6ZZX

Structure of low-light grown Chlorella ohadii Photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1741Chlorella ohadiiMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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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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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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit chloroplastic143Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-F165Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit chloroplastic99Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-chloroplastic-like94Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth J]41Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit chloroplasticJ [auth K]86Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIK [auth L]157Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIL [auth M]31Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]35Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit ON [auth O]87Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 1],
P [auth a]
192Chlorella ohadiiMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione reductaseQ [auth 3]241Chlorella ohadiiMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca4R [auth 4]207Chlorella ohadiiMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticS [auth 5]229Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticT [auth 6]231Chlorella ohadiiMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca7U [auth 7]221Chlorella ohadiiMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticV [auth 8]219Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth 2]215Chlorella ohadiiMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticX [auth 9]183Chlorella ohadiiMutation(s): 0 
UniProt
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Small Molecules
Ligands 30 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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DE [auth B],
ON [auth 8],
TM [auth 8],
UL [auth 7]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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AN [auth 8]
DP [auth 9]
EI [auth 3]
FI [auth 3]
FP [auth 9]
AN [auth 8],
DP [auth 9],
EI [auth 3],
FI [auth 3],
FP [auth 9],
GK [auth 5],
GL [auth 6],
GN [auth 8],
HH [auth a],
HJ [auth 4],
HK [auth 5],
HL [auth 6],
HP [auth 9],
IM [auth 7],
IO [auth 2],
JH [auth a],
JI [auth 3],
JK [auth 5],
JL [auth 6],
JN [auth 8],
JO [auth 2],
KG [auth 1],
KM [auth 7],
LI [auth 3],
LJ [auth 4],
LL [auth 6],
LM [auth 7],
LO [auth 2],
MH [auth a],
MK [auth 5],
MM [auth 7],
NA [auth A],
NH [auth a],
NK [auth 5],
NL [auth 6],
PG [auth 1],
PJ [auth 4],
QG [auth 1],
QH [auth a],
SG [auth 1],
TL [auth 7],
UK [auth 6],
WO [auth 9],
XM [auth 8],
YG [auth 1],
YO [auth 9],
ZM [auth 8]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AC [auth A]
AD [auth B]
AF [auth H]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth B],
AF [auth H],
AG [auth O],
AJ [auth 4],
AK [auth 5],
AL [auth 6],
AM [auth 7],
AO [auth 2],
AP [auth 9],
BA [auth A],
BB [auth A],
BC [auth A],
BD [auth B],
BG [auth O],
BJ [auth 4],
BK [auth 5],
BL [auth 6],
BM [auth 7],
BN [auth 8],
BO [auth 2],
BP [auth 9],
CA [auth A],
CB [auth A],
CD [auth B],
CG [auth O],
CI [auth 3],
CJ [auth 4],
CK [auth 5],
CL [auth 6],
CM [auth 7],
CN [auth 8],
CO [auth 2],
CP [auth 9],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth J],
DI [auth 3],
DJ [auth 4],
DK [auth 5],
DL [auth 6],
DM [auth 7],
DN [auth 8],
DO [auth 2],
EA [auth A],
EB [auth A],
ED [auth B],
EH [auth a],
EJ [auth 4],
EK [auth 5],
EL [auth 6],
EM [auth 7],
EN [auth 8],
EO [auth 2],
EP [auth 9],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FH [auth a],
FJ [auth 4],
FK [auth 5],
FL [auth 6],
FM [auth 7],
FN [auth 8],
FO [auth 2],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GH [auth a],
GI [auth 3],
GJ [auth 4],
GM [auth 7],
GO [auth 2],
GP [auth 9],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth B],
HG [auth 1],
HI [auth 3],
HM [auth 7],
HN [auth 8],
HO [auth 2],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IG [auth 1],
IH [auth a],
II [auth 3],
IJ [auth 4],
IK [auth 5],
IL [auth 6],
IN [auth 8],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JF [auth K],
JG [auth 1],
JJ [auth 4],
JM [auth 7],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth K],
KH [auth a],
KI [auth 3],
KJ [auth 4],
KK [auth 5],
KL [auth 6],
KN [auth 8],
KO [auth 2],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth K],
LG [auth 1],
LH [auth a],
LK [auth 5],
LN [auth 8],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MF [auth K],
MG [auth 1],
MI [auth 3],
ML [auth 6],
MN [auth 8],
MO [auth 2],
NC [auth B],
ND [auth B],
NG [auth 1],
NI [auth 3],
NO [auth 2],
OA [auth A],
OC [auth B],
OD [auth B],
OG [auth 1],
OH [auth a],
OI [auth 3],
PA [auth A],
PC [auth B],
PD [auth B],
PE [auth F],
PH [auth a],
QA [auth A],
QC [auth B],
QD [auth B],
QF [auth L],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RF [auth L],
RG [auth 1],
RH [auth a],
RI [auth 3],
SA [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SF [auth L],
TA [auth A],
TC [auth B],
TD [auth B],
TE [auth G],
TF [auth L],
TG [auth 1],
TK [auth 6],
UA [auth A],
UC [auth B],
VA [auth A],
VC [auth B],
WA [auth A],
WC [auth B],
WI [auth 4],
XA [auth A],
XC [auth B],
XI [auth 4],
XJ [auth 5],
XO [auth 9],
YA [auth A],
YC [auth B],
YE [auth H],
YI [auth 4],
YJ [auth 5],
YM [auth 8],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZE [auth H],
ZI [auth 4],
ZJ [auth 5],
ZK [auth 6],
ZL [auth 7],
ZO [auth 9]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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

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SM [auth 7]Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD
Query on SQD

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CF [auth H],
RM [auth 7],
VE [auth G],
XB [auth A],
ZF [auth I]
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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QN [auth 8]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
LMG
Query on LMG

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WB [auth A]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PCW
Query on PCW

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FE [auth B],
OF [auth K],
PF [auth K],
PL [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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GF [auth J]
IE [auth B]
JP [auth 9]
PK [auth 5]
QI [auth 3]
GF [auth J],
IE [auth B],
JP [auth 9],
PK [auth 5],
QI [auth 3],
QM [auth 7],
TH [auth a],
WE [auth G],
XE [auth G],
YB [auth A],
ZG [auth a]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG
Query on LHG

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BE [auth B]
CC [auth A]
CE [auth B]
IP [auth 9]
MJ [auth 4]
BE [auth B],
CC [auth A],
CE [auth B],
IP [auth 9],
MJ [auth 4],
NM [auth 7],
NN [auth 8],
OE [auth F],
OK [auth 5],
OL [auth 6],
OM [auth 7],
OO [auth 2],
PI [auth 3],
PM [auth 7],
PO [auth 2],
QE [auth F],
QJ [auth 4],
RO [auth 9],
SH [auth a],
SK [auth 6],
UB [auth A],
UG [auth 1],
VB [auth A],
VG [auth 1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH

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

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PN [auth 8],
QK [auth 5],
QO [auth 2],
SI [auth 3]
DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
XAT
Query on XAT

Download Ideal Coordinates CCD File 
UO [auth 9],
VO [auth 9],
WL [auth 7],
XN [auth 2]
(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

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NE [auth F](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
AXT
Query on AXT

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FG [auth 1],
YL [auth 7]
ASTAXANTHIN
C40 H52 O4
MQZIGYBFDRPAKN-UWFIBFSHSA-N
LUT
Query on LUT

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AH [auth a]
BH [auth a]
CH [auth a]
EG [auth 1]
GG [auth 1]
AH [auth a],
BH [auth a],
CH [auth a],
EG [auth 1],
GG [auth 1],
SJ [auth 5],
SO [auth 9],
TI [auth 4],
TJ [auth 5],
TO [auth 9],
UI [auth 4],
UM [auth 8],
VK [auth 6],
VL [auth 7],
VM [auth 8],
WH [auth 3],
WJ [auth 5],
WK [auth 6],
XH [auth 3],
YN [auth 2],
ZN [auth 2]
(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 
BI [auth 3],
FF [auth J]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
ECH
Query on ECH

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XF [auth M]beta,beta-caroten-4-one
C40 H54 O
QXNWZXMBUKUYMD-QQGJMDNJSA-N
BCR
Query on BCR

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AE [auth B]
AI [auth 3]
BF [auth H]
DG [auth O]
EE [auth B]
AE [auth B],
AI [auth 3],
BF [auth H],
DG [auth O],
EE [auth B],
EF [auth J],
IF [auth K],
NF [auth K],
PB [auth A],
QB [auth A],
RB [auth A],
SB [auth A],
TB [auth A],
UE [auth G],
UF [auth L],
UJ [auth 5],
VD [auth B],
VF [auth L],
VI [auth 4],
VJ [auth 5],
WD [auth B],
WF [auth L],
WM [auth 8],
XD [auth B],
XK [auth 6],
XL [auth 7],
YD [auth B],
YF [auth I],
YH [auth 3],
YK [auth 6],
ZD [auth B],
ZH [auth 3]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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EC [auth A],
GE [auth B],
WN [auth 2],
XG [auth 1]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LPX
Query on LPX

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LE [auth F](2S)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-hydroxypropyl hexadecanoate
C21 H44 N O7 P
YVYMBNSKXOXSKW-FQEVSTJZSA-N
PQN
Query on PQN

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NB [auth A],
UD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
LAP
Query on LAP

Download Ideal Coordinates CCD File 
VN [auth 8][2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
C20 H43 N O7 P
BWKILASWCLJPBO-UHFFFAOYSA-O
SF4
Query on SF4

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JE [auth C],
KE [auth C],
OB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
SPH
Query on SPH

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HF [auth J],
KP [auth 9],
OJ [auth 4],
SL [auth 6]
SPHINGOSINE
C18 H37 N O2
WWUZIQQURGPMPG-MSOLQXFVSA-N
OLA
Query on OLA

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TN [auth 8],
UN [auth 8],
VH [auth a],
WG [auth 1]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
QTB
Query on QTB

Download Ideal Coordinates CCD File 
DH [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 
NJ [auth 4]
QL [auth 6]
RJ [auth 4]
RK [auth 5]
RN [auth 8]
NJ [auth 4],
QL [auth 6],
RJ [auth 4],
RK [auth 5],
RN [auth 8],
SN [auth 8],
UH [auth a]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
13X
Query on 13X

Download Ideal Coordinates CCD File 
RL [auth 6]benzene-1,3,5-triol
C6 H6 O3
QCDYQQDYXPDABM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.7
MODEL REFINEMENTPHENIX

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