8Z11 | pdb_00008z11

Cryo-EM structure of haptophyte photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into the assembly and energy transfer of haptophyte photosystem I-light-harvesting supercomplex.

He, F.Y.Zhao, L.S.Qu, X.X.Li, K.Guo, J.P.Zhao, F.Wang, N.Qin, B.Y.Chen, X.L.Gao, J.Liu, L.N.Zhang, Y.Z.

(2024) Proc Natl Acad Sci U S A 121: e2413678121-e2413678121

  • DOI: https://doi.org/10.1073/pnas.2413678121
  • Primary Citation of Related Structures:  
    8Z11

  • PubMed Abstract: 

    Haptophyta represents a major taxonomic group, with plastids derived from the primary plastids of red algae. Here, we elucidated the cryoelectron microscopy structure of the photosystem I-light-harvesting complex I (PSI-LHCI) supercomplex from the haptophyte Isochrysis galbana . The PSI core comprises 12 subunits, which have evolved differently from red algae and cryptophytes by losing the PsaO subunit while incorporating the PsaK subunit, which is absent in diatoms and dinoflagellates. The PSI core is encircled by 22 fucoxanthin-chlorophyll a / c -binding light-harvesting antenna proteins (iFCPIs) that form a trilayered antenna arrangement. Moreover, a pigment-binding subunit, L iFP , which has not been identified in any other previously characterized PSI-LHCI supercomplexes, was determined in I. galbana PSI-iFCPI, presumably facilitating the interactions and energy transfer between peripheral iFCPIs and the PSI core. Calculation of excitation energy transfer rates by computational simulations revealed that the intricate pigment network formed within PSI-iFCPI ensures efficient transfer of excitation energy. Overall, our study provides a solid structural foundation for understanding the light-harvesting and energy transfer mechanisms in haptophyte PSI-iFCPI and provides insights into the evolution and structural variations of red-lineage PSI-LHCIs.


  • Organizational Affiliation
    • Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-7209Isochrysis galbanaMutation(s): 0 
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Find proteins for Q2IA66 (Isochrysis galbana)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-1209Isochrysis galbanaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-11205Isochrysis galbanaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-6245Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-5206Isochrysis galbanaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-8240Isochrysis galbanaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-13198Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-10198Isochrysis galbanaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-3194Isochrysis galbanaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-9200Isochrysis galbanaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-4202Isochrysis galbanaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-12229Isochrysis galbanaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-15/14/16
M, P, W
217Isochrysis galbanaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-17224Isochrysis galbanaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-20/19/21
O, R, T
206Isochrysis galbanaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-18187Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-22235Isochrysis galbanaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
iFCPI-2203Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
L-iFP122Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1X [auth a]752Isochrysis galbanaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2Y [auth b]734Isochrysis galbanaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerZ [auth c]81Isochrysis galbanaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIAA [auth d]142Isochrysis galbanaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEBA [auth e]124Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIICA [auth f]184Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIDA [auth i]36Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXEA [auth j]40Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
PsaKFA [auth k]92Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIGA [auth l]145Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIHA [auth m]30Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRIA [auth r]133Isochrysis galbanaMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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VL [auth Q],
ZS [auth b]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AC [auth D]
AD [auth E]
AF [auth H]
AI [auth L]
AO [auth U]
AC [auth D],
AD [auth E],
AF [auth H],
AI [auth L],
AO [auth U],
AQ [auth a],
AS [auth b],
BB [auth B],
BC [auth D],
BD [auth E],
BE [auth F],
BH [auth K],
BK [auth O],
BM [auth R],
BO [auth U],
BQ [auth a],
BS [auth b],
BU [auth r],
CB [auth B],
CC [auth D],
CD [auth E],
CF [auth H],
CK [auth O],
CM [auth R],
CQ [auth a],
CS [auth b],
CU [auth r],
DB [auth B],
DC [auth D],
DD [auth E],
DF [auth H],
DH [auth K],
DK [auth O],
DM [auth R],
DQ [auth a],
DR [auth a],
DS [auth b],
DT [auth f],
EB [auth B],
EC [auth D],
ED [auth E],
EF [auth H],
EG [auth I],
EH [auth K],
EK [auth O],
EL [auth Q],
EM [auth R],
EP [auth a],
EQ [auth a],
ER [auth a],
ES [auth b],
FB [auth B],
FC [auth D],
FD [auth E],
FF [auth H],
FH [auth K],
FK [auth O],
FM [auth R],
FO [auth V],
FP [auth a],
FQ [auth a],
FS [auth b],
FT [auth f],
GB [auth B],
GC [auth D],
GD [auth E],
GF [auth H],
GG [auth J],
GK [auth O],
GL [auth Q],
GP [auth a],
GQ [auth a],
GR [auth b],
GS [auth b],
GT [auth f],
HC [auth D],
HF [auth H],
HG [auth J],
HH [auth K],
HJ [auth N],
HL [auth Q],
HN [auth T],
HO [auth V],
HP [auth a],
HQ [auth a],
HR [auth b],
HS [auth b],
IC [auth D],
ID [auth E],
IF [auth H],
IL [auth Q],
IO [auth V],
IP [auth a],
IQ [auth a],
IR [auth b],
IS [auth b],
JA [auth A],
JB [auth B],
JC [auth D],
JD [auth E],
JG [auth J],
JL [auth Q],
JP [auth a],
JQ [auth a],
JR [auth b],
JS [auth b],
JT [auth j],
KA [auth A],
KB [auth C],
KC [auth D],
KG [auth J],
KL [auth Q],
KM [auth S],
KN [auth T],
KP [auth a],
KQ [auth a],
KR [auth b],
KS [auth b],
LA [auth A],
LB [auth C],
LG [auth J],
LI [auth M],
LJ [auth N],
LL [auth Q],
LN [auth T],
LP [auth a],
LQ [auth a],
LR [auth b],
LS [auth b],
MA [auth A],
ME [auth F],
MG [auth J],
MI [auth M],
MJ [auth N],
ML [auth Q],
MN [auth T],
MP [auth a],
MQ [auth a],
MR [auth b],
MS [auth b],
NA [auth A],
NB [auth C],
NE [auth G],
NG [auth J],
NH [auth L],
NJ [auth N],
NL [auth Q],
NM [auth S],
NN [auth T],
NP [auth a],
NQ [auth a],
NR [auth b],
NS [auth b],
OA [auth A],
OB [auth C],
OF [auth I],
OG [auth J],
OI [auth M],
OJ [auth N],
OK [auth P],
OM [auth S],
ON [auth T],
OP [auth a],
OQ [auth a],
OR [auth b],
OS [auth b],
OT [auth k],
PA [auth A],
PB [auth C],
PE [auth G],
PF [auth I],
PI [auth M],
PJ [auth N],
PK [auth P],
PN [auth T],
PO [auth W],
PP [auth a],
PQ [auth a],
PR [auth b],
PS [auth b],
PT [auth k],
QA [auth A],
QB [auth C],
QE [auth G],
QF [auth I],
QG [auth J],
QH [auth L],
QI [auth M],
QM [auth S],
QO [auth W],
QP [auth a],
QQ [auth a],
QR [auth b],
QS [auth b],
QT [auth k],
RA [auth A],
RB [auth C],
RD [auth F],
RE [auth G],
RF [auth I],
RG [auth J],
RI [auth M],
RK [auth P],
RM [auth S],
RP [auth a],
RQ [auth a],
RR [auth b],
RS [auth b],
SB [auth C],
SE [auth G],
SF [auth I],
SI [auth M],
SK [auth P],
SM [auth S],
SO [auth W],
SP [auth a],
SQ [auth a],
SR [auth b],
SS [auth b],
TA [auth A],
TD [auth F],
TE [auth G],
TF [auth I],
TH [auth L],
TK [auth P],
TM [auth S],
TO [auth W],
TP [auth a],
TQ [auth a],
TR [auth b],
TS [auth b],
UD [auth F],
UE [auth G],
UF [auth I],
UH [auth L],
UK [auth P],
UM [auth S],
UO [auth W],
UP [auth a],
UR [auth b],
VD [auth F],
VF [auth I],
VH [auth L],
VK [auth P],
VN [auth U],
VO [auth W],
VP [auth a],
VR [auth b],
VT [auth l],
WD [auth F],
WH [auth L],
WL [auth R],
WM [auth S],
WN [auth U],
WO [auth W],
WP [auth a],
WR [auth b],
WT [auth l],
XC [auth E],
XD [auth F],
XH [auth L],
XN [auth U],
XP [auth a],
XR [auth b],
XT [auth l],
YC [auth E],
YD [auth F],
YG [auth K],
YH [auth L],
YJ [auth O],
YP [auth a],
YR [auth b],
ZB [auth D],
ZC [auth E],
ZD [auth F],
ZE [auth H],
ZL [auth R],
ZN [auth U],
ZP [auth a],
ZR [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

Download Ideal Coordinates CCD File 
NF [auth H],
TT [auth k]
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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AB [auth A]
AJ [auth M]
CL [auth P]
DJ [auth N]
DP [auth W]
AB [auth A],
AJ [auth M],
CL [auth P],
DJ [auth N],
DP [auth W],
FN [auth S],
GI [auth L],
GN [auth T],
JE [auth F],
KE [auth F],
MT [auth j],
OD [auth E],
QC [auth D],
QD [auth E],
UC [auth D],
UT [auth l],
WC [auth E],
XB [auth D],
YB [auth D],
ZA [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
AR [auth a]
BG [auth I]
BL [auth P]
BR [auth a]
CP [auth W]
AR [auth a],
BG [auth I],
BL [auth P],
BR [auth a],
CP [auth W],
CR [auth a],
FG [auth I],
HT [auth f],
IB [auth B],
IE [auth F],
LE [auth F],
PC [auth D],
PD [auth E],
VC [auth E],
YA [auth A],
ZI [auth M]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86 (Subject of Investigation/LOI)
Query on A86

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AL [auth P]
AN [auth S]
BI [auth L]
BN [auth S]
BP [auth W]
AL [auth P],
AN [auth S],
BI [auth L],
BN [auth S],
BP [auth W],
CE [auth F],
CI [auth L],
CJ [auth M],
CN [auth S],
CO [auth U],
DE [auth F],
DI [auth L],
DL [auth P],
DN [auth S],
EI [auth L],
EU [auth r],
HE [auth F],
HI [auth M],
HM [auth R],
IH [auth K],
IK [auth O],
IM [auth R],
JH [auth K],
JK [auth O],
LH [auth K],
LO [auth W],
MF [auth H],
OL [auth Q],
RC [auth D],
RJ [auth N],
RN [auth T],
SC [auth D],
SG [auth J],
SJ [auth N],
SN [auth T],
TJ [auth N],
TL [auth Q],
UB [auth C],
UI [auth M],
UN [auth T],
VB [auth C],
VI [auth M],
WE [auth G],
WJ [auth N],
XE [auth G],
XI [auth M],
XK [auth P],
XM [auth S],
YI [auth M],
YK [auth P],
YM [auth S],
YO [auth W],
ZM [auth S],
ZO [auth W]
(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
KC2 (Subject of Investigation/LOI)
Query on KC2

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AE [auth F]
AH [auth K]
AK [auth O]
AM [auth R]
BF [auth H]
AE [auth F],
AH [auth K],
AK [auth O],
AM [auth R],
BF [auth H],
BJ [auth M],
CH [auth K],
DG [auth I],
EJ [auth N],
FJ [auth N],
FL [auth Q],
GH [auth K],
GJ [auth N],
GM [auth R],
HD [auth E],
HK [auth O],
IG [auth J],
II [auth M],
IJ [auth N],
IN [auth T],
JI [auth M],
JJ [auth N],
JN [auth T],
KI [auth M],
KJ [auth N],
KO [auth W],
LK [auth P],
LM [auth S],
MB [auth C],
MK [auth P],
MM [auth S],
MO [auth W],
NI [auth M],
NK [auth P],
NO [auth W],
OE [auth G],
OH [auth L],
OO [auth W],
PG [auth J],
PH [auth L],
PM [auth S],
QJ [auth N],
QK [auth P],
QN [auth T],
RH [auth L],
RO [auth W],
SA [auth A],
SD [auth F],
SH [auth L],
TI [auth M],
UL [auth Q],
VE [auth G],
VM [auth S],
WF [auth I],
WK [auth P],
XL [auth R],
XO [auth W],
YL [auth R],
YN [auth U],
ZG [auth K],
ZH [auth L],
ZJ [auth O]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

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AG [auth I]
AP [auth W]
DO [auth U]
EE [auth F]
EN [auth S]
AG [auth I],
AP [auth W],
DO [auth U],
EE [auth F],
EN [auth S],
FE [auth F],
FI [auth L],
GE [auth F],
GO [auth V],
HB [auth B],
JF [auth H],
JM [auth R],
KD [auth E],
KF [auth H],
KH [auth K],
KK [auth O],
LC [auth D],
LD [auth E],
LF [auth H],
LT [auth j],
MC [auth D],
MD [auth E],
MH [auth K],
NC [auth D],
ND [auth E],
OC [auth D],
PL [auth Q],
QL [auth Q],
RL [auth Q],
SL [auth Q],
ST [auth k],
TB [auth C],
TG [auth J],
TN [auth T],
UA [auth A],
UG [auth J],
UJ [auth N],
VA [auth A],
VG [auth J],
VJ [auth N],
WA [auth A],
WB [auth D],
WG [auth J],
WI [auth M],
XA [auth A],
XF [auth I],
XJ [auth N],
YE [auth G],
YF [auth I],
ZF [auth I],
ZK [auth P]
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AU [auth m]
DU [auth r]
EO [auth U]
ET [auth f]
FR [auth a]
AU [auth m],
DU [auth r],
EO [auth U],
ET [auth f],
FR [auth a],
FU [auth r],
IT [auth i],
KT [auth j],
RT [auth k],
UQ [auth a],
US [auth b],
VQ [auth a],
VS [auth b],
WQ [auth a],
WS [auth b],
XQ [auth a],
XS [auth b],
YS [auth b],
YT [auth l],
ZT [auth l]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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CG [auth I],
JO [auth V],
NT [auth j],
TC [auth D],
XG [auth J]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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AT [auth b],
ZQ [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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BT [auth c],
CT [auth c],
YQ [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China2023YFA0914600

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release