6J40 | pdb_00006j40

Structure of C2S2M2-type PSII-FCPII supercomplex from diatom

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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This is version 2.1 of the entry. See complete history. 


Literature

Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.

Nagao, R., Kato, K., Suzuki, T., Ifuku, K., Uchiyama, I., Kashino, Y., Dohmae, N., Akimoto, S., Shen, J.R., Miyazaki, N., Akita, F.

(2019) Nat Plants 5: 890-901

  • DOI: https://doi.org/10.1038/s41477-019-0477-x
  • Primary Citation of Related Structures:  
    6J3Y, 6J3Z, 6J40

  • PubMed Abstract: 

    Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.

    • Organizational Affiliation: 
    • Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D1A,
Y [auth a]		344Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP47B,
Z [auth b]		509Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II chlorophyll protein CP43AA [auth c],
C		471Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein D2BA [auth d],
D		351Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaCA [auth e],
E		84Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaDA [auth f],
F		43Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HEA [auth h],
G [auth H]		67Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IFA [auth i],
H [auth I]		38Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JGA [auth j],
I [auth J]		39Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KHA [auth k],
J [auth K]		44Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LIA [auth l],
K [auth L]		38Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MJA [auth m],
L [auth M]		131Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIKA [auth o],
M [auth O]		248Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TLA [auth t],
N [auth T]		31Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIMA [auth u],
O [auth U]		93Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550NA [auth v],
P [auth V]		137Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12OA [auth y],
Q [auth Y]		34Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinPA [auth x],
R [auth X]		38Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZQA [auth z],
S [auth Z]		61Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Extrinsic protein in photosystem IIRA [auth q],
T [auth Q]		155Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein WSA [auth w],
U [auth W]		72Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 0TA [auth 5],
V [auth 0]		31Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 1UA [auth 6],
W [auth 1]		30Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown protein 2VA [auth 7],
X [auth 2]		10Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1207Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein monomer 1EB [auth 19],
PB [auth 39]		215Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein monomer 2FB [auth 20],
QB [auth 40]		143Chaetoceros neogracilisMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein monomer 3GB [auth 21],
RB [auth 41]		155Chaetoceros neogracilisMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
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FE [auth H]
GE [auth J]
KH [auth h]
LH [auth j]
OD [auth C]
FE [auth H],
GE [auth J],
KH [auth h],
LH [auth j],
OD [auth C],
PD [auth C],
PG [auth c],
QG [auth c]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
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AD [auth C]
AG [auth c]
AI [auth 11]
AK [auth 14]
AL [auth 16]
AD [auth C],
AG [auth c],
AI [auth 11],
AK [auth 14],
AL [auth 16],
AP [auth 32],
AR [auth 35],
AS [auth 37],
AT [auth 39],
AU [auth 41],
BC [auth B],
BD [auth C],
BG [auth c],
BI [auth 11],
BK [auth 14],
BL [auth 16],
BP [auth 32],
BS [auth 37],
BT [auth 39],
BU [auth 41],
CC [auth B],
CD [auth C],
CF [auth b],
CG [auth c],
CH [auth d],
CI [auth 11],
CK [auth 14],
CL [auth 16],
CP [auth 32],
CS [auth 37],
CT [auth 39],
CU [auth 41],
DC [auth B],
DD [auth C],
DF [auth b],
DG [auth c],
DH [auth d],
DI [auth 11],
DK [auth 14],
DL [auth 16],
DM [auth 18],
DP [auth 32],
DS [auth 37],
DT [auth 39],
DU [auth 41],
EC [auth B],
ED [auth C],
EF [auth b],
EG [auth c],
EI [auth 11],
EK [auth 14],
EL [auth 16],
EN [auth 20],
EO [auth 31],
EP [auth 32],
EQ [auth 34],
ES [auth 37],
ET [auth 39],
EU [auth 41],
FC [auth B],
FD [auth C],
FF [auth b],
FG [auth c],
FK [auth 14],
FL [auth 16],
FM [auth 18],
FN [auth 20],
FO [auth 31],
FP [auth 32],
FQ [auth 34],
FT [auth 39],
FU [auth 41],
GC [auth B],
GD [auth C],
GF [auth b],
GG [auth c],
GJ [auth 13],
GL [auth 16],
GM [auth 18],
GN [auth 20],
GO [auth 31],
GP [auth 32],
GQ [auth 34],
GT [auth 39],
GU [auth 41],
HC [auth B],
HD [auth C],
HF [auth b],
HG [auth c],
HJ [auth 13],
HL [auth 16],
HM [auth 18],
HN [auth 20],
HO [auth 31],
HQ [auth 34],
HT [auth 39],
IC [auth B],
ID [auth C],
IF [auth b],
IG [auth c],
IJ [auth 13],
IL [auth 16],
IM [auth 18],
IN [auth 20],
IO [auth 31],
IQ [auth 34],
IR [auth 36],
JC [auth B],
JD [auth C],
JF [auth b],
JG [auth c],
JJ [auth 13],
JM [auth 18],
JN [auth 20],
JO [auth 31],
JQ [auth 34],
JR [auth 36],
KC [auth B],
KD [auth C],
KE [auth M],
KF [auth b],
KG [auth c],
KI [auth 11],
KJ [auth 13],
KK [auth 15],
KM [auth 18],
KN [auth 20],
KO [auth 31],
KQ [auth 34],
KR [auth 36],
LC [auth B],
LD [auth C],
LF [auth b],
LG [auth c],
LJ [auth 13],
LK [auth 15],
LM [auth 18],
LN [auth 20],
LO [auth 31],
LQ [auth 34],
LR [auth 36],
LS [auth 38],
MC [auth B],
MD [auth C],
MF [auth b],
MG [auth c],
MJ [auth 13],
MK [auth 15],
MM [auth 18],
MO [auth 31],
MQ [auth 34],
MR [auth 36],
MT [auth 40],
NC [auth B],
NF [auth b],
NJ [auth 13],
NK [auth 15],
NL [auth 17],
NM [auth 18],
NP [auth 33],
NQ [auth 34],
NR [auth 36],
NS [auth 38],
NT [auth 40],
OC [auth B],
OF [auth b],
OH [auth m],
OI [auth 12],
OJ [auth 13],
OK [auth 15],
OM [auth 18],
OR [auth 36],
OS [auth 38],
OT [auth 40],
PC [auth B],
PE [auth Z],
PF [auth b],
PK [auth 15],
PL [auth 17],
PP [auth 33],
PR [auth 36],
PS [auth 38],
PT [auth 40],
QF [auth b],
QI [auth 12],
QK [auth 15],
QL [auth 17],
QN [auth 21],
QP [auth 33],
QR [auth 36],
QS [auth 38],
QT [auth 40],
RD [auth C],
RI [auth 12],
RK [auth 15],
RL [auth 17],
RN [auth 21],
RP [auth 33],
RS [auth 38],
RT [auth 40],
SD [auth C],
SE [auth W],
SH [auth z],
SI [auth 12],
SK [auth 15],
SL [auth 17],
SM [auth 19],
SN [auth 21],
SO [auth 31],
SP [auth 33],
SQ [auth 35],
SS [auth 38],
ST [auth 40],
TB [auth A],
TD [auth C],
TE [auth W],
TI [auth 12],
TL [auth 17],
TM [auth 19],
TN [auth 21],
TP [auth 33],
TQ [auth 35],
TS [auth 38],
TT [auth 40],
UD [auth D],
UG [auth c],
UH [auth w],
UI [auth 12],
UL [auth 17],
UM [auth 19],
UN [auth 21],
UP [auth 33],
UQ [auth 35],
US [auth 38],
VB [auth A],
VD [auth D],
VE [auth a],
VG [auth c],
VH [auth w],
VI [auth 12],
VL [auth 17],
VM [auth 19],
VN [auth 21],
VP [auth 33],
VQ [auth 35],
VR [auth 37],
VS [auth 38],
WE [auth a],
WG [auth c],
WH [auth 11],
WI [auth 12],
WJ [auth 14],
WL [auth 17],
WM [auth 19],
WN [auth 21],
WO [auth 32],
WP [auth 33],
WQ [auth 35],
WS [auth 38],
XC [auth B],
XF [auth b],
XG [auth d],
XH [auth 11],
XI [auth 12],
XJ [auth 14],
XM [auth 19],
XN [auth 21],
XP [auth 33],
XQ [auth 35],
XR [auth 37],
YD [auth D],
YG [auth d],
YH [auth 11],
YI [auth 12],
YJ [auth 14],
YM [auth 19],
YN [auth 21],
YO [auth 32],
YQ [auth 35],
YR [auth 37],
YT [auth 41],
ZD [auth D],
ZH [auth 11],
ZI [auth 12],
ZJ [auth 14],
ZM [auth 19],
ZO [auth 32],
ZQ [auth 35],
ZR [auth 37],
ZT [auth 41]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
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AH [auth d],
UB [auth A],
WD [auth D],
ZG [auth d]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
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JE [auth L]
MH [auth l]
VC [auth B]
VF [auth b]
XB [auth A]
JE [auth L],
MH [auth l],
VC [auth B],
VF [auth b],
XB [auth A],
YE [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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BE [auth D]
GH [auth d]
LE [auth M]
MI [auth 12]
PH [auth m]
BE [auth D],
GH [auth d],
LE [auth M],
MI [auth 12],
PH [auth m],
QE [auth Q],
RE [auth W],
RG [auth c],
TC [auth B],
TF [auth b],
TH [auth w],
UC [auth B],
UF [auth b],
UO [auth 32]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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AE [auth D],
BH [auth d],
EH [auth d],
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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AF [auth a]
FH [auth d]
HE [auth L]
IE [auth L]
NH [auth l]
AF [auth a],
FH [auth d],
HE [auth L],
IE [auth L],
NH [auth l],
WC [auth B],
WF [auth b],
ZB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86
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AJ [auth 12]
AM [auth 17]
AN [auth 19]
AO [auth 21]
AQ [auth 33]
AJ [auth 12],
AM [auth 17],
AN [auth 19],
AO [auth 21],
AQ [auth 33],
BJ [auth 12],
BM [auth 17],
BN [auth 19],
BO [auth 21],
BQ [auth 33],
BR [auth 35],
CJ [auth 12],
CM [auth 17],
CN [auth 19],
CO [auth 21],
CQ [auth 33],
CR [auth 35],
DJ [auth 12],
DN [auth 20],
DO [auth 21],
DQ [auth 33],
DR [auth 35],
EJ [auth 12],
EM [auth 18],
ER [auth 35],
FI [auth 11],
FJ [auth 13],
FR [auth 35],
FS [auth 37],
GI [auth 11],
GK [auth 14],
GR [auth 35],
GS [auth 37],
HI [auth 11],
HK [auth 14],
HP [auth 32],
HR [auth 35],
HS [auth 37],
HU [auth 41],
II [auth 11],
IK [auth 14],
IP [auth 32],
IS [auth 37],
IT [auth 39],
IU [auth 41],
JI [auth 11],
JK [auth 14],
JL [auth 16],
JP [auth 32],
JS [auth 37],
JT [auth 39],
JU [auth 41],
KL [auth 16],
KP [auth 32],
KS [auth 37],
KT [auth 39],
KU [auth 41],
LI [auth 11],
LL [auth 16],
LP [auth 32],
LT [auth 40],
LU [auth 41],
ML [auth 16],
MN [auth 20],
MP [auth 32],
MS [auth 38],
NN [auth 20],
NO [auth 31],
OL [auth 17],
ON [auth 20],
OO [auth 31],
OP [auth 33],
OQ [auth 34],
PI [auth 12],
PJ [auth 13],
PM [auth 18],
PN [auth 20],
PO [auth 31],
PQ [auth 34],
QJ [auth 13],
QM [auth 18],
QO [auth 31],
QQ [auth 34],
RJ [auth 13],
RM [auth 18],
RO [auth 31],
RQ [auth 34],
RR [auth 36],
SJ [auth 13],
SR [auth 36],
TJ [auth 13],
TK [auth 15],
TO [auth 31],
TR [auth 36],
UJ [auth 13],
UK [auth 15],
UR [auth 36],
UT [auth 40],
VJ [auth 13],
VK [auth 15],
VT [auth 40],
WK [auth 15],
WR [auth 37],
WT [auth 40],
XK [auth 15],
XL [auth 17],
XO [auth 32],
XS [auth 38],
XT [auth 40],
YK [auth 15],
YL [auth 17],
YP [auth 33],
YS [auth 38],
ZK [auth 15],
ZL [auth 17],
ZN [auth 21],
ZP [auth 33],
ZS [auth 38]
(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
Query on HEM
Download Ideal Coordinates CCD File 
CE [auth E],
HH [auth e],
ME [auth V],
RH [auth v]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
Download Ideal Coordinates CCD File 
AC [auth A]
BF [auth a]
DE [auth F]
EE [auth H]
IH [auth f]
AC [auth A],
BF [auth a],
DE [auth F],
EE [auth H],
IH [auth f],
JH [auth h],
ND [auth C],
NE [auth Y],
NG [auth c],
OE [auth Z],
OG [auth c],
QC [auth B],
QD [auth C],
QH [auth m],
RC [auth B],
RF [auth b],
SC [auth B],
SF [auth b],
SG [auth c],
TG [auth c],
WB [auth A],
XE [auth a],
YC [auth B],
YF [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU
Download Ideal Coordinates CCD File 
NI [auth 12],
VO [auth 32]		DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX
Query on OEX
Download Ideal Coordinates CCD File 
ZC [auth C],
ZF [auth c]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT
Download Ideal Coordinates CCD File 
YB [auth A],
ZE [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
Download Ideal Coordinates CCD File 
SB [auth A],
UE [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-07
    Type: Initial release
  • Version 1.1: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-06
    Changes: Data collection, Other
  • Version 2.0: 2025-04-09
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2025-09-17
    Changes: Advisory, Data collection, Derived calculations, Structure summary