6KAF | pdb_00006kaf

C2S2M2N2-type PSII-LHCII


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6KAF

This is version 2.1 of the entry. See complete history

Literature

Structure of a C2S2M2N2-type PSII-LHCII supercomplex from the green algaChlamydomonas reinhardtii.

Shen, L.Huang, Z.Chang, S.Wang, W.Wang, J.Kuang, T.Han, G.Shen, J.R.Zhang, X.

(2019) Proc Natl Acad Sci U S A 116: 21246-21255

  • DOI: https://doi.org/10.1073/pnas.1912462116
  • Primary Citation Related Structures: 
    6KAF

  • PubMed Abstract: 

    Photosystem II (PSII) in the thylakoid membranes of plants, algae, and cyanobacteria catalyzes light-induced oxidation of water by which light energy is converted to chemical energy and molecular oxygen is produced. In higher plants and most eukaryotic algae, the PSII core is surrounded by variable numbers of light-harvesting antenna complex II (LHCII), forming a PSII-LHCII supercomplex. In order to harvest energy efficiently at low-light-intensity conditions under water, a complete PSII-LHCII supercomplex (C 2 S 2 M 2 N 2 ) of the green alga Chlamydomonas reinhardtii (Cr) contains more antenna subunits and pigments than the dominant PSII-LHCII supercomplex (C 2 S 2 M 2 ) of plants. The detailed structure and energy transfer pathway of the Cr-PSII-LHCII remain unknown. Here we report a cryoelectron microscopy structure of a complete, C 2 S 2 M 2 N 2 -type PSII-LHCII supercomplex from C. reinhardtii at 3.37-Å resolution. The results show that the Cr-C 2 S 2 M 2 N 2 supercomplex is organized as a dimer, with 3 LHCII trimers, 1 CP26, and 1 CP29 peripheral antenna subunits surrounding each PSII core. The N-LHCII trimer partially occupies the position of CP24, which is present in the higher-plant PSII-LHCII but absent in the green alga. The M trimer is rotated relative to the corresponding M trimer in plant PSII-LHCII. In addition, some unique features were found in the green algal PSII core. The arrangement of a huge number of pigments allowed us to deduce possible energy transfer pathways from the peripheral antennae to the PSII core.


  • Organizational Affiliation
    • Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 1,662.09 kDa 
  • Atom Count: 104,363 
  • Modeled Residue Count: 9,607 
  • Deposited Residue Count: 11,214 
  • Unique protein chains: 21

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein CP29A [auth r],
VA [auth R]
280Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93WD2 (Chlamydomonas reinhardtii)
Explore Q93WD2 
Go to UniProtKB:  Q93WD2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WD2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1B [auth a],
Q [auth A]
352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P07753 (Chlamydomonas reinhardtii)
Explore P07753 
Go to UniProtKB:  P07753
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07753
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinAB [auth D],
C [auth d]
352Chlamydomonas reinhardtiiMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
Find proteins for P06007 (Chlamydomonas reinhardtii)
Explore P06007 
Go to UniProtKB:  P06007
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06007
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaD [auth f],
S [auth F]
44Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q08363 (Chlamydomonas reinhardtii)
Explore Q08363 
Go to UniProtKB:  Q08363
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08363
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HE [auth h],
T [auth H]
88Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P22666 (Chlamydomonas reinhardtii)
Explore P22666 
Go to UniProtKB:  P22666
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22666
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IF [auth i],
U [auth I]
37Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P59763 (Chlamydomonas reinhardtii)
Explore P59763 
Go to UniProtKB:  P59763
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59763
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein J, PsbJG [auth j],
V [auth J]
50Chlamydomonas reinhardtiiMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KH [auth k],
W [auth K]
46Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P18263 (Chlamydomonas reinhardtii)
Explore P18263 
Go to UniProtKB:  P18263
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18263
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LI [auth l],
X [auth L]
38Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P32974 (Chlamydomonas reinhardtii)
Explore P32974 
Go to UniProtKB:  P32974
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32974
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MJ [auth m],
Y [auth M]
34Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92277 (Chlamydomonas reinhardtii)
Explore P92277 
Go to UniProtKB:  P92277
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92277
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1 of photosystem IIK [auth o],
ZA [auth O]
291Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8J0E4 (Chlamydomonas reinhardtii)
Explore A8J0E4 
Go to UniProtKB:  A8J0E4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8J0E4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TL [auth t],
Z [auth T]
31Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37256 (Chlamydomonas reinhardtii)
Explore P37256 
Go to UniProtKB:  P37256
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37256
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W protein, chloroplasticAA [auth W],
M [auth w]
115Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SPI9 (Chlamydomonas reinhardtii)
Explore Q9SPI9 
Go to UniProtKB:  Q9SPI9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9SPI9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
4.1 kDa photosystem II subunitBB [auth X],
N [auth x]
101Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A8I846 (Chlamydomonas reinhardtii)
Explore A8I846 
Go to UniProtKB:  A8I846
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8I846
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZBA [auth Z],
O [auth z]
62Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P92276 (Chlamydomonas reinhardtii)
Explore P92276 
Go to UniProtKB:  P92276
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP92276
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein 30, Psb30CA [auth y],
P [auth Y]
33Chlamydomonas reinhardtiiMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaDB [auth e],
R [auth E]
82Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P48268 (Chlamydomonas reinhardtii)
Explore P48268 
Go to UniProtKB:  P48268
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48268
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic257Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93WL4 (Chlamydomonas reinhardtii)
Explore Q93WL4 
Go to UniProtKB:  Q93WL4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WL4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticFB [auth s],
WA [auth S]
289Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q9FEK6 (Chlamydomonas reinhardtii)
Explore Q9FEK6 
Go to UniProtKB:  Q9FEK6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FEK6
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinEB [auth c],
XA [auth C]
461Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P10898 (Chlamydomonas reinhardtii)
Explore P10898 
Go to UniProtKB:  P10898
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10898
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinCB [auth b],
YA [auth B]
508Chlamydomonas reinhardtiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P37255 (Chlamydomonas reinhardtii)
Explore P37255 
Go to UniProtKB:  P37255
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37255
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
LS [auth C]
MS [auth C]
OC [auth a]
OV [auth c]
PV [auth c]
LS [auth C],
MS [auth C],
OC [auth a],
OV [auth c],
PV [auth c],
QV [auth c],
RS [auth B],
SD [auth A],
UD [auth J],
ZT [auth b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
AG [auth 3]
AI [auth 6]
AK [auth q]
AR [auth R]
BG [auth 3]
AG [auth 3],
AI [auth 6],
AK [auth q],
AR [auth R],
BG [auth 3],
BI [auth 6],
BK [auth q],
BM [auth Q],
BR [auth R],
CI [auth 6],
CK [auth q],
CM [auth Q],
CO [auth G],
DK [auth q],
DM [auth Q],
DO [auth G],
EK [auth q],
EM [auth Q],
EO [auth G],
FF [auth 2],
FH [auth 5],
FM [auth Q],
FO [auth G],
FQ [auth g],
GF [auth 2],
GH [auth 5],
GM [auth Q],
GO [auth G],
GQ [auth g],
HF [auth 2],
HH [auth 5],
HO [auth G],
HQ [auth g],
HW [auth s],
IF [auth 2],
IH [auth 5],
IQ [auth g],
IW [auth s],
JF [auth 2],
JH [auth 5],
JJ [auth p],
JQ [auth g],
JW [auth s],
KF [auth 2],
KH [auth 5],
KJ [auth p],
KQ [auth g],
KW [auth s],
LJ [auth p],
LL [auth P],
MH [auth 6],
MJ [auth p],
ML [auth P],
MN [auth N],
NE [auth 1],
NJ [auth p],
NL [auth P],
NN [auth N],
OE [auth 1],
OG [auth 4],
OJ [auth p],
OL [auth P],
ON [auth N],
OP [auth n],
OR [auth S],
PE [auth 1],
PG [auth 4],
PI [auth v],
PJ [auth p],
PL [auth P],
PN [auth N],
PP [auth n],
PR [auth S],
QE [auth 1],
QG [auth 4],
QI [auth v],
QL [auth P],
QN [auth N],
QP [auth n],
QR [auth S],
RE [auth 1],
RG [auth 4],
RI [auth v],
RK [auth V],
RP [auth n],
RR [auth S],
SE [auth 1],
SG [auth 4],
SI [auth v],
SK [auth V],
SP [auth n],
TB [auth r],
TI [auth v],
TK [auth V],
TM [auth U],
TP [auth n],
UB [auth r],
UI [auth v],
UK [auth V],
UM [auth U],
UO [auth u],
VB [auth r],
VK [auth V],
VM [auth U],
VO [auth u],
WF [auth 3],
WK [auth V],
WM [auth U],
WO [auth u],
XF [auth 3],
XH [auth 6],
XM [auth U],
XO [auth u],
YB [auth r],
YF [auth 3],
YH [auth 6],
YO [auth u],
ZF [auth 3],
ZH [auth 6],
ZM [auth U],
ZO [auth u],
ZQ [auth R]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AF [auth 2]
AH [auth 5]
AJ [auth p]
AL [auth P]
AN [auth N]
AF [auth 2],
AH [auth 5],
AJ [auth p],
AL [auth P],
AN [auth N],
AQ [auth g],
AS [auth C],
AT [auth B],
AU [auth b],
AV [auth c],
AW [auth s],
BE [auth 1],
BJ [auth p],
BL [auth P],
BN [auth N],
BQ [auth g],
BS [auth C],
BT [auth B],
BU [auth b],
BV [auth c],
BW [auth s],
CC [auth a],
CD [auth x],
CE [auth 1],
CG [auth 4],
CJ [auth p],
CL [auth P],
CN [auth N],
CP [auth n],
CQ [auth g],
CR [auth S],
CS [auth C],
CT [auth B],
CU [auth b],
CV [auth c],
CW [auth s],
DC [auth a],
DE [auth 1],
DG [auth 4],
DI [auth v],
DJ [auth p],
DL [auth P],
DN [auth N],
DP [auth n],
DR [auth S],
DS [auth C],
DT [auth B],
DU [auth b],
DV [auth c],
DW [auth s],
EC [auth a],
EE [auth 1],
EG [auth 4],
EI [auth v],
EJ [auth p],
EL [auth P],
EN [auth N],
EP [auth n],
ER [auth S],
ES [auth C],
ET [auth B],
EU [auth b],
EV [auth c],
FE [auth 1],
FG [auth 4],
FI [auth v],
FK [auth V],
FL [auth P],
FN [auth N],
FP [auth n],
FR [auth S],
FS [auth C],
FT [auth B],
FU [auth b],
FV [auth c],
GB [auth r],
GC [auth a],
GE [auth 1],
GG [auth 4],
GI [auth v],
GK [auth V],
GL [auth P],
GN [auth N],
GP [auth n],
GR [auth S],
GS [auth C],
GT [auth B],
GU [auth b],
GV [auth c],
HB [auth r],
HE [auth 1],
HG [auth 4],
HI [auth v],
HK [auth V],
HM [auth U],
HN [auth N],
HP [auth n],
HR [auth S],
HS [auth C],
HT [auth B],
HU [auth b],
HV [auth c],
IB [auth r],
ID [auth A],
IE [auth 1],
IG [auth 4],
II [auth v],
IK [auth V],
IM [auth U],
IO [auth u],
IP [auth n],
IR [auth S],
IU [auth b],
IV [auth c],
JB [auth r],
JD [auth A],
JG [auth 4],
JI [auth v],
JK [auth V],
JM [auth U],
JO [auth u],
JP [auth n],
JR [auth S],
JU [auth b],
JV [auth c],
KB [auth r],
KD [auth A],
KI [auth v],
KK [auth V],
KM [auth U],
KO [auth u],
KR [auth S],
KU [auth b],
KV [auth c],
LB [auth r],
LK [auth V],
LM [auth U],
LO [auth u],
LU [auth b],
LV [auth c],
MB [auth r],
MD [auth A],
MF [auth 3],
MK [auth V],
MM [auth U],
MO [auth u],
MQ [auth R],
MU [auth b],
NB [auth r],
NF [auth 3],
NH [auth 6],
NM [auth U],
NO [auth u],
NQ [auth R],
NU [auth b],
OB [auth r],
OF [auth 3],
OH [auth 6],
OM [auth U],
OO [auth u],
OQ [auth R],
OU [auth b],
PB [auth r],
PF [auth 3],
PH [auth 6],
PO [auth u],
PQ [auth R],
PU [auth b],
QC [auth d],
QF [auth 3],
QH [auth 6],
QJ [auth q],
QQ [auth R],
RF [auth 3],
RH [auth 6],
RJ [auth q],
RL [auth Q],
RQ [auth R],
RT [auth D],
SF [auth 3],
SH [auth 6],
SJ [auth q],
SL [auth Q],
SN [auth G],
SQ [auth R],
SS [auth B],
TE [auth 2],
TF [auth 3],
TG [auth 5],
TH [auth 6],
TJ [auth q],
TL [auth Q],
TN [auth G],
TQ [auth R],
TS [auth B],
UE [auth 2],
UG [auth 5],
UH [auth 6],
UJ [auth q],
UL [auth Q],
UN [auth G],
UQ [auth R],
US [auth B],
VE [auth 2],
VG [auth 5],
VJ [auth q],
VL [auth Q],
VN [auth G],
VP [auth g],
VQ [auth R],
VR [auth C],
VS [auth B],
VV [auth s],
WE [auth 2],
WG [auth 5],
WJ [auth q],
WL [auth Q],
WN [auth G],
WP [auth g],
WR [auth C],
WS [auth B],
WV [auth s],
XE [auth 2],
XG [auth 5],
XI [auth p],
XJ [auth q],
XL [auth Q],
XN [auth G],
XP [auth g],
XR [auth C],
XS [auth B],
XV [auth s],
YE [auth 2],
YG [auth 5],
YI [auth p],
YL [auth Q],
YN [auth G],
YP [auth g],
YR [auth C],
YS [auth B],
YT [auth X],
YV [auth s],
ZE [auth 2],
ZG [auth 5],
ZI [auth p],
ZK [auth P],
ZN [auth G],
ZP [auth g],
ZR [auth C],
ZS [auth B],
ZU [auth c],
ZV [auth s]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
(Subject of Investigation/LOI)

Query on PHO



Download:Ideal Coordinates CCD File
FC [auth a],
LD [auth A],
PC [auth d],
PT [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
IC [auth a]
LC [auth a]
QD [auth A]
TR [auth C]
XD [auth L]
IC [auth a],
LC [auth a],
QD [auth A],
TR [auth C],
XD [auth L],
YC [auth l],
YD [auth M],
ZC [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
AE [auth W]
BD [auth w]
KC [auth a]
LT [auth B]
NS [auth C]
AE [auth W],
BD [auth w],
KC [auth a],
LT [auth B],
NS [auth C],
OT [auth B],
PD [auth A],
RV [auth c],
TU [auth b],
UR [auth C],
VC [auth d],
WT [auth D],
WU [auth b],
YU [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
JC [auth a],
OD [auth A],
SC [auth d],
TT [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
AM [auth Q]
BO [auth G]
EF [auth 2]
EH [auth 5]
EQ [auth g]
AM [auth Q],
BO [auth G],
EF [auth 2],
EH [auth 5],
EQ [auth g],
GW [auth s],
IJ [auth p],
KL [auth P],
LN [auth N],
ME [auth 1],
MT [auth B],
NC [auth a],
NG [auth 4],
NP [auth n],
NR [auth S],
NT [auth B],
OI [auth v],
OS [auth C],
PS [auth C],
QK [auth V],
QS [auth C],
RD [auth A],
SB [auth r],
SM [auth U],
SV [auth c],
TC [auth d],
TO [auth u],
TV [auth c],
UC [auth d],
UT [auth D],
UU [auth b],
UV [auth c],
VF [auth 3],
VT [auth D],
VU [auth b],
WD [auth L],
WH [auth 6],
XC [auth l],
YQ [auth R],
ZJ [auth q]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
TD [auth E],
XU [auth e]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NEX

Query on NEX



Download:Ideal Coordinates CCD File
AP [auth u]
BP [auth u]
LF [auth 2]
LH [auth 5]
LQ [auth R]
AP [auth u],
BP [auth u],
LF [auth 2],
LH [auth 5],
LQ [auth R],
LW [auth s],
RN [auth N],
SR [auth S],
UP [auth n],
VI [auth v],
WB [auth r],
WI [auth p],
XB [auth r],
XK [auth V],
YK [auth P],
YM [auth U]
(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
XAT

Query on XAT



Download:Ideal Coordinates CCD File
AO [auth G]
DF [auth 2]
DH [auth 5]
DQ [auth g]
HJ [auth p]
AO [auth G],
DF [auth 2],
DH [auth 5],
DQ [auth g],
HJ [auth p],
JL [auth P],
KN [auth N],
LE [auth 1],
MG [auth 4],
MP [auth n],
NI [auth v],
PK [auth V],
RB [auth r],
RM [auth U],
SO [auth u],
UF [auth 3],
VH [auth 6],
XQ [auth R],
YJ [auth q],
ZL [auth Q]
(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
LUT

Query on LUT



Download:Ideal Coordinates CCD File
BF [auth 2]
BH [auth 5]
CF [auth 2]
CH [auth 5]
EW [auth s]
BF [auth 2],
BH [auth 5],
CF [auth 2],
CH [auth 5],
EW [auth s],
FJ [auth p],
FW [auth s],
GJ [auth p],
HL [auth P],
IL [auth P],
IN [auth N],
JE [auth 1],
JN [auth N],
KE [auth 1],
KG [auth 4],
KP [auth n],
LG [auth 4],
LI [auth v],
LP [auth n],
LR [auth S],
MI [auth v],
MR [auth S],
NK [auth V],
OK [auth V],
PM [auth U],
QB [auth r],
QM [auth U],
QO [auth u],
RO [auth u],
WQ [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
AD [auth t]
DD [auth x]
ED [auth z]
HC [auth a]
IS [auth C]
AD [auth t],
DD [auth x],
ED [auth z],
HC [auth a],
IS [auth C],
IT [auth B],
JS [auth C],
JT [auth B],
KS [auth C],
KT [auth B],
MV [auth c],
ND [auth A],
NV [auth c],
QU [auth b],
RC [auth d],
RU [auth b],
ST [auth D],
SU [auth b],
VD [auth K],
WC [auth k],
XT [auth X],
ZD [auth T]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
MC [auth a],
QT [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
FD [auth A],
ZB [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AC [auth a],
BC [auth a],
GD [auth A],
HD [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDY-SSW-SMC003
Chinese Academy of SciencesChinaXDB17000000
National Basic Research Program of China (973 Program)China2015CB150100

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Derived calculations
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Non-polymer description, Structure summary
  • Version 2.1: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations