7Y7B | pdb_00007y7b

Cryo-EM structure of cryptophyte photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae.

Zhao, L.S.Wang, P.Li, K.Zhang, Q.B.He, F.Y.Li, C.Y.Su, H.N.Chen, X.L.Liu, L.N.Zhang, Y.Z.

(2023) Plant Cell 35: 2449-2463

  • DOI: https://doi.org/10.1093/plcell/koad087
  • Primary Citation Related Structures: 
    7Y7B, 7Y8A

  • PubMed Abstract: 

    Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI-ACPI represents a unique PSI-LHCI intermediate in the evolution from red algal to diatom PSI-LHCI. The PSI-ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI-LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI-ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI-LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI-LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis.


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

Macromolecule Content 

  • Total Structure Weight: 975.35 kDa 
  • Atom Count: 60,515 
  • Modeled Residue Count: 5,227 
  • Deposited Residue Count: 6,066 
  • Unique protein chains: 28

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-1A [auth 1]222Chroomonas placoideaMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-2B [auth 2]216Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-3C [auth 3]236Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-4D [auth 4]217Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-5E [auth 5]229Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-6F [auth 6]215Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-7G [auth 7]230Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-8H [auth 8]227Chroomonas placoideaMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-12I [auth 9]220Chroomonas placoideaMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1J [auth A]752Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AIB4 (Chroomonas placoidea)
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UniProt GroupA0A222AIB4
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2K [auth B]734Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI95 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerL [auth C]81Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI25 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIM [auth D]141Chroomonas placoideaMutation(s): 0 
UniProt
Find proteins for A0A222AIA6 (Chroomonas placoidea)
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UniProt GroupA0A222AIA6
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVN [auth E]64Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AIF3 (Chroomonas placoidea)
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UniProt GroupA0A222AIF3
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIO [auth F]183Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI52 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIP [auth I]36Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI78 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXQ [auth J]42Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI55 (Chroomonas placoidea)
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UniProt GroupA0A222AI55
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKR [auth K]87Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI34 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIS [auth L]153Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI68 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIT [auth M]30Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI28 (Chroomonas placoidea)
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaOU [auth O]99Chroomonas placoideaMutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaRV [auth R]133Chroomonas placoideaMutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Unk1W [auth X]164Chroomonas placoideaMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-SX [auth Z]242Chroomonas placoideaMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-13/10BA [auth d],
Y [auth a]
215Chroomonas placoideaMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-14Z [auth b]218Chroomonas placoideaMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-9AA [auth c]257Chroomonas placoideaMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-11CA [auth e]208Chroomonas placoideaMutation(s): 0 

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
IM [auth Z],
RK [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
AB [auth 2]
AC [auth 3]
AE [auth 6]
AF [auth 7]
AH [auth A]
AB [auth 2],
AC [auth 3],
AE [auth 6],
AF [auth 7],
AH [auth A],
AI [auth A],
AJ [auth B],
AK [auth B],
AL [auth F],
AN [auth a],
AO [auth c],
AP [auth d],
BB [auth 2],
BC [auth 3],
BE [auth 6],
BF [auth 7],
BG [auth 8],
BH [auth A],
BI [auth A],
BJ [auth B],
BK [auth B],
BN [auth a],
BO [auth c],
BP [auth d],
CB [auth 2],
CE [auth 6],
CH [auth A],
CI [auth A],
CJ [auth B],
CK [auth B],
CO [auth c],
CP [auth d],
DA [auth 1],
DB [auth 2],
DE [auth 6],
DF [auth 7],
DG [auth 9],
DH [auth A],
DI [auth A],
DJ [auth B],
DK [auth B],
DM [auth R],
DO [auth c],
EA [auth 1],
EB [auth 2],
EE [auth 6],
EF [auth 7],
EG [auth 9],
EH [auth A],
EI [auth A],
EJ [auth B],
EK [auth B],
EO [auth c],
EP [auth d],
FA [auth 1],
FE [auth 6],
FG [auth 9],
FH [auth A],
FI [auth A],
FJ [auth B],
FK [auth B],
FL [auth J],
FO [auth c],
FP [auth d],
GA [auth 1],
GB [auth 2],
GD [auth 5],
GE [auth 6],
GG [auth 9],
GH [auth A],
GI [auth A],
GJ [auth B],
GK [auth B],
GM [auth Z],
GO [auth c],
HA [auth 1],
HB [auth 2],
HD [auth 5],
HE [auth 6],
HG [auth 9],
HH [auth A],
HI [auth A],
HJ [auth B],
HK [auth B],
HO [auth c],
IA [auth 1],
ID [auth 5],
IE [auth 6],
IG [auth 9],
IH [auth A],
II [auth A],
IJ [auth B],
IK [auth B],
IL [auth K],
JA [auth 1],
JD [auth 5],
JG [auth 9],
JH [auth A],
JI [auth A],
JJ [auth B],
JK [auth B],
JL [auth K],
JM [auth Z],
JN [auth b],
KA [auth 1],
KD [auth 5],
KE [auth 6],
KG [auth 9],
KH [auth A],
KI [auth A],
KJ [auth B],
KK [auth B],
KM [auth Z],
KN [auth b],
KO [auth c],
LA [auth 1],
LD [auth 5],
LE [auth 6],
LG [auth 9],
LH [auth A],
LI [auth A],
LJ [auth B],
LM [auth Z],
LN [auth b],
LO [auth c],
MD [auth 5],
MH [auth A],
MI [auth A],
MJ [auth B],
ML [auth L],
MN [auth b],
MO [auth c],
NA [auth 1],
NC [auth 4],
ND [auth 5],
NF [auth 8],
NG [auth 9],
NH [auth A],
NI [auth A],
NJ [auth B],
NL [auth L],
NP [auth e],
OA [auth 1],
OC [auth 4],
OD [auth 5],
OF [auth 8],
OG [auth 9],
OH [auth A],
OJ [auth B],
OL [auth L],
ON [auth b],
OP [auth e],
PA [auth 1],
PC [auth 4],
PF [auth 8],
PG [auth 9],
PH [auth A],
PJ [auth B],
PL [auth L],
PN [auth b],
PP [auth e],
QB [auth 3],
QC [auth 4],
QD [auth 5],
QF [auth 8],
QG [auth 9],
QH [auth A],
QJ [auth B],
QM [auth a],
QN [auth b],
QP [auth e],
RB [auth 3],
RD [auth 5],
RF [auth 8],
RH [auth A],
RJ [auth B],
RM [auth a],
SB [auth 3],
SC [auth 4],
SD [auth 5],
SF [auth 8],
SH [auth A],
SJ [auth B],
SL [auth L],
SM [auth a],
SN [auth b],
SP [auth e],
TB [auth 3],
TC [auth 4],
TE [auth 7],
TF [auth 8],
TH [auth A],
TJ [auth B],
TM [auth a],
TN [auth b],
TP [auth e],
UB [auth 3],
UC [auth 4],
UE [auth 7],
UF [auth 8],
UH [auth A],
UJ [auth B],
UM [auth a],
UO [auth d],
UP [auth e],
VC [auth 4],
VE [auth 7],
VH [auth A],
VJ [auth B],
VL [auth O],
VM [auth a],
VO [auth d],
WA [auth 2],
WB [auth 3],
WC [auth 4],
WE [auth 7],
WG [auth A],
WH [auth A],
WJ [auth B],
WL [auth O],
WM [auth a],
WO [auth d],
WP [auth e],
XA [auth 2],
XB [auth 3],
XC [auth 4],
XE [auth 7],
XG [auth A],
XH [auth A],
XI [auth B],
XJ [auth B],
XL [auth O],
XM [auth a],
XO [auth d],
XP [auth e],
YA [auth 2],
YB [auth 3],
YG [auth A],
YH [auth A],
YI [auth B],
YJ [auth B],
YK [auth F],
YM [auth a],
YO [auth d],
ZA [auth 2],
ZB [auth 3],
ZE [auth 7],
ZG [auth A],
ZH [auth A],
ZI [auth B],
ZJ [auth B],
ZK [auth F],
ZN [auth c],
ZO [auth d]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD

Query on SQD



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AM [auth O],
KC [auth 3]
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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AG [auth 8]
BL [auth F]
DL [auth I]
HC [auth 3]
JC [auth 3]
AG [auth 8],
BL [auth F],
DL [auth I],
HC [auth 3],
JC [auth 3],
MB [auth 2],
SE [auth 6]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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DD [auth 4]
FD [auth 4]
HN [auth a]
IC [auth 3]
KF [auth 7]
DD [auth 4],
FD [auth 4],
HN [auth a],
IC [auth 3],
KF [auth 7],
LC [auth 3],
LF [auth 7],
LP [auth d],
MC [auth 3],
MP [auth d],
NB [auth 2],
OB [auth 2],
PB [auth 2],
PM [auth Z],
RE [auth 6],
SK [auth B],
TI [auth A],
TL [auth L],
TO [auth c],
UI [auth A],
YD [auth 5],
YN [auth b],
ZF [auth 8]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2
(Subject of Investigation/LOI)

Query on KC2



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CF [auth 7]
DP [auth d]
FB [auth 2]
IO [auth c]
JE [auth 6]
CF [auth 7],
DP [auth d],
FB [auth 2],
IO [auth c],
JE [auth 6],
JO [auth c],
MA [auth 1],
ME [auth 6],
MG [auth 9],
MM [auth Z],
NN [auth b],
NO [auth c],
PD [auth 5],
RC [auth 4],
RN [auth b],
RP [auth e],
VB [auth 3],
VP [auth e],
YE [auth 7],
ZM [auth a]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II3
(Subject of Investigation/LOI)

Query on II3



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RA [auth 1],
VN [auth b],
ZP [auth e]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
VAGYSFRRYPPSFX-RLVOMNFVSA-N
II0
(Subject of Investigation/LOI)

Query on II0



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AD [auth 4]
AQ [auth e]
BD [auth 4]
BQ [auth e]
CC [auth 3]
AD [auth 4],
AQ [auth e],
BD [auth 4],
BQ [auth e],
CC [auth 3],
CG [auth 8],
CN [auth a],
DC [auth 3],
DN [auth a],
EC [auth 3],
EL [auth J],
EN [auth a],
FC [auth 3],
FF [auth 7],
FM [auth R],
FN [auth a],
GC [auth 3],
GF [auth 7],
GP [auth d],
HF [auth 7],
HP [auth d],
IB [auth 2],
IF [auth 7],
IN [auth a],
IP [auth d],
JB [auth 2],
JP [auth d],
KB [auth 2],
MK [auth B],
NE [auth 6],
OE [auth 6],
OO [auth c],
PE [auth 6],
PO [auth c],
QA [auth 1],
QO [auth c],
RG [auth 9],
RO [auth c],
SA [auth 1],
SG [auth 9],
TA [auth 1],
TD [auth 5],
TG [auth 9],
UD [auth 5],
UG [auth 9],
UN [auth b],
VA [auth 1],
VD [auth 5],
WD [auth 5],
WF [auth 8],
WN [auth b],
XF [auth 8],
YC [auth 4],
YF [auth 8],
YL [auth O],
YP [auth e],
ZC [auth 4],
ZD [auth 5],
ZL [auth O]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT
(Subject of Investigation/LOI)

Query on IHT



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GN [auth a]
HM [auth Z]
KP [auth d]
LB [auth 2]
LL [auth K]
GN [auth a],
HM [auth Z],
KP [auth d],
LB [auth 2],
LL [auth K],
QE [auth 6],
QL [auth L],
SO [auth c],
UA [auth 1],
VF [auth 8],
VG [auth 9],
XD [auth 5]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
8CT
(Subject of Investigation/LOI)

Query on 8CT



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CD [auth 4]
CL [auth I]
CM [auth R]
CQ [auth e]
EM [auth R]
CD [auth 4],
CL [auth I],
CM [auth R],
CQ [auth e],
EM [auth R],
GL [auth J],
JF [auth 7],
KL [auth K],
NK [auth B],
NM [auth Z],
OI [auth A],
OK [auth B],
OM [auth Z],
PI [auth A],
PK [auth B],
QI [auth A],
QK [auth B],
RI [auth A],
RL [auth L],
TK [auth B],
UK [auth B],
UL [auth M],
VI [auth A],
XK [auth F],
XN [auth b]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
LMU

Query on LMU



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BM [auth O],
DQ [auth e],
ED [auth 4],
HL [auth J],
MF [auth 7]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN



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LK [auth B],
SI [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
VK [auth C],
WI [auth B],
WK [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Structure summary
  • Version 1.3: 2023-07-12
    Changes: Database references
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary