

  • DOI: https://doi.org/10.1038/s41598-021-94914-x
  • Primary Citation Related Structures: 
    7OUI

  • PubMed Abstract: 

    In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn 4 CaO 5 -site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

    • Organizational Affiliation: 
    • Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.

Macromolecule Content 

  • Total Structure Weight: 1,321.04 kDa 
  • Atom Count: 84,427 
  • Modeled Residue Count: 8,342 
  • Deposited Residue Count: 9,282 
  • Unique protein chains: 23

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1],
AA [auth 5],
C [auth 3],
CA [auth 7]		266Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q39142 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3, chloroplasticB [auth 2],
BA [auth 6]		243Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9S7M0 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 4],
DA [auth 8]		212Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9LMQ2 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1E [auth A],
EA [auth a]		352Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P83755 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinF [auth B],
FA [auth b]		508Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56777 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinG [auth C],
GA [auth c]		459Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56778 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinH [auth D],
HA [auth d]		352Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P56761 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaI [auth E],
IA [auth e]		83Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56779 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit beta (PsbF)J [auth F],
JA [auth f]		39Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P62095 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HK [auth H],
KA [auth h]		72Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56780 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IL [auth I],
LA [auth i]		36Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P62100 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KM [auth K],
MA [auth k]		37Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56782 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LN [auth L],
NA [auth l]		38Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P60129 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MO [auth M],
OA [auth m]		34Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P62109 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1-1, chloroplasticP [auth O],
PA [auth o]		247Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23321 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TQ [auth T],
QA [auth t]		33Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P61839 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticR [auth W],
RA [auth w]		54Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q39194 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
(thale cress) hypothetical proteinS [auth X],
SA [auth x]		42Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A7G2E9B1 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZT [auth Z],
TA [auth z]		62Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56790 (Arabidopsis thaliana)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP26, chloroplasticU [auth S],
UA [auth s]		232Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9XF89 (Arabidopsis thaliana)
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1, chloroplastic232Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P04778 (Arabidopsis thaliana)
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29.1, chloroplasticY [auth R],
YA [auth r]		250Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q07473 (Arabidopsis thaliana)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticZ [auth U],
ZA [auth u]		28Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q39195 (Arabidopsis thaliana)
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Reference Sequence

Small Molecules

Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
(Subject of Investigation/LOI)

Query on AJP


Download:Ideal Coordinates CCD File
AK [auth b]
CF [auth S]
HM [auth s]
IH [auth Y]
JH [auth Y]
AK [auth b],
CF [auth S],
HM [auth s],
IH [auth Y],
JH [auth Y],
KH [auth Y],
LH [auth Y],
MH [auth Y],
NG [auth N],
NO [auth y],
OG [auth N],
OO [auth y],
PO [auth y],
QO [auth y],
RO [auth y],
SN [auth n],
TB [auth A],
TN [auth n],
UF [auth G],
VC [auth B],
ZI [auth a],
ZM [auth g]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
DGD

Query on DGD


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CK [auth b]
ND [auth C]
NI [auth a]
OD [auth C]
SK [auth c]
CK [auth b],
ND [auth C],
NI [auth a],
OD [auth C],
SK [auth c],
TK [auth c],
WB [auth A],
XC [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL


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AB [auth 1]
AG [auth N]
AN [auth n]
AO [auth y]
BB [auth 1]
AB [auth 1],
AG [auth N],
AN [auth n],
AO [auth y],
BB [auth 1],
BG [auth N],
BO [auth y],
CB [auth 2],
CG [auth N],
CO [auth y],
DF [auth G],
DG [auth N],
DO [auth y],
EB [auth 2],
EN [auth n],
EP [auth r],
FI [auth 5],
FN [auth n],
GI [auth 5],
GN [auth n],
HF [auth G],
HI [auth 6],
HN [auth n],
IF [auth G],
IM [auth g],
IN [auth n],
JF [auth G],
JI [auth 6],
KF [auth G],
LE [auth S],
LF [auth G],
MM [auth g],
NM [auth g],
OM [auth g],
PE [auth S],
PM [auth g],
QE [auth S],
QG [auth Y],
QL [auth s],
QM [auth g],
RE [auth S],
RH [auth R],
SH [auth R],
TH [auth R],
UG [auth Y],
UL [auth s],
VF [auth N],
VG [auth Y],
VL [auth s],
VN [auth y],
WG [auth Y],
WL [auth s],
WO [auth r],
XG [auth Y],
XO [auth r],
YG [auth Y],
YO [auth r],
ZF [auth N],
ZH [auth R],
ZN [auth y]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA


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AC [auth B]
AD [auth C]
AH [auth Y]
AI [auth R]
AL [auth d]
AC [auth B],
AD [auth C],
AH [auth Y],
AI [auth R],
AL [auth d],
AM [auth s],
AP [auth r],
BC [auth B],
BD [auth C],
BH [auth Y],
BM [auth s],
BN [auth n],
BP [auth r],
CC [auth B],
CD [auth C],
CH [auth Y],
CM [auth s],
CN [auth n],
CP [auth r],
DB [auth 2],
DC [auth B],
DD [auth C],
DH [auth Y],
DJ [auth b],
DN [auth n],
DP [auth r],
EC [auth B],
ED [auth C],
EF [auth G],
EG [auth N],
EJ [auth b],
EK [auth c],
EO [auth y],
FB [auth 2],
FC [auth B],
FD [auth C],
FF [auth G],
FG [auth N],
FJ [auth b],
FK [auth c],
FO [auth y],
FP [auth r],
GB [auth 2],
GC [auth B],
GD [auth C],
GF [auth G],
GG [auth N],
GJ [auth b],
GK [auth c],
GO [auth y],
HC [auth B],
HD [auth C],
HG [auth N],
HJ [auth b],
HK [auth c],
HO [auth y],
IB [auth A],
IC [auth B],
ID [auth C],
IG [auth N],
II [auth 6],
IJ [auth b],
IK [auth c],
IO [auth y],
JB [auth A],
JC [auth B],
JD [auth C],
JJ [auth b],
JK [auth c],
JM [auth g],
JN [auth n],
KC [auth B],
KD [auth C],
KI [auth 6],
KJ [auth b],
KK [auth c],
KM [auth g],
KN [auth n],
LC [auth B],
LD [auth C],
LI [auth 6],
LJ [auth b],
LK [auth c],
LM [auth g],
LN [auth n],
MB [auth A],
MC [auth B],
ME [auth S],
MF [auth G],
MJ [auth b],
MK [auth c],
MN [auth n],
NC [auth B],
NE [auth S],
NF [auth G],
NH [auth R],
NJ [auth b],
NK [auth c],
NN [auth n],
OE [auth S],
OF [auth G],
OH [auth R],
OI [auth a],
OJ [auth b],
OK [auth c],
PF [auth G],
PH [auth R],
PI [auth a],
PJ [auth b],
PK [auth c],
QF [auth G],
QH [auth R],
QJ [auth b],
QK [auth c],
RG [auth Y],
RJ [auth b],
RL [auth s],
RM [auth g],
SE [auth S],
SG [auth Y],
SI [auth a],
SJ [auth b],
SL [auth s],
SM [auth g],
SO [auth r],
TD [auth D],
TE [auth S],
TG [auth Y],
TL [auth s],
TM [auth g],
TO [auth r],
UD [auth D],
UE [auth S],
UH [auth R],
UM [auth g],
UO [auth r],
VD [auth D],
VE [auth S],
VH [auth R],
VM [auth g],
VO [auth r],
WE [auth S],
WF [auth N],
WH [auth R],
WN [auth y],
XE [auth S],
XF [auth N],
XH [auth R],
XL [auth s],
XN [auth y],
YB [auth B],
YF [auth N],
YH [auth R],
YK [auth d],
YL [auth s],
YN [auth y],
ZB [auth B],
ZC [auth C],
ZG [auth Y],
ZK [auth d],
ZL [auth s],
ZO [auth r]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


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KB [auth A],
LB [auth A],
QI [auth a],
RI [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


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FE [auth L]
HE [auth L]
KL [auth l]
LL [auth l]
OB [auth A]
FE [auth L],
HE [auth L],
KL [auth l],
LL [auth l],
OB [auth A],
SB [auth A],
UI [auth a],
YI [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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EL [auth d]
PB [auth A]
RB [auth A]
RC [auth B]
SD [auth C]
EL [auth d],
PB [auth A],
RB [auth A],
RC [auth B],
SD [auth C],
UC [auth B],
VI [auth a],
WJ [auth b],
XI [auth a],
XK [auth c],
ZD [auth D],
ZJ [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


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CL [auth d],
QB [auth A],
WI [auth a],
XD [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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BF [auth S]
BK [auth b]
DL [auth d]
EI [auth R]
GE [auth L]
BF [auth S],
BK [auth b],
DL [auth d],
EI [auth R],
GE [auth L],
GM [auth s],
HB [auth 2],
HH [auth Y],
JP [auth r],
KE [auth S],
MG [auth N],
MI [auth 6],
ML [auth l],
MO [auth y],
PD [auth C],
PG [auth Y],
PL [auth s],
QD [auth C],
RD [auth C],
RN [auth n],
SC [auth B],
TC [auth B],
UK [auth c],
UN [auth y],
VK [auth c],
WC [auth B],
WK [auth c],
XJ [auth b],
YD [auth D],
YJ [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM


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BE [auth F],
GL [auth f]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
XAT

Query on XAT


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CI [auth R],
HP [auth r]		(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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AF [auth S]
DI [auth R]
FM [auth s]
GH [auth Y]
IP [auth r]
AF [auth S],
DI [auth R],
FM [auth s],
GH [auth Y],
IP [auth r],
LG [auth N],
LO [auth y],
QN [auth n],
TF [auth G],
YM [auth g]
(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
BI [auth R]
DM [auth s]
EH [auth Y]
EM [auth s]
FH [auth Y]
BI [auth R],
DM [auth s],
EH [auth Y],
EM [auth s],
FH [auth Y],
GP [auth r],
JG [auth N],
JO [auth y],
KG [auth N],
KO [auth y],
ON [auth n],
PN [auth n],
RF [auth G],
SF [auth G],
WM [auth g],
XM [auth g],
YE [auth S],
ZE [auth S]
(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
BL [auth d]
CE [auth H]
DE [auth I]
EE [auth K]
HL [auth h]
BL [auth d],
CE [auth H],
DE [auth I],
EE [auth K],
HL [auth h],
IE [auth T],
IL [auth i],
JE [auth Z],
JL [auth k],
MD [auth C],
NB [auth A],
NL [auth t],
OC [auth B],
OL [auth z],
PC [auth B],
QC [auth B],
RK [auth c],
TI [auth a],
TJ [auth b],
UJ [auth b],
VJ [auth b],
WD [auth D]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
AJ [auth a],
UB [auth A]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
BJ [auth a],
VB [auth A]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA


Download:Ideal Coordinates CCD File
CJ [auth a],
DK [auth b],
XB [auth A],
YC [auth B]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
AE [auth D],
FL [auth d]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-05009
Other privateSwedenCarl Trygger

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-18
    Type: Initial release
  • Version 2.0: 2025-07-02
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary