7XQP | pdb_00007xqp

PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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 insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens.

Zhang, S.Tang, K.Yan, Q.Li, X.Shen, L.Wang, W.He, Y.K.Kuang, T.Han, G.Shen, J.R.Zhang, X.

(2023) Nat Plants 9: 832-846

  • DOI: https://doi.org/10.1038/s41477-023-01401-4
  • Primary Citation Related Structures: 
    7XQP

  • PubMed Abstract: 

    Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.


  • Organizational Affiliation
    • Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Macromolecule Content 

  • Total Structure Weight: 857.08 kDa 
  • Atom Count: 56,417 
  • Modeled Residue Count: 5,076 
  • Deposited Residue Count: 5,104 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1742Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA3 (Physcomitrium patens)
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UniProt GroupQ8MFA3
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q8MFA2 (Physcomitrium patens)
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UniProt GroupQ8MFA2
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Physcomitrium patensMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXQ2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Predicted protein PsaD141Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A0A2K1JKF2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaE62Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IKE2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-F159Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1J0L9 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI-G98Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JC42 (Physcomitrium patens)
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UniProt GroupA0A2K1JC42
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaH photosystem I reaction center subunit95Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9SL09 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII34Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXR3 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IX41Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXM2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaK81Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KU02 (Physcomitrium patens)
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UniProt GroupA0A2K1KU02
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
PSI subunit V163Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1IAD0 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII32Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q6YXK4 (Physcomitrium patens)
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UniProt GroupQ6YXK4
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaON [auth O]89Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1JDE1 (Physcomitrium patens)
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UniProt GroupA0A2K1JDE1
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticO [auth 1],
S [auth 5]
192Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KU97 (Physcomitrium patens)
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UniProt GroupA0A2K1KU97
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticP [auth 2],
T [auth 6]
211Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1K0C7 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticQ [auth 3],
U [auth 7]
216Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1KGQ2 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticR [auth 4],
V [auth 8]
205Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2K1K0E4 (Physcomitrium patens)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth 9]225Physcomitrium patensMutation(s): 0 
UniProt
Find proteins for A0A2K1KKR9 (Physcomitrium patens)
Explore A0A2K1KKR9 
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UniProt GroupA0A2K1KKR9
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticX [auth a],
Y [auth b],
Z [auth c]
227Physcomitrium patensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A9RT62 (Physcomitrium patens)
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
YD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL

Query on CHL



Download:Ideal Coordinates CCD File
AM [auth a]
BJ [auth 6]
BM [auth a]
CJ [auth 6]
CM [auth a]
AM [auth a],
BJ [auth 6],
BM [auth a],
CJ [auth 6],
CM [auth a],
DH [auth 3],
DM [auth a],
EG [auth 2],
EI [auth 4],
EL [auth 9],
EM [auth a],
FG [auth 2],
FJ [auth 6],
GJ [auth 6],
HJ [auth 6],
HN [auth c],
IG [auth 2],
IL [auth 9],
JG [auth 2],
JL [auth 9],
KG [auth 2],
KI [auth 5],
KL [auth 9],
LL [auth 9],
LN [auth c],
MF [auth 1],
ML [auth 9],
MN [auth c],
NN [auth c],
OJ [auth 6],
ON [auth c],
PI [auth 5],
PM [auth b],
PN [auth c],
QK [auth 8],
RF [auth 1],
RG [auth 2],
RK [auth 8],
SK [auth 8],
TM [auth b],
UM [auth b],
VH [auth 4],
VM [auth b],
WH [auth 4],
WL [auth a],
WM [auth b],
XH [auth 4],
XM [auth b],
YK [auth 8],
ZJ [auth 7]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AF [auth L]
AG [auth 1]
AA [auth A],
AB [auth A],
AD [auth B],
AF [auth L],
AG [auth 1],
AH [auth 3],
AI [auth 4],
AK [auth 7],
AN [auth b],
BA [auth A],
BB [auth A],
BD [auth B],
BF [auth L],
BH [auth 3],
BI [auth 4],
BK [auth 7],
BN [auth b],
CA [auth A],
CB [auth A],
CD [auth B],
CE [auth F],
CH [auth 3],
CI [auth 4],
CK [auth 7],
CN [auth b],
DA [auth A],
DB [auth A],
DD [auth B],
DI [auth 4],
DJ [auth 6],
DK [auth 7],
DL [auth 8],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth F],
EH [auth 3],
EJ [auth 6],
EK [auth 7],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FE [auth F],
FF [auth O],
FH [auth 3],
FK [auth 7],
FL [auth 9],
FM [auth a],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth O],
GG [auth 2],
GH [auth 3],
GK [auth 7],
GL [auth 9],
GM [auth a],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HE [auth G],
HF [auth O],
HG [auth 2],
HH [auth 3],
HK [auth 7],
HL [auth 9],
HM [auth a],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth G],
IF [auth O],
IH [auth 3],
IJ [auth 6],
IM [auth a],
IN [auth c],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth G],
JH [auth 3],
JJ [auth 6],
JM [auth a],
JN [auth c],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KH [auth 3],
KJ [auth 6],
KN [auth c],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LG [auth 2],
LH [auth 3],
LI [auth 5],
LJ [auth 6],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth H],
MG [auth 2],
MI [auth 5],
MJ [auth 6],
MK [auth 8],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth 1],
NG [auth 2],
NI [auth 5],
NJ [auth 6],
NK [auth 8],
NL [auth 9],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth 1],
OG [auth 2],
OI [auth 5],
OK [auth 8],
OL [auth 9],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PE [auth J],
PF [auth 1],
PG [auth 2],
PK [auth 8],
PL [auth 9],
QA [auth A],
QC [auth B],
QD [auth B],
QF [auth 1],
QG [auth 2],
QI [auth 5],
QL [auth 9],
QM [auth b],
QN [auth c],
RA [auth A],
RC [auth B],
RD [auth B],
RH [auth 4],
RI [auth 5],
RM [auth b],
RN [auth c],
SA [auth A],
SC [auth B],
SF [auth 1],
SH [auth 4],
SI [auth 5],
SM [auth b],
SN [auth c],
TA [auth A],
TC [auth B],
TE [auth K],
TF [auth 1],
TH [auth 4],
TI [auth 5],
TK [auth 8],
TN [auth c],
UA [auth A],
UC [auth B],
UE [auth K],
UF [auth 1],
UH [auth 4],
UI [auth 5],
UJ [auth 7],
UK [auth 8],
UN [auth c],
VA [auth A],
VC [auth B],
VE [auth K],
VF [auth 1],
VI [auth 5],
VJ [auth 7],
VK [auth 8],
WA [auth A],
WC [auth B],
WE [auth K],
WF [auth 1],
WI [auth 5],
WJ [auth 7],
WK [auth 8],
XA [auth A],
XC [auth B],
XF [auth 1],
XG [auth 3],
XI [auth 5],
XJ [auth 7],
XK [auth 8],
XL [auth a],
YA [auth A],
YC [auth B],
YF [auth 1],
YG [auth 3],
YH [auth 4],
YJ [auth 7],
YL [auth a],
YM [auth b],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZE [auth L],
ZF [auth 1],
ZG [auth 3],
ZH [auth 4],
ZL [auth a],
ZM [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



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LE [auth G],
PJ [auth 6],
SE [auth J],
SG [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG

Query on LHG



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AJ [auth 5]
CC [auth A]
CL [auth 8]
DG [auth 1]
GN [auth b]
AJ [auth 5],
CC [auth A],
CL [auth 8],
DG [auth 1],
GN [auth b],
II [auth 4],
JI [auth 4],
LF [auth 1],
MM [auth a],
RB [auth A],
SB [auth A],
TJ [auth 6],
VL [auth 9],
WG [auth 2],
ZN [auth c]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX

Query on NEX



Download:Ideal Coordinates CCD File
FN [auth b],
UL [auth 9],
YN [auth c]
(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
XAT

Query on XAT



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AL [auth 8]
CG [auth 1]
GI [auth 4]
JK [auth 7]
NH [auth 3]
AL [auth 8],
CG [auth 1],
GI [auth 4],
JK [auth 7],
NH [auth 3],
NM [auth a],
RJ [auth 6],
TL [auth 9],
UG [auth 2],
XN [auth c],
ZI [auth 5]
(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
LUT

Query on LUT



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BG [auth 1]
DN [auth b]
EN [auth b]
FI [auth 4]
IK [auth 7]
BG [auth 1],
DN [auth b],
EN [auth b],
FI [auth 4],
IK [auth 7],
KM [auth a],
LM [auth a],
MH [auth 3],
QJ [auth 6],
RL [auth 9],
SL [auth 9],
TG [auth 2],
VN [auth c],
WN [auth c],
YI [auth 5],
ZK [auth 8]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR

Query on BCR



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BC [auth A]
BE [auth F]
BL [auth 8]
CF [auth L]
DE [auth F]
BC [auth A],
BE [auth F],
BL [auth 8],
CF [auth L],
DE [auth F],
DF [auth L],
EF [auth M],
GE [auth G],
HI [auth 4],
JF [auth O],
KE [auth G],
KK [auth 7],
LK [auth 7],
NE [auth I],
OE [auth J],
OH [auth 3],
PH [auth 3],
QE [auth J],
RE [auth J],
SJ [auth 6],
TB [auth A],
TD [auth B],
UB [auth A],
UD [auth B],
VB [auth A],
VD [auth B],
VG [auth 2],
WB [auth A],
WD [auth B],
XB [auth A],
XD [auth B],
XE [auth K],
YE [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
(Subject of Investigation/LOI)

Query on LMU



Download:Ideal Coordinates CCD File
AC [auth A],
DC [auth A],
KF [auth O],
OM [auth b],
QH [auth 3]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN

Query on PQN



Download:Ideal Coordinates CCD File
QB [auth A],
SD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
AE [auth C],
YB [auth A],
ZD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
X [auth a],
Y [auth b],
Z [auth c]
L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2020YFA0907600
Chinese Academy of SciencesChinaYSBR-004

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2023-05-10
    Changes: Database references
  • Version 1.3: 2023-06-07
    Changes: Database references
  • Version 1.4: 2024-11-06
    Changes: Data collection, Structure summary