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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for P50155 (Picea abies)
Explore P50155 
Go to UniProtKB:  P50155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50155
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore R4ZGX1 
Go to UniProtKB:  R4ZGX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGX1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
Z [auth c]
473Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGZ0 (Picea abies)
Explore R4ZGZ0 
Go to UniProtKB:  R4ZGZ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGZ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for R4ZGX6 (Picea abies)
Explore R4ZGX6 
Go to UniProtKB:  R4ZGX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGX6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaBA [auth e],
E
83Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGW6 (Picea abies)
Explore R4ZGW6 
Go to UniProtKB:  R4ZGW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGW6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaCA [auth f],
F
39Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGT7 (Picea abies)
Explore R4ZGT7 
Go to UniProtKB:  R4ZGT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGT7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic275Picea abiesMutation(s): 0 
UniProt
Find proteins for Q40771 (Picea abies)
Explore Q40771 
Go to UniProtKB:  Q40771
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ40771
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEA [auth h],
H
75Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGS7 (Picea abies)
Explore R4ZGS7 
Go to UniProtKB:  R4ZGS7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGS7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IFA [auth i],
I
36Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGS4 (Picea abies)
Explore R4ZGS4 
Go to UniProtKB:  R4ZGS4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGS4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for R4ZGX8 (Picea abies)
Explore R4ZGX8 
Go to UniProtKB:  R4ZGX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGX8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for R4ZGV2 (Picea abies)
Explore R4ZGV2 
Go to UniProtKB:  R4ZGV2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGV2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for A2CHR7 (Picea abies)
Explore A2CHR7 
Go to UniProtKB:  A2CHR7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2CHR7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for A9NRV4 (Picea sitchensis)
Explore A9NRV4 
Go to UniProtKB:  A9NRV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NRV4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticLA [auth r],
O [auth R]
300Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9NKX0 (Picea sitchensis)
Explore A9NKX0 
Go to UniProtKB:  A9NKX0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NKX0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticMA [auth s],
P [auth S]
303Picea abiesMutation(s): 0 
UniProt
Find proteins for A9NKM0 (Picea sitchensis)
Explore A9NKM0 
Go to UniProtKB:  A9NKM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NKM0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TNA [auth t],
Q [auth T]
35Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for R4ZGU2 (Picea abies)
Explore R4ZGU2 
Go to UniProtKB:  R4ZGU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGU2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticOA [auth u],
R [auth U]
133Picea abiesMutation(s): 0 
UniProt
Find proteins for A9NJW3 (Picea sitchensis)
Explore A9NJW3 
Go to UniProtKB:  A9NJW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NJW3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for R4ZGY5 (Picea abies)
Explore R4ZGY5 
Go to UniProtKB:  R4ZGY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGY5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PSII 6.1 kDa proteinQA [auth w],
T [auth W]
146Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9NLC2 (Picea sitchensis)
Explore A9NLC2 
Go to UniProtKB:  A9NLC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NLC2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II PsbXRA [auth x],
U [auth X]
129Picea abiesMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9NTS2 (Picea sitchensis)
Explore A9NTS2 
Go to UniProtKB:  A9NTS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9NTS2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for R4ZGT1 (Picea abies)
Explore R4ZGT1 
Go to UniProtKB:  R4ZGT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupR4ZGT1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 21 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

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

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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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