6ZZY | pdb_00006zzy

Structure of high-light grown Chlorella ohadii photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Cryo-EM photosystem I structure reveals adaptation mechanisms to extreme high light in Chlorella ohadii.

Caspy, I.Neumann, E.Fadeeva, M.Liveanu, V.Savitsky, A.Frank, A.Kalisman, Y.L.Shkolnisky, Y.Murik, O.Treves, H.Hartmann, V.Nowaczyk, M.M.Schuhmann, W.Rogner, M.Willner, I.Kaplan, A.Schuster, G.Nelson, N.Lubitz, W.Nechushtai, R.

(2021) Nat Plants 7: 1314-1322

  • DOI: https://doi.org/10.1038/s41477-021-00983-1
  • Primary Citation Related Structures: 
    6ZZX, 6ZZY, 7A4P

  • PubMed Abstract: 

    Photosynthesis in deserts is challenging since it requires fast adaptation to rapid night-to-day changes, that is, from dawn's low light (LL) to extreme high light (HL) intensities during the daytime. To understand these adaptation mechanisms, we purified photosystem I (PSI) from Chlorella ohadii, a green alga that was isolated from a desert soil crust, and identified the essential functional and structural changes that enable the photosystem to perform photosynthesis under extreme high light conditions. The cryo-electron microscopy structures of PSI from cells grown under low light (PSI LL ) and high light (PSI HL ), obtained at 2.70 and 2.71 Å, respectively, show that part of light-harvesting antenna complex I (LHCI) and the core complex subunit (PsaO) are eliminated from PSI HL to minimize the photodamage. An additional change is in the pigment composition and their number in LHCI HL ; about 50% of chlorophyll b is replaced by chlorophyll a. This leads to higher electron transfer rates in PSI HL and might enable C. ohadii PSI to act as a natural photosynthesiser in photobiocatalytic systems. PSI HL or PSI LL were attached to an electrode and their induced photocurrent was determined. To obtain photocurrents comparable with PSI HL , 25 times the amount of PSI LL was required, demonstrating the high efficiency of PSI HL . Hence, we suggest that C. ohadii PSI HL is an ideal candidate for the design of desert artificial photobiocatalytic systems.


  • Organizational Affiliation
    • Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

Macromolecule Content 

  • Total Structure Weight: 801.81 kDa 
  • Atom Count: 54,609 
  • Modeled Residue Count: 4,594 
  • Deposited Residue Count: 4,594 
  • Unique protein chains: 22

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1741Chlorella ohadiiMutation(s): 2 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2731Chlorella ohadiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Chlorella ohadiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit chloroplastic143Chlorella ohadiiMutation(s): 2 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Chlorella ohadiiMutation(s): 5 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-F165Chlorella ohadiiMutation(s): 11 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit chloroplastic99Chlorella ohadiiMutation(s): 8 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-KI [auth K]86Chlorella ohadiiMutation(s): 7 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]31Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIK [auth I]35Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-chloroplastic-likeL [auth H]94Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2P6TPU7 (Chlorella sorokiniana)
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit VM [auth L]157Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0A2P6TC44 (Chlorella sorokiniana)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 1],
O [auth a]
192Chlorella ohadiiMutation(s): 0 
UniProt
Find proteins for A0A2P6TT36 (Chlorella sorokiniana)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione reductaseP [auth 3]241Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 4]207Chlorella ohadiiMutation(s): 1 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 5]227Chlorella ohadiiMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 6]231Chlorella ohadiiMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 7]221Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticU [auth 8]219Chlorella ohadiiMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticV [auth 2]215Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth 9]182Chlorella ohadiiMutation(s): 0 
UniProt
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Reference Sequence

Small Molecules

Ligands 30 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
CE [auth B],
UM [auth 8],
ZB [auth A]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



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AH [auth a]
BH [auth a]
DM [auth 8]
EG [auth 1]
EH [auth a]
AH [auth a],
BH [auth a],
DM [auth 8],
EG [auth 1],
EH [auth a],
GM [auth 8],
GO [auth 9],
IG [auth 1],
IO [auth 9],
OK [auth 6],
PK [auth 6],
PM [auth 8],
QI [auth 4],
QJ [auth 5],
RJ [auth 5],
RK [auth 6],
RL [auth 7],
TJ [auth 5],
UI [auth 4],
VK [auth 6],
WH [auth 3],
XG [auth a],
YH [auth 3],
YI [auth 4]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



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AA [auth A]
AB [auth A]
AD [auth B]
AF [auth K]
AG [auth 1]
AA [auth A],
AB [auth A],
AD [auth B],
AF [auth K],
AG [auth 1],
AI [auth 3],
AO [auth 9],
BA [auth A],
BB [auth A],
BD [auth B],
BF [auth K],
BG [auth 1],
BI [auth 3],
BO [auth 9],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CF [auth K],
CG [auth 1],
CH [auth a],
CI [auth 3],
CO [auth 9],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DG [auth 1],
DH [auth a],
DN [auth 2],
DO [auth 9],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EM [auth 8],
EN [auth 2],
EO [auth 9],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FG [auth 1],
FH [auth a],
FK [auth 6],
FL [auth 7],
FM [auth 8],
FN [auth 2],
FO [auth 9],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GG [auth 1],
GK [auth 6],
GL [auth 7],
GN [auth 2],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HG [auth 1],
HJ [auth 5],
HK [auth 6],
HL [auth 7],
HM [auth 8],
HN [auth 2],
HO [auth 9],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IF [auth H],
II [auth 4],
IJ [auth 5],
IK [auth 6],
IL [auth 7],
IM [auth 8],
IN [auth 2],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JF [auth H],
JG [auth 1],
JI [auth 4],
JJ [auth 5],
JK [auth 6],
JL [auth 7],
JM [auth 8],
JN [auth 2],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KE [auth F],
KF [auth H],
KI [auth 4],
KJ [auth 5],
KK [auth 6],
KL [auth 7],
KM [auth 8],
KN [auth 2],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LI [auth 4],
LJ [auth 5],
LK [auth 6],
LL [auth 7],
LM [auth 8],
LN [auth 2],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MI [auth 4],
MJ [auth 5],
MK [auth 6],
ML [auth 7],
MM [auth 8],
MN [auth 2],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth L],
NI [auth 4],
NJ [auth 5],
NK [auth 6],
NL [auth 7],
NM [auth 8],
NN [auth 2],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth L],
OI [auth 4],
OJ [auth 5],
OL [auth 7],
OM [auth 8],
ON [auth 2],
PA [auth A],
PC [auth B],
PD [auth B],
PE [auth G],
PF [auth L],
PH [auth 3],
PI [auth 4],
PJ [auth 5],
PL [auth 7],
PN [auth 2],
QA [auth A],
QC [auth B],
QD [auth B],
QE [auth G],
QH [auth 3],
QK [auth 6],
QL [auth 7],
QM [auth 8],
QN [auth 2],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RH [auth 3],
RI [auth 4],
RM [auth 8],
SA [auth A],
SC [auth B],
SG [auth a],
SH [auth 3],
SI [auth 4],
SJ [auth 5],
SK [auth 6],
SL [auth 7],
SM [auth 8],
TA [auth A],
TC [auth B],
TG [auth a],
TH [auth 3],
TI [auth 4],
TK [auth 6],
TL [auth 7],
UA [auth A],
UC [auth B],
UG [auth a],
UH [auth 3],
UJ [auth 5],
UK [auth 6],
VA [auth A],
VC [auth B],
VE [auth J],
VG [auth a],
VH [auth 3],
VI [auth 4],
VJ [auth 5],
WA [auth A],
WC [auth B],
WF [auth 1],
WG [auth a],
WI [auth 4],
WJ [auth 5],
XA [auth A],
XC [auth B],
XF [auth 1],
XH [auth 3],
XI [auth 4],
XJ [auth 5],
XN [auth 9],
Y [auth A],
YA [auth A],
YC [auth B],
YF [auth 1],
YG [auth a],
YN [auth 9],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZE [auth K],
ZF [auth 1],
ZG [auth a],
ZH [auth 3],
ZN [auth 9]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0

Query on CL0



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X [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
4RF

Query on 4RF



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XM [auth 8],
YM [auth 8],
ZL [auth 7]
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD

Query on SQD



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MF [auth H],
TE [auth G],
YL [auth 7]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
P5S

Query on P5S



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WM [auth 8]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
PCW

Query on PCW



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DE [auth B],
YK [auth 6]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
PTY

Query on PTY



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AN [auth 8]
EE [auth B]
EI [auth 3]
LO [auth 9]
XL [auth 7]
AN [auth 8],
EE [auth B],
EI [auth 3],
LO [auth 9],
XL [auth 7],
ZJ [auth 5]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG

Query on LHG



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AE [auth B]
AJ [auth 4]
BE [auth B]
DI [auth 3]
GH [auth a]
AE [auth B],
AJ [auth 4],
BE [auth B],
DI [auth 3],
GH [auth a],
JO [auth 9],
KG [auth 1],
KO [auth 9],
LG [auth 1],
ME [auth F],
NE [auth F],
RN [auth 2],
SN [auth 2],
TM [auth 8],
UL [auth 7],
VL [auth 7],
WB [auth A],
WK [auth 6],
WL [auth 7],
XB [auth A],
XK [auth 6],
YB [auth A],
YJ [auth 5],
ZI [auth 4]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH

Query on 3PH



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AC [auth A]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA

Query on DGA



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AK [auth 5],
VM [auth 8]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
XAT

Query on XAT



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CL [auth 7](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
C7Z

Query on C7Z



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EL [auth 7](1~{S})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{S})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohex-3-en-1-ol
C40 H56 O2
JKQXZKUSFCKOGQ-ANDPMPNWSA-N
LUT

Query on LUT



Download:Ideal Coordinates CCD File
AM [auth 8]
BK [auth 6]
BL [auth 7]
BM [auth 8]
BN [auth 2]
AM [auth 8],
BK [auth 6],
BL [auth 7],
BM [auth 8],
BN [auth 2],
CJ [auth 5],
CK [auth 6],
CN [auth 2],
DJ [auth 5],
FI [auth 4],
GI [auth 4],
GJ [auth 5],
JH [auth 3],
KH [auth 3],
OG [auth a],
PG [auth a],
QG [auth a],
TF [auth 1],
UF [auth 1],
UN [auth 9],
VF [auth 1],
VN [auth 9]
(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
XE [auth J](3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
ECH

Query on ECH



Download:Ideal Coordinates CCD File
GF [auth M]beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR

Query on BCR



Download:Ideal Coordinates CCD File
CM [auth 8]
DF [auth K]
DK [auth 6]
DL [auth 7]
EF [auth K]
CM [auth 8],
DF [auth K],
DK [auth 6],
DL [auth 7],
EF [auth K],
EJ [auth 5],
EK [auth 6],
FJ [auth 5],
HF [auth I],
HI [auth 4],
LE [auth F],
LF [auth H],
LH [auth 3],
MH [auth 3],
NH [auth 3],
QF [auth L],
RB [auth A],
RF [auth L],
SB [auth A],
SE [auth G],
SF [auth L],
TB [auth A],
TD [auth B],
UB [auth A],
UD [auth B],
VB [auth A],
VD [auth B],
WD [auth B],
WE [auth J],
XD [auth B],
YD [auth B],
ZD [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
BC [auth A],
FE [auth B],
NG [auth 1],
TN [auth 2]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX

Query on LPX



Download:Ideal Coordinates CCD File
HH [auth a],
YE [auth J]
(2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
PB [auth A],
SD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
LAP

Query on LAP



Download:Ideal Coordinates CCD File
FF [auth K],
GE [auth B],
OE [auth F]
[2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
C20 H43 N O7 P
BWKILASWCLJPBO-UHFFFAOYSA-O
ERG

Query on ERG



Download:Ideal Coordinates CCD File
UE [auth G]ERGOSTEROL
C28 H44 O
DNVPQKQSNYMLRS-APGDWVJJSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
HE [auth C],
IE [auth C],
QB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SPH

Query on SPH



Download:Ideal Coordinates CCD File
AL [auth 6]SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
MG [auth 1],
ZM [auth 8]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
A8S

Query on A8S



Download:Ideal Coordinates CCD File
WN [auth 9](2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
C15 H20 O4
JLIDBLDQVAYHNE-YKALOCIXSA-N
QTB

Query on QTB



Download:Ideal Coordinates CCD File
OH [auth 3],
RG [auth a]
(3~{E},5~{E},7~{E})-6-methyl-8-[(6~{R})-2,2,6-trimethylcyclohexyl]octa-3,5,7-trien-2-one
C18 H28 O
WXNCHUZBWWHNPM-FHRFKLSGSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
BJ [auth 4],
ZK [auth 6]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
GG0

Query on GG0



Download:Ideal Coordinates CCD File
IH [auth a]2-(2-azanylethanoylamino)ethanoic acid
C4 H8 N2 O3
YMAWOPBAYDPSLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
German-Israeli Foundation for Research and DevelopmentIsraelG-1483-207/2018

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-28
    Type: Initial release
  • Version 1.1: 2021-09-08
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection, Refinement description, Structure summary