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 7YMM | pdb_00007ymm

PSII-Pcb Tetramer of Acaryochloris Marina

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.2 of the entry. See complete history. 

Literature

Structure of a unique PSII-Pcb tetrameric megacomplex in a chlorophyll d -containing cyanobacterium.

Shen, L., Gao, Y., Tang, K., Qi, R., Fu, L., Chen, J.H., Wang, W., Ma, X., Li, P., Chen, M., Kuang, T., Zhang, X., Shen, J.R., Wang, P., Han, G.

(2024) Sci Adv 10: eadk7140-eadk7140

  • DOI: https://doi.org/10.1126/sciadv.adk7140
  • Primary Citation Related Structures: 
    7YMI, 7YMM

  • PubMed Abstract: 

    Acaryochloris marina is a unique cyanobacterium using chlorophyll d (Chl d ) as its major pigment and thus can use far-red light for photosynthesis. Photosystem II (PSII) of A. marina associates with a number of prochlorophyte Chl-binding (Pcb) proteins to act as the light-harvesting system. We report here the cryo-electron microscopic structure of a PSII-Pcb megacomplex from A. marina at a 3.6-angstrom overall resolution and a 3.3-angstrom local resolution. The megacomplex is organized as a tetramer consisting of two PSII core dimers flanked by sixteen symmetrically related Pcb proteins, with a total molecular weight of 1.9 megadaltons. The structure reveals the detailed organization of PSII core consisting of 15 known protein subunits and an unknown subunit, the assembly of 4 Pcb antennas within each PSII monomer, and possible pathways of energy transfer within the megacomplex, providing deep insights into energy transfer and dissipation mechanisms within the PSII-Pcb megacomplex involved in far-red light utilization.

    • Organizational Affiliation: 
    • Cryo-EM Centre, Southern University of Science and Technology, Shenzhen 518055, China.

Macromolecule Content 

  • Total Structure Weight: 2,158.03 kDa 
  • Atom Count: 136,856 
  • Modeled Residue Count: 13,384 
  • Deposited Residue Count: 14,996 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 2A [auth 1A],
IB [auth 4A],
OA [auth 3A],
U [auth 2A]		360Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for A5A8K9 (Acaryochloris marina (strain MBIC 11017))
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UniProt GroupA5A8K9
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB [auth 1B],
JB [auth 4B],
PA [auth 3B],
V [auth 2B]		506Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0CFM2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC [auth 1C],
KB [auth 4C],
QA [auth 3C],
W [auth 2C]		490Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C1V7 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 protein 1D [auth 1D],
LB [auth 4D],
RA [auth 3D],
X [auth 2D]		351Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.10.3.9
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE [auth 1E],
MB [auth 4E],
SA [auth 3E],
Y [auth 2E]		83Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C6T2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein YF [auth 1F],
NB [auth 4F],
TA [auth 3F],
Z [auth 2F]		99Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C2V2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 10 kDa phosphoprotein PsbHAA [auth 2H],
G [auth 1H],
OB [auth 4H],
UA [auth 3H]		71Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0CDZ2 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein PsbIBA [auth 2I],
H [auth 1I],
PB [auth 4I],
VA [auth 3I]		34Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KCA [auth 2K],
I [auth 1K],
QB [auth 4K],
WA [auth 3K]		45Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LDA [auth 2L],
J [auth 1L],
RB [auth 4L],
XA [auth 3L]		38Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MEA [auth 2M],
K [auth 1M],
SB [auth 4M],
YA [auth 3M]		34Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TFA [auth 2T],
L [auth 1T],
TB [auth 4T],
ZA [auth 3T]		46Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C605 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinAB [auth 3X],
GA [auth 2X],
M [auth 1X],
UB [auth 4X]		40Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0BYW9 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12BB [auth 3Y],
HA [auth 2Y],
N [auth 1Y],
VB [auth 4Y]		39Acaryochloris marina MBIC11017Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZCB [auth 3Z],
IA [auth 2Z],
O [auth 1Z],
WB [auth 4Z]		62Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinDB [auth 32],
JA [auth 22],
P [auth 12],
XB [auth 42]		352Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown proteinEB [auth 3G],
KA [auth 2G],
Q [auth 1G],
YB [auth 4G]		41Acaryochloris marina MBIC11017Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinFB [auth 31],
LA [auth 21],
R [auth 11],
ZB [auth 41]		356Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C576 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinAC [auth 43],
GB [auth 33],
MA [auth 23],
S [auth 13]		349Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C6I0 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
High light inducible proteinBC [auth 44],
HB [auth 34],
NA [auth 24],
T [auth 14]		353Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C3E6 (Acaryochloris marina (strain MBIC 11017))
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD


Download:Ideal Coordinates CCD File
HD [auth 1B]
HP [auth 3B]
IJ [auth 2B]
IV [auth 4B]
ZD [auth 1C]
HD [auth 1B],
HP [auth 3B],
IJ [auth 2B],
IV [auth 4B],
ZD [auth 1C],
ZJ [auth 2C],
ZP [auth 3C],
ZV [auth 4C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CL7
(Subject of Investigation/LOI)

Query on CL7


Download:Ideal Coordinates CCD File
AE [auth 1C]
AF [auth 12]
AG [auth 11]
AH [auth 13]
AJ [auth 2B]
AE [auth 1C],
AF [auth 12],
AG [auth 11],
AH [auth 13],
AJ [auth 2B],
AK [auth 2C],
AL [auth 22],
AM [auth 21],
AN [auth 23],
AQ [auth 3C],
AR [auth 32],
AS [auth 31],
AT [auth 33],
AV [auth 4B],
AW [auth 4C],
AX [auth 42],
AY [auth 41],
AZ [auth 43],
BF [auth 12],
BG [auth 11],
BL [auth 22],
BM [auth 21],
BN [auth 23],
BR [auth 32],
BS [auth 31],
BX [auth 42],
BY [auth 41],
BZ [auth 43],
CC [auth 1A],
CF [auth 12],
CG [auth 11],
CI [auth 2A],
CL [auth 22],
CM [auth 21],
CO [auth 3A],
CR [auth 32],
CS [auth 31],
CU [auth 4A],
CX [auth 42],
CY [auth 41],
DE [auth 1D],
DF [auth 12],
DG [auth 11],
DK [auth 2D],
DL [auth 22],
DM [auth 21],
DQ [auth 3D],
DR [auth 32],
DS [auth 31],
DW [auth 4D],
DX [auth 42],
DY [auth 41],
EC [auth 1A],
EF [auth 12],
EG [auth 11],
EI [auth 2A],
EL [auth 22],
EM [auth 21],
EO [auth 3A],
ER [auth 32],
ES [auth 31],
EU [auth 4A],
EX [auth 42],
EY [auth 41],
FD [auth 1B],
FE [auth 1D],
FF [auth 12],
FG [auth 11],
FK [auth 2D],
FL [auth 22],
FM [auth 21],
FP [auth 3B],
FQ [auth 3D],
FR [auth 32],
FS [auth 31],
FW [auth 4D],
FX [auth 42],
FY [auth 41],
GE [auth 1D],
GJ [auth 2B],
GK [auth 2D],
GQ [auth 3D],
GV [auth 4B],
GW [auth 4D],
IC [auth 1A],
II [auth 2A],
IO [auth 3A],
IU [auth 4A],
JG [auth 13],
JS [auth 33],
KC [auth 1B],
KD [auth 1C],
KG [auth 13],
KJ [auth 2C],
KM [auth 23],
KO [auth 3B],
KP [auth 3C],
KS [auth 33],
KV [auth 4C],
KY [auth 43],
LC [auth 1B],
LD [auth 1C],
LG [auth 13],
LH [auth 14],
LI [auth 2B],
LJ [auth 2C],
LM [auth 23],
LN [auth 24],
LO [auth 3B],
LP [auth 3C],
LS [auth 33],
LT [auth 34],
LU [auth 4B],
LV [auth 4C],
LY [auth 43],
LZ [auth 44],
MC [auth 1B],
MD [auth 1C],
MG [auth 13],
MH [auth 14],
MI [auth 2B],
MJ [auth 2C],
MM [auth 23],
MN [auth 24],
MO [auth 3B],
MP [auth 3C],
MS [auth 33],
MT [auth 34],
MU [auth 4B],
MV [auth 4C],
MY [auth 43],
MZ [auth 44],
NC [auth 1B],
ND [auth 1C],
NF [auth 11],
NG [auth 13],
NH [auth 14],
NI [auth 2B],
NJ [auth 2C],
NL [auth 21],
NM [auth 23],
NN [auth 24],
NO [auth 3B],
NP [auth 3C],
NR [auth 31],
NS [auth 33],
NT [auth 34],
NU [auth 4B],
NV [auth 4C],
NX [auth 41],
NY [auth 43],
NZ [auth 44],
OC [auth 1B],
OD [auth 1C],
OE [auth 12],
OF [auth 11],
OG [auth 13],
OH [auth 14],
OI [auth 2B],
OJ [auth 2C],
OK [auth 22],
OL [auth 21],
OM [auth 23],
ON [auth 24],
OO [auth 3B],
OP [auth 3C],
OQ [auth 32],
OR [auth 31],
OS [auth 33],
OT [auth 34],
OU [auth 4B],
OV [auth 4C],
OW [auth 42],
OX [auth 41],
OY [auth 43],
OZ [auth 44],
PC [auth 1B],
PD [auth 1C],
PE [auth 12],
PF [auth 11],
PG [auth 13],
PH [auth 14],
PI [auth 2B],
PJ [auth 2C],
PK [auth 22],
PL [auth 21],
PM [auth 23],
PN [auth 24],
PO [auth 3B],
PP [auth 3C],
PQ [auth 32],
PR [auth 31],
PS [auth 33],
PT [auth 34],
PU [auth 4B],
PV [auth 4C],
PW [auth 42],
PX [auth 41],
PY [auth 43],
PZ [auth 44],
QC [auth 1B],
QD [auth 1C],
QE [auth 12],
QF [auth 11],
QG [auth 13],
QH [auth 14],
QI [auth 2B],
QJ [auth 2C],
QK [auth 22],
QL [auth 21],
QM [auth 23],
QN [auth 24],
QO [auth 3B],
QP [auth 3C],
QQ [auth 32],
QR [auth 31],
QS [auth 33],
QT [auth 34],
QU [auth 4B],
QV [auth 4C],
QW [auth 42],
QX [auth 41],
QY [auth 43],
QZ [auth 44],
RC [auth 1B],
RD [auth 1C],
RE [auth 12],
RF [auth 11],
RG [auth 13],
RH [auth 14],
RI [auth 2B],
RJ [auth 2C],
RK [auth 22],
RL [auth 21],
RM [auth 23],
RN [auth 24],
RO [auth 3B],
RP [auth 3C],
RQ [auth 32],
RR [auth 31],
RS [auth 33],
RT [auth 34],
RU [auth 4B],
RV [auth 4C],
RW [auth 42],
RX [auth 41],
RY [auth 43],
RZ [auth 44],
SC [auth 1B],
SD [auth 1C],
SE [auth 12],
SF [auth 11],
SG [auth 13],
SH [auth 14],
SI [auth 2B],
SJ [auth 2C],
SK [auth 22],
SL [auth 21],
SM [auth 23],
SN [auth 24],
SO [auth 3B],
SP [auth 3C],
SQ [auth 32],
SR [auth 31],
SS [auth 33],
ST [auth 34],
SU [auth 4B],
SV [auth 4C],
SW [auth 42],
SX [auth 41],
SY [auth 43],
SZ [auth 44],
TC [auth 1B],
TD [auth 1C],
TE [auth 12],
TF [auth 11],
TG [auth 13],
TH [auth 14],
TI [auth 2B],
TJ [auth 2C],
TK [auth 22],
TL [auth 21],
TM [auth 23],
TN [auth 24],
TO [auth 3B],
TP [auth 3C],
TQ [auth 32],
TR [auth 31],
TS [auth 33],
TT [auth 34],
TU [auth 4B],
TV [auth 4C],
TW [auth 42],
TX [auth 41],
TY [auth 43],
TZ [auth 44],
UC [auth 1B],
UD [auth 1C],
UE [auth 12],
UF [auth 11],
UG [auth 13],
UH [auth 14],
UI [auth 2B],
UJ [auth 2C],
UK [auth 22],
UL [auth 21],
UM [auth 23],
UN [auth 24],
UO [auth 3B],
UP [auth 3C],
UQ [auth 32],
UR [auth 31],
US [auth 33],
UT [auth 34],
UU [auth 4B],
UV [auth 4C],
UW [auth 42],
UX [auth 41],
UY [auth 43],
UZ [auth 44],
VC [auth 1B],
VD [auth 1C],
VE [auth 12],
VF [auth 11],
VG [auth 13],
VH [auth 14],
VI [auth 2B],
VJ [auth 2C],
VK [auth 22],
VL [auth 21],
VM [auth 23],
VN [auth 24],
VO [auth 3B],
VP [auth 3C],
VQ [auth 32],
VR [auth 31],
VS [auth 33],
VT [auth 34],
VU [auth 4B],
VV [auth 4C],
VW [auth 42],
VX [auth 41],
VY [auth 43],
VZ [auth 44],
WC [auth 1B],
WD [auth 1C],
WE [auth 12],
WF [auth 11],
WG [auth 13],
WH [auth 14],
WI [auth 2B],
WJ [auth 2C],
WK [auth 22],
WL [auth 21],
WM [auth 23],
WN [auth 24],
WO [auth 3B],
WP [auth 3C],
WQ [auth 32],
WR [auth 31],
WS [auth 33],
WT [auth 34],
WU [auth 4B],
WV [auth 4C],
WW [auth 42],
WX [auth 41],
WY [auth 43],
WZ [auth 44],
XC [auth 1B],
XE [auth 12],
XF [auth 11],
XG [auth 13],
XH [auth 14],
XI [auth 2B],
XK [auth 22],
XL [auth 21],
XM [auth 23],
XN [auth 24],
XO [auth 3B],
XQ [auth 32],
XR [auth 31],
XS [auth 33],
XT [auth 34],
XU [auth 4B],
XW [auth 42],
XX [auth 41],
XY [auth 43],
XZ [auth 44],
YC [auth 1B],
YE [auth 12],
YF [auth 11],
YG [auth 13],
YH [auth 14],
YI [auth 2B],
YK [auth 22],
YL [auth 21],
YM [auth 23],
YN [auth 24],
YO [auth 3B],
YQ [auth 32],
YR [auth 31],
YS [auth 33],
YT [auth 34],
YU [auth 4B],
YW [auth 42],
YX [auth 41],
YY [auth 43],
YZ [auth 44],
ZC [auth 1B],
ZE [auth 12],
ZF [auth 11],
ZG [auth 13],
ZI [auth 2B],
ZK [auth 22],
ZL [auth 21],
ZM [auth 23],
ZO [auth 3B],
ZQ [auth 32],
ZR [auth 31],
ZS [auth 33],
ZU [auth 4B],
ZW [auth 42],
ZX [auth 41],
ZY [auth 43]
CHLOROPHYLL D
C54 H70 Mg N4 O6
FBCRYORFRGRJBC-ACDPFEIMSA-L
PHO
(Subject of Investigation/LOI)

Query on PHO


Download:Ideal Coordinates CCD File
DC [auth 1A]
DI [auth 2A]
DO [auth 3A]
DU [auth 4A]
JE [auth 1D]
DC [auth 1A],
DI [auth 2A],
DO [auth 3A],
DU [auth 4A],
JE [auth 1D],
JK [auth 2D],
JQ [auth 3D],
JW [auth 4D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
(Subject of Investigation/LOI)

Query on SQD


Download:Ideal Coordinates CCD File
DD [auth 1B]
DH [auth 13]
DP [auth 3B]
DT [auth 33]
EJ [auth 2B]
DD [auth 1B],
DH [auth 13],
DP [auth 3B],
DT [auth 33],
EJ [auth 2B],
EN [auth 23],
EV [auth 4B],
EZ [auth 43],
FH [auth 13],
FT [auth 33],
GN [auth 23],
GZ [auth 43],
HC [auth 1A],
HI [auth 2A],
HO [auth 3A],
HU [auth 4A],
IF [auth 12],
IG [auth 11],
IL [auth 22],
IM [auth 21],
IR [auth 32],
IS [auth 31],
IX [auth 42],
IY [auth 41],
KF [auth 12],
KL [auth 22],
KR [auth 32],
KX [auth 42]
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


Download:Ideal Coordinates CCD File
ED [auth 1B]
EP [auth 3B]
FJ [auth 2B]
FV [auth 4B]
GC [auth 1A]
ED [auth 1B],
EP [auth 3B],
FJ [auth 2B],
FV [auth 4B],
GC [auth 1A],
GI [auth 2A],
GO [auth 3A],
GU [auth 4A],
LE [auth 1D],
LK [auth 2D],
LQ [auth 3D],
LW [auth 4D],
MF [auth 11],
ML [auth 21],
MR [auth 31],
MX [auth 41]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
(Subject of Investigation/LOI)

Query on PL9


Download:Ideal Coordinates CCD File
IE [auth 1D],
IK [auth 2D],
IQ [auth 3D],
IW [auth 4D]		2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG


Download:Ideal Coordinates CCD File
GD [auth 1B]
GH [auth 13]
GP [auth 3B]
GT [auth 33]
HJ [auth 2B]
GD [auth 1B],
GH [auth 13],
GP [auth 3B],
GT [auth 33],
HJ [auth 2B],
HN [auth 23],
HV [auth 4B],
HZ [auth 43],
ID [auth 1B],
IH [auth 14],
IN [auth 24],
IP [auth 3B],
IT [auth 34],
IZ [auth 44],
JC [auth 1A],
JI [auth 2A],
JJ [auth 2B],
JO [auth 3A],
JU [auth 4A],
JV [auth 4B],
KE [auth 1D],
KK [auth 2D],
KQ [auth 3D],
KW [auth 4D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
(Subject of Investigation/LOI)

Query on HEM


Download:Ideal Coordinates CCD File
ME [auth 1F],
MK [auth 2F],
MQ [auth 3F],
MW [auth 4F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
ZEX
(Subject of Investigation/LOI)

Query on ZEX


Download:Ideal Coordinates CCD File
AAA [auth 44]
AI [auth 14]
AO [auth 24]
AU [auth 34]
BAA [auth 44]
AAA [auth 44],
AI [auth 14],
AO [auth 24],
AU [auth 34],
BAA [auth 44],
BH [auth 13],
BI [auth 14],
BO [auth 24],
BT [auth 33],
BU [auth 34],
CH [auth 13],
CN [auth 23],
CT [auth 33],
CZ [auth 43],
DN [auth 23],
DZ [auth 43],
EH [auth 13],
ET [auth 33],
FN [auth 23],
FZ [auth 43],
GF [auth 12],
GG [auth 11],
GL [auth 22],
GM [auth 21],
GR [auth 32],
GS [auth 31],
GX [auth 42],
GY [auth 41],
HF [auth 12],
HG [auth 11],
HH [auth 13],
HL [auth 22],
HM [auth 21],
HR [auth 32],
HS [auth 31],
HT [auth 33],
HX [auth 42],
HY [auth 41],
JF [auth 12],
JL [auth 22],
JM [auth 23],
JR [auth 32],
JX [auth 42],
JY [auth 43],
KH [auth 14],
KN [auth 24],
KT [auth 34],
KZ [auth 44],
LF [auth 12],
LL [auth 22],
LR [auth 32],
LX [auth 42],
ZH [auth 14],
ZN [auth 24],
ZT [auth 34],
ZZ [auth 44]
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
C40 H56 O2
YRMDXLDAZBQLBK-WIHRHFSMSA-N
8CT
(Subject of Investigation/LOI)

Query on 8CT


Download:Ideal Coordinates CCD File
AD [auth 1B]
AP [auth 3B]
BD [auth 1B]
BE [auth 1C]
BJ [auth 2B]
AD [auth 1B],
AP [auth 3B],
BD [auth 1B],
BE [auth 1C],
BJ [auth 2B],
BK [auth 2C],
BP [auth 3B],
BQ [auth 3C],
BV [auth 4B],
BW [auth 4C],
CD [auth 1B],
CJ [auth 2B],
CP [auth 3B],
CV [auth 4B],
DJ [auth 2B],
DV [auth 4B],
FC [auth 1A],
FI [auth 2A],
FO [auth 3A],
FU [auth 4A],
HE [auth 1D],
HK [auth 2D],
HQ [auth 3D],
HW [auth 4D],
JD [auth 1B],
JH [auth 14],
JN [auth 24],
JP [auth 3B],
JT [auth 34],
JZ [auth 44],
KI [auth 2B],
KU [auth 4B],
NE [auth 1K],
NK [auth 2K],
NQ [auth 3K],
NW [auth 4K],
XD [auth 1C],
XJ [auth 2C],
XP [auth 3C],
XV [auth 4C],
YD [auth 1C],
YJ [auth 2C],
YP [auth 3C],
YV [auth 4C]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
BCT
(Subject of Investigation/LOI)

Query on BCT


Download:Ideal Coordinates CCD File
EE [auth 1D],
EK [auth 2D],
EQ [auth 3D],
EW [auth 4D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
(Subject of Investigation/LOI)

Query on FE2


Download:Ideal Coordinates CCD File
CE [auth 1D],
CK [auth 2D],
CQ [auth 3D],
CW [auth 4D]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
UNK
Query on UNK		EB [auth 3G],
KA [auth 2G],
Q [auth 1G],
YB [auth 4G]		L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18.2_3874:

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDY-SSW-SMC003
Chinese Academy of SciencesChinaXDB17000000
National Basic Research Program of China (973 Program)China2015CB150100

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2024-09-04
    Changes: Data collection, Database references
  • Version 2.0: 2026-08-12
    Type: Remediation
    Reason: Metalloprotein remediation
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2026-09-16
    Changes: Data collection, Structure summary
  • Version 2.2: 2026-09-23
    Changes: Data collection