8J5K

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.

Zhao, S.Shen, L.Li, X.Tao, Q.Li, Z.Xu, C.Zhou, C.Yang, Y.Sang, M.Han, G.Yu, L.J.Kuang, T.Shen, J.R.Wang, W.

(2023) Nat Commun 14: 8164-8164

  • DOI: https://doi.org/10.1038/s41467-023-44055-8
  • Primary Citation of Related Structures:  
    8J5K, 8J7Z, 8W4O, 8W4P

  • PubMed Abstract: 

    Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PsbAA,
W [auth a]
333Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8F5GJ32 (Chaetoceros gracilis)
Explore A0A8F5GJ32 
Go to UniProtKB:  A0A8F5GJ32
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8F5GJ32
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PsbBB,
X [auth b]
481Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679C6E3 (Chaetoceros gracilis)
Explore A0A679C6E3 
Go to UniProtKB:  A0A679C6E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679C6E3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PsbCC,
Y [auth c]
450Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8F5GHI6 (Chaetoceros gracilis)
Explore A0A8F5GHI6 
Go to UniProtKB:  A0A8F5GHI6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8F5GHI6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
PsbDD,
Z [auth d]
340Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679C012 (Chaetoceros gracilis)
Explore A0A679C012 
Go to UniProtKB:  A0A679C012
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679C012
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
PsbEAA [auth e],
E
75Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679C209 (Chaetoceros gracilis)
Explore A0A679C209 
Go to UniProtKB:  A0A679C209
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679C209
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PsbFBA [auth f],
F
31Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0U1 (Thalassiosira pseudonana)
Explore A0T0U1 
Go to UniProtKB:  A0T0U1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0T0U1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
PsbHCA [auth h],
G [auth H]
65Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B7XBY7 (Chaetoceros gracilis)
Explore B7XBY7 
Go to UniProtKB:  B7XBY7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB7XBY7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
PsbIDA [auth i],
H [auth I]
34Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679BVT8 (Chaetoceros gracilis)
Explore A0A679BVT8 
Go to UniProtKB:  A0A679BVT8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679BVT8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsbJEA [auth j],
I [auth J]
34Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0T9 (Thalassiosira pseudonana)
Explore A0T0T9 
Go to UniProtKB:  A0T0T9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0T0T9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsbKFA [auth k],
J [auth K]
37Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2H5N031 (Citrus unshiu)
Explore A0A2H5N031 
Go to UniProtKB:  A0A2H5N031
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2H5N031
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PsbLGA [auth l],
K [auth L]
37Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A151DYG7 (Thermoplasmatales archaeon SG8-52-4)
Explore A0A151DYG7 
Go to UniProtKB:  A0A151DYG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A151DYG7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsbMHA [auth m],
L [auth M]
41Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679C2A0 (Chaetoceros gracilis)
Explore A0A679C2A0 
Go to UniProtKB:  A0A679C2A0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679C2A0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Psb34IA [auth n],
M [auth N]
30Stephanocyclus meneghinianusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsbOJA [auth o],
N [auth O]
248Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHE8 (Chaetoceros gracilis)
Explore B6ZHE8 
Go to UniProtKB:  B6ZHE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHE8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsbQ'KA [auth q],
O [auth Q]
145Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHE9 (Chaetoceros gracilis)
Explore B6ZHE9 
Go to UniProtKB:  B6ZHE9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHE9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PsbTLA [auth t],
P [auth T]
29Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679C6E6 (Chaetoceros gracilis)
Explore A0A679C6E6 
Go to UniProtKB:  A0A679C6E6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679C6E6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PsbUMA [auth u],
Q [auth U]
92Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHF0 (Chaetoceros gracilis)
Explore B6ZHF0 
Go to UniProtKB:  B6ZHF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsbVNA [auth v],
R [auth V]
136Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8F5GGT9 (Chaetoceros gracilis)
Explore A0A8F5GGT9 
Go to UniProtKB:  A0A8F5GGT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8F5GGT9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PsbWOA [auth w],
S [auth W]
50Stephanocyclus meneghinianusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
PsbXPA [auth x],
T [auth X]
34Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B6ZHF2 (Chaetoceros gracilis)
Explore B6ZHF2 
Go to UniProtKB:  B6ZHF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6ZHF2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsbYQA [auth y],
U [auth Y]
33Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0V3 (Thalassiosira pseudonana)
Explore A0T0V3 
Go to UniProtKB:  A0T0V3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0T0V3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsbZRA [auth z],
V [auth Z]
59Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0T3 (Thalassiosira pseudonana)
Explore A0T0T3 
Go to UniProtKB:  A0T0T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0T0T3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-G, fucoxanthin chlorophyll a/c binding proteinBB [auth 0],
SA [auth 5]
169Stephanocyclus meneghinianusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-H2, fucoxanthin chlorophyll a/c binding proteinCB [auth 2],
TA [auth 7]
164Stephanocyclus meneghinianusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-H1, fucoxanthin chlorophyll a/c binding proteinDB [auth 1],
UA [auth 6]
164Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8BX93 (Thalassiosira pseudonana)
Explore B8BX93 
Go to UniProtKB:  B8BX93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8BX93
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-I, fucoxanthin chlorophyll a/c binding proteinVA [auth p],
YA [auth P]
214Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8BUU4 (Thalassiosira pseudonana)
Explore B8BUU4 
Go to UniProtKB:  B8BUU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8BUU4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-K, fucoxanthin chlorophyll a/c binding proteinWA [auth 4],
ZA [auth 9]
153Stephanocyclus meneghinianusMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
FCPII-J, fucoxanthin chlorophyll a/c binding proteinAB [auth 8],
XA [auth 3]
163Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8BVI1 (Thalassiosira pseudonana)
Explore B8BVI1 
Go to UniProtKB:  B8BVI1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8BVI1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
FD [auth C]
GD [auth C]
HD [auth C]
HG [auth c]
IG [auth c]
FD [auth C],
GD [auth C],
HD [auth C],
HG [auth c],
IG [auth c],
JG [auth c],
XD [auth H],
ZG [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AC [auth B]
AD [auth C]
AF [auth b]
AG [auth c]
AJ [auth 6]
AC [auth B],
AD [auth C],
AF [auth b],
AG [auth c],
AJ [auth 6],
AK [auth 4],
AL [auth P],
AM [auth 8],
AN [auth 2],
AO [auth 1],
BC [auth B],
BD [auth C],
BF [auth b],
BG [auth c],
BJ [auth 6],
BK [auth 4],
BL [auth P],
BM [auth 8],
BN [auth 2],
BO [auth 1],
CC [auth B],
CF [auth b],
CG [auth c],
CJ [auth 6],
CK [auth 4],
CM [auth 8],
CN [auth 2],
DC [auth B],
DF [auth b],
DG [auth c],
DJ [auth 6],
DK [auth 4],
DM [auth 8],
DN [auth 2],
EC [auth B],
EF [auth b],
EJ [auth 6],
EK [auth 4],
EM [auth 8],
EN [auth 2],
FC [auth B],
FE [auth W],
FF [auth b],
FI [auth 7],
FJ [auth 6],
FN [auth 2],
GB [auth A],
GC [auth B],
GF [auth b],
GI [auth 7],
GJ [auth 6],
GN [auth 2],
HB [auth A],
HE [auth Z],
HF [auth b],
HH [auth w],
HI [auth 7],
HJ [auth p],
HL [auth 9],
HN [auth 2],
IF [auth b],
II [auth 7],
IJ [auth p],
IK [auth 3],
IL [auth 9],
IM [auth 0],
IN [auth 2],
JD [auth D],
JF [auth b],
JH [auth z],
JI [auth 7],
JJ [auth p],
JK [auth 3],
JL [auth 9],
JM [auth 0],
JN [auth 2],
KB [auth A],
KE [auth a],
KF [auth b],
KI [auth 7],
KJ [auth p],
KK [auth 3],
KL [auth 9],
KM [auth 0],
KN [auth 2],
LD [auth D],
LE [auth a],
LG [auth d],
LI [auth 7],
LJ [auth p],
LK [auth 3],
LL [auth 9],
LM [auth 0],
LN [auth 2],
MD [auth D],
MI [auth 7],
MJ [auth p],
MK [auth 3],
ML [auth 9],
MM [auth 0],
MN [auth 1],
NG [auth d],
NH [auth 5],
NI [auth 7],
NJ [auth p],
NK [auth 3],
NL [auth 9],
NM [auth 0],
OE [auth a],
OG [auth d],
OH [auth 5],
OI [auth 7],
OJ [auth p],
OK [auth 3],
OL [auth 9],
OM [auth 0],
PC [auth C],
PH [auth 5],
PI [auth 7],
PJ [auth p],
PK [auth 3],
PL [auth 9],
PM [auth 0],
QC [auth C],
QH [auth 5],
QI [auth 7],
QK [auth 3],
QL [auth 9],
QM [auth 0],
QN [auth 1],
RB [auth B],
RC [auth C],
RF [auth c],
RH [auth 5],
RI [auth 6],
RK [auth 3],
RM [auth 0],
RN [auth 1],
SB [auth B],
SC [auth C],
SF [auth c],
SH [auth 5],
SK [auth 3],
SM [auth 0],
SN [auth 1],
TB [auth B],
TC [auth C],
TF [auth c],
TH [auth 5],
TK [auth P],
TN [auth 1],
UB [auth B],
UC [auth C],
UF [auth c],
UH [auth 5],
UK [auth P],
UL [auth 8],
UN [auth 1],
VB [auth B],
VC [auth C],
VE [auth b],
VF [auth c],
VH [auth 5],
VI [auth 6],
VJ [auth 4],
VK [auth P],
VL [auth 8],
VN [auth 1],
WB [auth B],
WC [auth C],
WE [auth b],
WF [auth c],
WH [auth 5],
WI [auth 6],
WJ [auth 4],
WK [auth P],
WL [auth 8],
WN [auth 1],
XB [auth B],
XC [auth C],
XE [auth b],
XF [auth c],
XH [auth 5],
XI [auth 6],
XJ [auth 4],
XK [auth P],
XL [auth 8],
XN [auth 1],
YB [auth B],
YC [auth C],
YE [auth b],
YF [auth c],
YI [auth 6],
YJ [auth 4],
YK [auth P],
YL [auth 8],
YN [auth 1],
ZB [auth B],
ZC [auth C],
ZE [auth b],
ZF [auth c],
ZI [auth 6],
ZJ [auth 4],
ZK [auth P],
ZL [auth 8],
ZN [auth 1]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

Download Ideal Coordinates CCD File 
IB [auth A],
JB [auth A],
ME [auth a],
NE [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

Download Ideal Coordinates CCD File 
MB [auth A]
MC [auth B]
NC [auth B]
OB [auth A]
QE [auth a]
MB [auth A],
MC [auth B],
NC [auth B],
OB [auth A],
QE [auth a],
UE [auth b],
UM [auth 0],
ZH [auth 5]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
BE [auth M]
BH [auth j]
CE [auth M]
DH [auth m]
EE [auth W]
BE [auth M],
BH [auth j],
CE [auth M],
DH [auth m],
EE [auth W],
EH [auth m],
GE [auth Y],
GH [auth w],
ID [auth C],
IH [auth y],
KC [auth B],
KG [auth c],
OF [auth b],
QD [auth D],
RD [auth D],
SD [auth D],
SG [auth d],
TG [auth d],
TM [auth 0],
UG [auth d],
YH [auth 5],
ZD [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

Download Ideal Coordinates CCD File 
NB [auth A],
OD [auth D],
QG [auth d],
RE [auth a]
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 (Subject of Investigation/LOI)
Query on LHG

Download Ideal Coordinates CCD File 
AH [auth h]
LC [auth B]
PB [auth A]
PD [auth D]
PF [auth b]
AH [auth h],
LC [auth B],
PB [auth A],
PD [auth D],
PF [auth b],
QB [auth A],
RG [auth d],
SE [auth a],
TD [auth D],
TE [auth a],
UD [auth D],
VG [auth d],
WG [auth d],
YD [auth H]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86 (Subject of Investigation/LOI)
Query on A86

Download Ideal Coordinates CCD File 
AI [auth 5]
BI [auth 7]
CI [auth 7]
CL [auth P]
EL [auth 9]
AI [auth 5],
BI [auth 7],
CI [auth 7],
CL [auth P],
EL [auth 9],
FK [auth 3],
FL [auth 9],
FM [auth 0],
GK [auth 3],
GL [auth 9],
HM [auth 0],
KH [auth 5],
MH [auth 5],
NN [auth 1],
QJ [auth p],
RL [auth 8],
SI [auth 6],
SJ [auth 4],
SL [auth 8],
TJ [auth 4],
UJ [auth 4],
VM [auth 0],
WM [auth 2],
XM [auth 2]
(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 (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
DE [auth V],
FH [auth v],
VD [auth F],
XG [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

Download Ideal Coordinates CCD File 
DI [auth 7]
DL [auth P]
EI [auth 7]
HK [auth 3]
ON [auth 1]
DI [auth 7],
DL [auth P],
EI [auth 7],
HK [auth 3],
ON [auth 1],
PN [auth 1],
RJ [auth p],
TI [auth 6],
TL [auth 8],
UI [auth 6],
YM [auth 2],
ZM [auth 2]
(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
ET4 (Subject of Investigation/LOI)
Query on ET4

Download Ideal Coordinates CCD File 
GM [auth 0],
LH [auth 5]
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
HNYJHQMUSVNWPV-DRCJTWAYSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
AE [auth K]
CD [auth C]
CH [auth k]
DD [auth C]
ED [auth C]
AE [auth K],
CD [auth C],
CH [auth k],
DD [auth C],
ED [auth C],
EG [auth c],
FG [auth c],
GG [auth c],
HC [auth B],
IC [auth B],
JC [auth B],
LB [auth A],
LF [auth b],
MF [auth b],
ND [auth D],
NF [auth b],
PE [auth a],
PG [auth d],
WD [auth H],
YG [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX (Subject of Investigation/LOI)
Query on OEX

Download Ideal Coordinates CCD File 
EB [auth A],
IE [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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

Download Ideal Coordinates CCD File 
FB [auth A],
JE [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
OC [auth C],
QF [auth c]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release