9KQP | pdb_00009kqp

PSI-LHCI supercomplex binding with 10 Lhcas from C. subellipsoidea


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural study of the chlorophyll between Lhca8 and PsaJ in an Antarctica green algal photosystem I-LHCI supercomplex revealed by its atomic structure.

Tsai, P.C.Kato, K.Shen, J.R.Akita, F.

(2025) Biochim Biophys Acta Bioenerg 1866: 149543-149543

  • DOI: https://doi.org/10.1016/j.bbabio.2025.149543
  • Primary Citation of Related Structures:  
    9KQP, 9KQQ

  • PubMed Abstract: 

    Coccomyxa subellipsoidea is an oleaginous, non-motile unicellular green microalga isolated from Antarctica, and is an attractive candidate for CO 2 fixation and biomass production. C. subellipsoidea is the first polar green alga whose genome has been sequenced. Understanding the structure of photosystems from C. subellipsoidea can provide more information about the conversion of light energy into chemical energy under extreme environments. Photosystems I (PSI) is one of the two photosystems highly conserved from cyanobacteria to vascular plants, and associates with a large amount of outer light-harvesting complex (LHC) which absorb light energy and transfer them to the core complex. Here, we determined the structure of the PSI-10 LHCIs and PSI-8 LHCIs supercomplexes from C. subellipsoidea at 1.92 Å and 2.06 Å resolutions by cryo-electron microscopy, respectively. The supercomplex is similar to PSI-LHCI from other green algae, whereas a large amount of water molecules is observed in our structure because of the high-resolution map. Two novel chlorophylls (Chls), Chl a321 in Lhca4 and Chl a314 in Lhca8, are observed at the lumenal side in our structure, in which Lhca8-Chl a314 provides a potential excitation energy transfer (EET) pathway between the inner-belt of LHCI and the core at the lumenal side. A total of three major EET pathways from LHCIs to PSI core are proposed, and C. subellipsoidea might adapt to the extreme environment by transferring energy in these three different EET pathways instead of by two major pathways proposed in other organisms.


  • Organizational Affiliation
    • Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1751Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupE9NPS8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplastic192Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit IV/PsaE71Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III245Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplastic138Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit VI133Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII36Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-K131Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIL [auth M]31Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticM [auth a],
T [auth b]
229Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticN [auth 3]246Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 7]259Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 8]255Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 9]230Coccomyxa subellipsoidea C-169Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VR [auth L]210Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I PsaOS [auth O]142Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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UniProt GroupI0YWK6
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic/Lhca2U [auth 2]273Coccomyxa subellipsoidea C-169Mutation(s): 0 
EC: 1.97.1.12
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticV [auth 4]246Coccomyxa subellipsoidea C-169Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth 5]274Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticX [auth 6]272Coccomyxa subellipsoidea C-169Mutation(s): 0 
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Small Molecules
Ligands 20 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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EH [auth 7],
LC [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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AF [auth K]
AG [auth a]
AN [auth 6]
CB [auth A]
GK [auth b]
AF [auth K],
AG [auth a],
AN [auth 6],
CB [auth A],
GK [auth b],
IN [auth 6],
JJ [auth 9],
JL [auth 4],
JN [auth 6],
KB [auth A],
KI [auth 8],
KM [auth 5],
KN [auth 6],
LB [auth A],
LJ [auth 9],
LM [auth 5],
LN [auth 6],
ML [auth 4],
MN [auth 6],
NH [auth 7],
NI [auth 8],
NM [auth 5],
OH [auth 7],
PH [auth 7],
QH [auth 7],
QL [auth 4],
QM [auth 5],
RG [auth 3],
UH [auth 7],
XF [auth a],
YF [auth a]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AB [auth A]
AC [auth A]
AD [auth B]
AE [auth B]
AJ [auth 9]
AB [auth A],
AC [auth A],
AD [auth B],
AE [auth B],
AJ [auth 9],
AK [auth b],
BB [auth A],
BC [auth A],
BD [auth B],
BE [auth B],
BG [auth a],
BI [auth 8],
BJ [auth 9],
BK [auth b],
BM [auth 5],
BN [auth 6],
CC [auth A],
CD [auth B],
CG [auth a],
CI [auth 8],
CJ [auth 9],
CK [auth b],
CM [auth 5],
CN [auth 6],
DB [auth A],
DD [auth B],
DF [auth K],
DI [auth 8],
DJ [auth 9],
DK [auth b],
DM [auth 5],
DN [auth 6],
EB [auth A],
ED [auth B],
EF [auth K],
EI [auth 8],
EJ [auth 9],
EK [auth b],
EL [auth 4],
EM [auth 5],
EN [auth 6],
FB [auth A],
FD [auth B],
FE [auth F],
FF [auth K],
FH [auth 7],
FI [auth 8],
FJ [auth 9],
FK [auth b],
FL [auth 4],
FM [auth 5],
FN [auth 6],
GB [auth A],
GD [auth B],
GH [auth 7],
GI [auth 8],
GJ [auth 9],
GL [auth 4],
GM [auth 5],
GN [auth 6],
HB [auth A],
HD [auth B],
HH [auth 7],
HI [auth 8],
HJ [auth 9],
HK [auth b],
HL [auth 4],
HM [auth 5],
HN [auth 6],
IB [auth A],
ID [auth B],
IH [auth 7],
II [auth 8],
IJ [auth 9],
IK [auth b],
IL [auth 4],
IM [auth 5],
JB [auth A],
JD [auth B],
JE [auth F],
JG [auth 3],
JH [auth 7],
JI [auth 8],
JK [auth b],
JM [auth 5],
KD [auth B],
KE [auth F],
KG [auth 3],
KH [auth 7],
KJ [auth 9],
KK [auth b],
KL [auth 4],
LA [auth A],
LD [auth B],
LG [auth 3],
LH [auth 7],
LI [auth 8],
LL [auth 4],
MA [auth A],
MB [auth A],
MD [auth B],
MG [auth 3],
MH [auth 7],
MI [auth 8],
MM [auth 5],
NA [auth A],
NB [auth A],
ND [auth B],
NG [auth 3],
NL [auth 4],
NN [auth 6],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OE [auth G],
OG [auth 3],
OI [auth 8],
OK [auth 2],
OL [auth 4],
OM [auth 5],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth G],
PF [auth a],
PG [auth 3],
PI [auth 8],
PK [auth 2],
PL [auth 4],
PM [auth 5],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth G],
QF [auth a],
QG [auth 3],
QK [auth 2],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth H],
RF [auth a],
RH [auth 7],
RJ [auth L],
RK [auth 2],
RL [auth 4],
RM [auth 5],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth H],
SF [auth a],
SG [auth 3],
SH [auth 7],
SJ [auth L],
SK [auth 2],
SL [auth 4],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth H],
TF [auth a],
TG [auth 3],
TJ [auth L],
TK [auth 2],
TL [auth 4],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UF [auth a],
UG [auth 3],
UK [auth 2],
UL [auth 4],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VF [auth a],
VG [auth 3],
VJ [auth O],
VK [auth 2],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WF [auth a],
WG [auth 3],
WJ [auth O],
WK [auth 2],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XJ [auth O],
XK [auth 2],
XM [auth 6],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YK [auth 2],
YM [auth 6],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth J],
ZF [auth a],
ZJ [auth b],
ZK [auth 2],
ZM [auth 6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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KA [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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DL [auth 4]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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HF [auth a],
ME [auth G],
VE [auth J],
YE [auth J]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PTY (Subject of Investigation/LOI)
Query on PTY

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AM [auth 5]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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DH [auth 7]
GA [auth A]
HA [auth A]
IA [auth A]
KC [auth B]
DH [auth 7],
GA [auth A],
HA [auth A],
IA [auth A],
KC [auth B],
MF [auth a],
SM [auth 6],
WM [auth 6],
YG [auth 7],
YH [auth 8],
ZL [auth 5]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH

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XG [auth 7]1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
DGA (Subject of Investigation/LOI)
Query on DGA

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ZH [auth 8]DIACYL GLYCEROL
C39 H76 O5
UHUSDOQQWJGJQS-QNGWXLTQSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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CH [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
AXT (Subject of Investigation/LOI)
Query on AXT

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KF [auth a]ASTAXANTHIN
C40 H52 O4
MQZIGYBFDRPAKN-UWFIBFSHSA-N
LUT (Subject of Investigation/LOI)
Query on LUT

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BH [auth 7]
BL [auth 4]
CL [auth 4]
GG [auth 3]
HG [auth 3]
BH [auth 7],
BL [auth 4],
CL [auth 4],
GG [auth 3],
HG [auth 3],
IE [auth F],
JF [auth a],
LF [auth a],
LK [auth 2],
QJ [auth L],
RI [auth 9],
SI [auth 9],
UI [auth 9],
UM [auth 6],
VM [auth 6],
WH [auth 8],
XE [auth J],
XH [auth 8],
XL [auth 5],
YJ [auth b],
YL [auth 5]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AA [auth A]
AH [auth 7]
BA [auth A]
BF [auth K]
CA [auth A]
AA [auth A],
AH [auth 7],
BA [auth A],
BF [auth K],
CA [auth A],
CF [auth K],
DA [auth A],
DG [auth 3],
EG [auth 3],
FC [auth B],
FG [auth 3],
GC [auth B],
GE [auth F],
GF [auth M],
HC [auth B],
IC [auth B],
JC [auth B],
LE [auth G],
MK [auth 2],
NE [auth G],
NJ [auth L],
OJ [auth L],
PJ [auth L],
TM [auth 6],
UE [auth I],
UJ [auth O],
VH [auth 8],
WE [auth J],
WL [auth 5]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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EA [auth A],
FA [auth A],
VI [auth 9],
VL [auth 5]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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EC [auth B],
Y [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
LAP (Subject of Investigation/LOI)
Query on LAP

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CE [auth B][2-((1-OXODODECANOXY-(2-HYDROXY-3-PROPANYL))-PHOSPHONATE-OXY)-ETHYL]-TRIMETHYLAMMONIUM
C20 H43 N O7 P
BWKILASWCLJPBO-UHFFFAOYSA-O
SF4 (Subject of Investigation/LOI)
Query on SF4

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DE [auth C],
EE [auth C],
Z [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
QTB (Subject of Investigation/LOI)
Query on QTB

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HE [auth F],
IF [auth a],
TI [auth 9],
ZG [auth 7]
(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
UNL (Subject of Investigation/LOI)
Query on UNL

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AI [auth 8]
AL [auth 4]
DC [auth A]
IG [auth 3]
JA [auth A]
AI [auth 8],
AL [auth 4],
DC [auth A],
IG [auth 3],
JA [auth A],
MC [auth B],
MJ [auth 9],
NC [auth B],
NF [auth a],
NK [auth 2],
OF [auth a],
QI [auth 9],
TH [auth 7],
WI [auth 9],
XI [auth 9],
YI [auth 9],
ZI [auth 9]
Unknown ligand
WXNCHUZBWWHNPM-FHRFKLSGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22H04916

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-26
    Type: Initial release