8BD3 | pdb_00008bd3

Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.1 of the entry. See complete history. 

Literature

Structure of Chlorella ohadii Photosystem II Reveals Protective Mechanisms against Environmental Stress.

Fadeeva, M., Klaiman, D., Caspy, I., Nelson, N.

(2023) Cells 12

  • DOI: https://doi.org/10.3390/cells12151971
  • Primary Citation Related Structures: 
    8BD3

  • PubMed Abstract: 

    Green alga Chlorella ohadii is known for its ability to carry out photosynthesis under harsh conditions. Using cryogenic electron microscopy (cryoEM), we obtained a high-resolution structure of PSII at 2.72 Å. This structure revealed 64 subunits, which encompassed 386 chlorophylls, 86 carotenoids, four plastoquinones, and several structural lipids. At the luminal side of PSII, a unique subunit arrangement was observed to protect the oxygen-evolving complex. This arrangement involved PsbO (OEE1), PsbP (OEE2), PsbB, and PsbU (a homolog of plant OEE3). PsbU interacted with PsbO, PsbC, and PsbP, thereby stabilizing the shield of the oxygen-evolving complex. Significant changes were also observed at the stromal electron acceptor side. PsbY, identified as a transmembrane helix, was situated alongside PsbF and PsbE, which enclosed cytochrome b559 . Supported by the adjacent C-terminal helix of Psb10, these four transmembrane helices formed a bundle that shielded cytochrome b559 from the surrounding solvent. Moreover, the bulk of Psb10 formed a protective cap, which safeguarded the quinone site and likely contributed to the stacking of PSII complexes. Based on our findings, we propose a protective mechanism that prevents Q B (plastoquinone B) from becoming fully reduced. This mechanism offers insights into the regulation of electron transfer within PSII.

    • Organizational Affiliation: 
    • Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.

Macromolecule Content 

  • Total Structure Weight: 1,723.57 kDa 
  • Atom Count: 117,990 
  • Modeled Residue Count: 10,854 
  • Deposited Residue Count: 10,854 
  • Unique protein chains: 29

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1],
FA [auth 7]		214Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic222Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding of LHCII221Chlorella ohadiiMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding of LHCIIEA [auth 0],
F [auth 6]		217Chlorella ohadiiMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1G [auth A],
KA [auth a]		336Chlorella ohadiiMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinH [auth B],
LA [auth b]		504Chlorella ohadiiMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinI [auth C],
MA [auth c]		448Chlorella ohadiiMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinJ [auth D],
NA [auth d]		342Chlorella ohadiiMutation(s): 0 
EC: 1.10.3.9
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaK [auth E],
OA [auth e]		81Chlorella ohadiiMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaL [auth F],
PA [auth f]		37Chlorella ohadiiMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HN [auth H],
RA [auth h]		67Chlorella ohadiiMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IO [auth I],
SA [auth i]		34Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JP [auth J],
TA [auth j]		38Chlorella ohadiiMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KQ [auth K],
UA [auth k]		37Chlorella ohadiiMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LR [auth L],
VA [auth l]		37Chlorella ohadiiMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MS [auth M],
WA [auth m]		57Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chloroplast oxygen-evolving enhancer protein 1U [auth O],
YA [auth o]		240Chlorella ohadiiMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a b binding CP29V [auth R],
ZA [auth r]		236Chlorella ohadiiMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a b-binding CP26AB [auth s],
W [auth S]		257Chlorella ohadiiMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBB [auth t],
X [auth T]		30Chlorella ohadiiMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12CB [auth v],
Y [auth V]		32Chlorella ohadiiMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center W proteinDB [auth w],
Z [auth W]		60Chlorella ohadiiMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XAA [auth X],
EB [auth x]		37Chlorella ohadiiMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Multifunctional fusion proteinBA [auth Y],
FB [auth y]		221Chlorella ohadiiMutation(s): 0 
EC: 2.7.1.107
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZCA [auth Z],
GB [auth z]		62Chlorella ohadiiMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
Chloroplast oxygen-evolving enhancer protein 3DA [auth U],
HB [auth u]		144Chlorella ohadiiMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
Chloroplast PsbYIB [auth Q1],
KB [auth q1]		34Chlorella ohadiiMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
Chloroplast photosystem II 10 kDa proteinJB [auth P1],
LB [auth p1]		108Chlorella ohadiiMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II oxygen evolving enhancer 2MB [auth F1],
NB [auth f1]		188Chlorella ohadiiMutation(s): 0 

Small Molecules

Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


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LV [auth c]
MV [auth c]
NV [auth c]
OV [auth c]
PI [auth C]
LV [auth c],
MV [auth c],
NV [auth c],
OV [auth c],
PI [auth C],
QI [auth C],
RI [auth C],
TI [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL


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AF [auth 5]
AL [auth N]
AQ [auth 8]
AR [auth 9]
BE [auth 4]
AF [auth 5],
AL [auth N],
AQ [auth 8],
AR [auth 9],
BE [auth 4],
BR [auth 9],
CE [auth 4],
CR [auth 9],
DD [auth 3],
DE [auth 4],
ED [auth 3],
EE [auth 4],
EQ [auth 8],
FE [auth 4],
FP [auth 7],
FQ [auth 8],
FZ [auth s],
GC [auth 1],
GQ [auth 8],
HC [auth 2],
HK [auth G],
HQ [auth 8],
ID [auth 3],
IO [auth 0],
JD [auth 3],
JP [auth 7],
JW [auth g],
KAA [auth y],
KD [auth 3],
KM [auth S],
KP [auth 7],
KS [auth q],
KZ [auth s],
LC [auth 2],
LD [auth 3],
LJ [auth G],
LP [auth 7],
LZ [auth s],
MC [auth 2],
MO [auth 0],
MP [auth 7],
MX [auth n],
MZ [auth s],
NC [auth 2],
NF [auth 6],
NN [auth Y],
NO [auth 0],
NP [auth 7],
NW [auth g],
NX [auth n],
OAA [auth y],
OB [auth 1],
OC [auth 2],
ON [auth Y],
OO [auth 0],
OR [auth p],
OS [auth q],
OW [auth g],
PAA [auth y],
PJ [auth G],
PM [auth S],
PO [auth 0],
PS [auth q],
PW [auth g],
PY [auth r],
QAA [auth y],
QJ [auth G],
QM [auth S],
QO [auth 0],
QS [auth q],
QW [auth g],
QY [auth r],
RAA [auth y],
RF [auth 6],
RJ [auth G],
RM [auth S],
RS [auth q],
RX [auth n],
RY [auth r],
SAA [auth y],
SB [auth 1],
SE [auth 5],
SF [auth 6],
SJ [auth G],
SK [auth N],
SN [auth Y],
SR [auth p],
SS [auth q],
SX [auth n],
TB [auth 1],
TF [auth 6],
TK [auth N],
TN [auth Y],
TR [auth p],
TX [auth n],
UB [auth 1],
UF [auth 6],
UL [auth R],
UN [auth Y],
UQ [auth 9],
UR [auth p],
UX [auth n],
VB [auth 1],
VF [auth 6],
VL [auth R],
VN [auth Y],
VR [auth p],
VX [auth n],
WB [auth 1],
WE [auth 5],
WL [auth R],
WR [auth p],
XD [auth 4],
XE [auth 5],
XK [auth N],
YE [auth 5],
YK [auth N],
YP [auth 7],
YQ [auth 9],
ZE [auth 5],
ZK [auth N],
ZQ [auth 9]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

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AC [auth 1]
AE [auth 4]
AG [auth 6]
AI [auth C]
AJ [auth D]
AC [auth 1],
AE [auth 4],
AG [auth 6],
AI [auth C],
AJ [auth D],
AM [auth R],
AO [auth Y],
AS [auth p],
AU [auth b],
AV [auth c],
AY [auth n],
BC [auth 1],
BF [auth 5],
BG [auth 6],
BH [auth B],
BI [auth C],
BJ [auth D],
BL [auth N],
BM [auth R],
BQ [auth 8],
BS [auth p],
BU [auth b],
BV [auth c],
BY [auth n],
CD [auth 3],
CF [auth 5],
CH [auth B],
CI [auth C],
CL [auth N],
CM [auth R],
CQ [auth 8],
CS [auth p],
CU [auth b],
CV [auth c],
DF [auth 5],
DH [auth B],
DI [auth C],
DL [auth N],
DQ [auth 8],
DR [auth 9],
DU [auth b],
DV [auth c],
EF [auth 5],
EH [auth B],
EI [auth C],
EL [auth N],
ER [auth 9],
EU [auth b],
EV [auth c],
FD [auth 3],
FF [auth 5],
FH [auth B],
FI [auth C],
FL [auth N],
FR [auth 9],
FU [auth b],
FV [auth c],
GD [auth 3],
GE [auth 4],
GF [auth 5],
GH [auth B],
GI [auth C],
GL [auth N],
GP [auth 7],
GR [auth 9],
GU [auth b],
GV [auth c],
GZ [auth s],
HD [auth 3],
HE [auth 4],
HH [auth B],
HI [auth C],
HP [auth 7],
HR [auth 9],
HU [auth b],
HV [auth c],
HZ [auth s],
IC [auth 2],
IE [auth 4],
IH [auth B],
II [auth C],
IP [auth 7],
IQ [auth 8],
IT [auth a],
IU [auth b],
IV [auth c],
IZ [auth s],
JC [auth 2],
JE [auth 4],
JH [auth B],
JI [auth C],
JO [auth 0],
JQ [auth 8],
JT [auth a],
JU [auth b],
JZ [auth s],
KC [auth 2],
KE [auth 4],
KH [auth B],
KI [auth C],
KO [auth 0],
KQ [auth 8],
KW [auth g],
KY [auth r],
LAA [auth y],
LH [auth B],
LI [auth C],
LM [auth S],
LO [auth 0],
LQ [auth 8],
LS [auth q],
LT [auth a],
LW [auth g],
LY [auth r],
MAA [auth y],
MD [auth 3],
MH [auth B],
MI [auth C],
MJ [auth G],
ML [auth N],
MM [auth S],
MQ [auth 8],
MS [auth q],
MW [auth g],
MY [auth r],
NAA [auth y],
ND [auth 3],
NG [auth A],
NH [auth B],
NJ [auth G],
NM [auth S],
NQ [auth 8],
NS [auth q],
NY [auth r],
NZ [auth s],
OD [auth 3],
OF [auth 6],
OG [auth A],
OH [auth B],
OJ [auth G],
OM [auth S],
OP [auth 7],
OX [auth n],
OY [auth r],
OZ [auth s],
PB [auth 1],
PC [auth 2],
PD [auth 3],
PF [auth 6],
PG [auth A],
PH [auth B],
PL [auth R],
PN [auth Y],
PP [auth 7],
PR [auth p],
PX [auth n],
PZ [auth s],
QB [auth 1],
QC [auth 2],
QD [auth 3],
QF [auth 6],
QH [auth B],
QL [auth R],
QN [auth Y],
QP [auth 7],
QR [auth p],
QX [auth n],
QZ [auth s],
RB [auth 1],
RC [auth 2],
RD [auth 3],
RG [auth A],
RL [auth R],
RN [auth Y],
RO [auth 0],
RP [auth 7],
RR [auth p],
RW [auth g],
RZ [auth s],
SC [auth 2],
SL [auth R],
SM [auth S],
SO [auth 0],
SP [auth 7],
SW [auth g],
SY [auth r],
SZ [auth s],
TAA [auth y],
TC [auth 2],
TE [auth 5],
TJ [auth G],
TL [auth R],
TM [auth S],
TO [auth 0],
TP [auth 7],
TS [auth q],
TW [auth g],
TY [auth r],
TZ [auth s],
UAA [auth y],
UE [auth 5],
UJ [auth G],
UK [auth N],
UM [auth S],
UO [auth 0],
US [auth q],
UT [auth b],
UV [auth d],
UW [auth g],
UY [auth r],
VAA [auth y],
VE [auth 5],
VJ [auth G],
VK [auth N],
VM [auth S],
VO [auth 0],
VQ [auth 9],
VS [auth q],
VT [auth b],
VW [auth g],
VY [auth r],
WAA [auth y],
WF [auth 6],
WJ [auth G],
WK [auth N],
WM [auth S],
WN [auth Y],
WO [auth 0],
WQ [auth 9],
WS [auth q],
WT [auth b],
WU [auth c],
WX [auth n],
WY [auth r],
XAA [auth y],
XB [auth 1],
XF [auth 6],
XJ [auth G],
XL [auth R],
XM [auth S],
XN [auth Y],
XQ [auth 9],
XR [auth p],
XS [auth q],
XT [auth b],
XU [auth c],
XV [auth d],
XX [auth n],
XY [auth r],
YAA [auth y],
YB [auth 1],
YD [auth 4],
YF [auth 6],
YL [auth R],
YM [auth S],
YN [auth Y],
YR [auth p],
YT [auth b],
YU [auth c],
YV [auth d],
YX [auth n],
ZB [auth 1],
ZD [auth 4],
ZF [auth 6],
ZL [auth R],
ZN [auth Y],
ZR [auth p],
ZT [auth b],
ZU [auth c],
ZX [auth n]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


Download:Ideal Coordinates CCD File
KT [auth a],
QG [auth A],
VV [auth d],
YI [auth D]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
BK [auth G]
CP [auth 0]
DZ [auth r]
EBA [auth y]
EZ [auth s]
BK [auth G],
CP [auth 0],
DZ [auth r],
EBA [auth y],
EZ [auth s],
GO [auth Y],
IAA [auth x],
IK [auth G],
IM [auth R],
IW [auth g],
JM [auth S],
KN [auth X],
KX [auth m],
MF [auth 6],
NT [auth a],
NU [auth b],
OT [auth a],
RK [auth M],
TG [auth A],
TU [auth b],
UH [auth B],
VG [auth A],
XH [auth B],
ZW [auth g]
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
AD [auth 2]
AH [auth A]
BD [auth 2]
BP [auth 0]
BX [auth g]
AD [auth 2],
AH [auth A],
BD [auth 2],
BP [auth 0],
BX [auth g],
CW [auth d],
CZ [auth r],
DAA [auth w],
DBA [auth y],
DK [auth G],
DN [auth S],
DP [auth 0],
DT [auth a],
DW [auth d],
DX [auth g],
EAA [auth w],
EP [auth 7],
EW [auth d],
FAA [auth w],
FC [auth 1],
FK [auth G],
FO [auth Y],
FX [auth j],
GAA [auth w],
GG [auth 6],
GJ [auth D],
GK [auth G],
GY [auth n],
HAA [auth w],
HBA [auth Q1],
HG [auth 6],
HJ [auth D],
HM [auth R],
HN [auth W],
HS [auth p],
HW [auth f],
HX [auth k],
HY [auth n],
IBA [auth q1],
IG [auth 6],
IJ [auth D],
IN [auth W],
IS [auth q],
IX [auth k],
JAA [auth x],
JJ [auth D],
JN [auth W],
JS [auth q],
KK [auth I],
LF [auth 5],
LK [auth J],
LL [auth N],
LN [auth X],
LX [auth m],
MK [auth J],
MN [auth X],
MR [auth 9],
OU [auth b],
PT [auth a],
PU [auth b],
PV [auth c],
QE [auth 4],
QU [auth b],
QV [auth c],
RE [auth 4],
SI [auth C],
SQ [auth 9],
ST [auth a],
SU [auth b],
TQ [auth 9],
TT [auth b],
TV [auth c],
UG [auth A],
UI [auth C],
VH [auth B],
VI [auth C],
VU [auth b],
WD [auth 3],
WG [auth A],
WH [auth B],
XI [auth C],
XP [auth 7],
YC [auth 2],
YZ [auth s],
ZH [auth B],
ZP [auth 7]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


Download:Ideal Coordinates CCD File
AW [auth d],
DJ [auth D],
QT [auth a],
YG [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

Query on LHG


Download:Ideal Coordinates CCD File
AP [auth 0]
AX [auth g]
BAA [auth t]
BT [auth q]
BW [auth d]
AP [auth 0],
AX [auth g],
BAA [auth t],
BT [auth q],
BW [auth d],
BZ [auth r],
CBA [auth y],
CK [auth G],
CN [auth S],
EC [auth 1],
EJ [auth D],
EN [auth S],
EO [auth Y],
FG [auth 6],
FJ [auth D],
FW [auth e],
FY [auth n],
GBA [auth z],
GM [auth R],
GS [auth p],
GX [auth j],
JBA [auth F1],
JX [auth l],
KF [auth 5],
KL [auth N],
LR [auth 9],
OE [auth 4],
OK [auth K],
PK [auth L],
QK [auth M],
RQ [auth 8],
RT [auth a],
RU [auth b],
RV [auth c],
UU [auth b],
VD [auth 3],
WI [auth C],
WP [auth 7],
XC [auth 2],
XG [auth A],
XZ [auth s],
YH [auth B],
ZG [auth A],
ZZ [auth s]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM


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

Query on XAT


Download:Ideal Coordinates CCD File
CT [auth q]
CX [auth g]
EK [auth G]
EM [auth R]
NR [auth 9]
CT [auth q],
CX [auth g],
EK [auth G],
EM [auth R],
NR [auth 9],
PE [auth 4],
ZC [auth 2],
ZY [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


Download:Ideal Coordinates CCD File
AK [auth G]
AT [auth q]
AZ [auth r]
BBA [auth y]
BN [auth S]
AK [auth G],
AT [auth q],
AZ [auth r],
BBA [auth y],
BN [auth S],
DO [auth Y],
EG [auth 6],
EY [auth n],
FM [auth R],
FS [auth p],
IY [auth r],
JF [auth 5],
JL [auth N],
KR [auth 9],
NE [auth 4],
NL [auth R],
QQ [auth 8],
UD [auth 3],
WC [auth 2],
WZ [auth s],
YW [auth g],
ZO [auth 0]
(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
ABA [auth y]
AN [auth S]
BO [auth Y]
CC [auth 1]
CG [auth 6]
ABA [auth y],
AN [auth S],
BO [auth Y],
CC [auth 1],
CG [auth 6],
CO [auth Y],
CY [auth n],
DC [auth 1],
DG [auth 6],
DM [auth R],
DS [auth p],
DY [auth n],
ES [auth p],
HF [auth 5],
HL [auth N],
IF [auth 5],
IL [auth N],
JR [auth 9],
ME [auth 4],
OQ [auth 8],
PQ [auth 8],
SD [auth 3],
TD [auth 3],
UP [auth 7],
UZ [auth s],
VC [auth 2],
VP [auth 7],
VZ [auth s],
XO [auth 0],
XW [auth g],
YO [auth 0],
YY [auth r],
ZAA [auth y],
ZJ [auth G],
ZM [auth S],
ZS [auth q]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
RRX

Query on RRX


Download:Ideal Coordinates CCD File
IR [auth 9]
LE [auth 4]
UC [auth 2]
WW [auth g]
YJ [auth G]
IR [auth 9],
LE [auth 4],
UC [auth 2],
WW [auth g],
YJ [auth G],
YS [auth q]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AAA [auth t]
CAA [auth v]
CJ [auth D]
EX [auth h]
FBA [auth z]
AAA [auth t],
CAA [auth v],
CJ [auth D],
EX [auth h],
FBA [auth z],
FN [auth T],
GN [auth V],
HO [auth Z],
JK [auth H],
JV [auth c],
KU [auth b],
KV [auth c],
LU [auth b],
MT [auth a],
MU [auth b],
NI [auth C],
OI [auth C],
RH [auth B],
SG [auth A],
SH [auth B],
TH [auth B],
ZV [auth d]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU

Query on LMU


Download:Ideal Coordinates CCD File
JY [auth r],
NK [auth K],
OL [auth R],
SV [auth c]		DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX

Query on OEX


Download:Ideal Coordinates CCD File
ET [auth a],
JG [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
WV [auth d],
ZI [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


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

Query on CL


Download:Ideal Coordinates CCD File
GT [auth a],
HT [auth a],
LG [auth A],
MG [auth A]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK		S [auth M],
WA [auth m]		L-PEPTIDE LINKINGC4 H9 N O2

--

CSU
Query on CSU		V [auth R],
ZA [auth r]		L-PEPTIDE LINKINGC3 H7 N O5 S2CYS

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael199/21

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references