LC3B OPTN-LIR Ptot complex structure
GAMGKTFKQR RTFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT KFLVPDHVNM SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE SEKDEDGFLY MVYASQETF
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 92.3 % (1483 of 1606) | 97.9 % (826 of 844) | 85.4 % (533 of 624) | 89.9 % (124 of 138) |
Backbone | 91.8 % (712 of 776) | 98.1 % (258 of 263) | 88.1 % (341 of 387) | 89.7 % (113 of 126) |
Sidechain | 92.6 % (884 of 955) | 97.8 % (568 of 581) | 84.3 % (305 of 362) | 91.7 % (11 of 12) |
Aromatic | 78.2 % (97 of 124) | 100.0 % (62 of 62) | 56.5 % (35 of 62) | |
Methyl | 91.8 % (134 of 146) | 94.5 % (69 of 73) | 89.0 % (65 of 73) |
1. entity 1
GAMGKTFKQR RTFEQRVEDV RLIREQHPTK IPVIIERYKG EKQLPVLDKT KFLVPDHVNM SELIKIIRRR LQLNANQAFF LLVNGHSMVS VSTPISEVYE SEKDEDGFLY MVYASQETF2. entity 2
NXXGXXEDXF VEIRMAESolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of OPTN-LIR in complex with LC3B Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | entity_1 | [U-98% 13C; U-98% 15N] | 2.5 (±0.05) mM | |
10 | entity_2 | natural abundance | 0.4 (±0.04) mM | |
11 | sodium phosphate | natural abundance | 70 mM | |
12 | sodium chloride | natural abundance | 30 mM | |
13 | DSS | natural abundance | 0.3 mM | |
14 | Protease inhibitors cocktail | natural abundance | 5 mM | |
15 | H2O | natural abundance | 95 % | |
16 | D2O | natural abundance | 5 % |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 600 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 900 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Bruker Avance - 700 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of OPTN-LIR in complex with LC3B Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | entity_1 | [U-98% 13C; U-98% 15N] | 2.5 (±0.05) mM | |
10 | entity_2 | natural abundance | 0.4 (±0.04) mM | |
11 | sodium phosphate | natural abundance | 70 mM | |
12 | sodium chloride | natural abundance | 30 mM | |
13 | DSS | natural abundance | 0.3 mM | |
14 | Protease inhibitors cocktail | natural abundance | 5 mM | |
15 | H2O | natural abundance | 95 % | |
16 | D2O | natural abundance | 5 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 288 K, pH 6.8, Details Assignment and distance restraints of LC3B in complex with OPTN-LIR Ptot
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | entity_1 | [U-98% 13C; U-98% 15N] | 0.6 (±0.05) mM | |
2 | entity_2 | natural abundance | 4.9 (±0.5) mM | |
3 | sodium phosphate | natural abundance | 70 mM | |
4 | sodium chloride | natural abundance | 30 mM | |
5 | DSS | natural abundance | 0.3 mM | |
6 | Protease inhibitors cocktail | natural abundance | 5 mM | |
7 | H2O | natural abundance | 95 % | |
8 | D2O | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18518_2lue.nef |
Input source #2: Coordindates | 2lue.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | None |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
NoneOther bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Å) |
---|---|---|---|---|
2:1:ASN:C | 2:2:SEP:N | unknown | unknown | n/a |
2:2:SEP:C | 2:3:SEP:N | unknown | unknown | n/a |
2:3:SEP:C | 2:4:GLY:N | unknown | unknown | n/a |
2:4:GLY:C | 2:5:SEP:N | unknown | unknown | n/a |
2:5:SEP:C | 2:6:SEP:N | unknown | unknown | n/a |
2:6:SEP:C | 2:7:GLU:N | unknown | unknown | n/a |
2:8:ASP:C | 2:9:SEP:N | unknown | unknown | n/a |
2:9:SEP:C | 2:10:PHE:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 170 | SEP | PHOSPHOSERINE | Assigned chemical shifts, Coordinates |
B | 171 | SEP | PHOSPHOSERINE | Assigned chemical shifts, Coordinates |
B | 173 | SEP | PHOSPHOSERINE | Assigned chemical shifts, Coordinates |
B | 174 | SEP | PHOSPHOSERINE | Assigned chemical shifts, Coordinates |
B | 177 | SEP | PHOSPHOSERINE | Assigned chemical shifts, Coordinates |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE -------110--------- SEKDEDGFLYMVYASQETF ||||||||||||||||||| SEKDEDGFLYMVYASQETF
-170-----180----- NXXGXXEDXFVEIRMAE ||||||||||||||||| NXXGXXEDXFVEIRMAE --------10-------
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 119 | 0 | 0 | 100.0 |
B | B | 17 | 0 | 0 | 100.0 |
Content subtype: combined_18518_2lue.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE -------110--------- SEKDEDGFLYMVYASQETF ||||||||||||||||||| SEKDEDGFLYMVYASQETF
-170-----180----- NXXGXXEDXFVEIRMAE ||||||||||||||||| NXXGXXEDXFVEIRMAE
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
9 | GLN | CD | 180.738 |
10 | ARG | HH12 | 6.88 |
10 | ARG | HH22 | 7.56 |
11 | ARG | HH12 | 7.215 |
11 | ARG | HH22 | 7.256 |
11 | ARG | NH1 | 72.531 |
11 | ARG | NH2 | 72.478 |
15 | GLN | CD | 180.549 |
21 | ARG | HH11 | 7.053 |
21 | ARG | HH12 | 6.835 |
21 | ARG | HH21 | 7.118 |
21 | ARG | HH22 | 6.99 |
21 | ARG | NH1 | 71.77 |
21 | ARG | NH2 | 71.77 |
24 | ARG | HH12 | 6.53 |
24 | ARG | HH22 | 7.116 |
24 | ARG | NH1 | 71.595 |
24 | ARG | NH2 | 71.595 |
26 | GLN | CD | 179.885 |
37 | ARG | HH12 | 6.498 |
37 | ARG | HH22 | 6.555 |
37 | ARG | NH1 | 69.721 |
37 | ARG | NH2 | 70.893 |
43 | GLN | CD | 180.164 |
59 | ASN | CG | 175.864 |
68 | ARG | HH22 | 7.488 |
69 | ARG | HH22 | 7.5 |
70 | ARG | HH12 | 7.215 |
70 | ARG | HH22 | 7.256 |
70 | ARG | NH1 | 72.531 |
70 | ARG | NH2 | 72.478 |
72 | GLN | CD | 181.782 |
74 | ASN | CG | 176.469 |
76 | ASN | CG | 177.398 |
77 | GLN | CD | 180.096 |
84 | ASN | CG | 178.541 |
116 | GLN | CD | 180.772 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 773 | 767 | 99.2 |
13C chemical shifts | 572 | 537 | 93.9 |
15N chemical shifts | 134 | 131 | 97.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 238 | 236 | 99.2 |
13C chemical shifts | 238 | 228 | 95.8 |
15N chemical shifts | 114 | 112 | 98.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 535 | 531 | 99.3 |
13C chemical shifts | 334 | 309 | 92.5 |
15N chemical shifts | 20 | 19 | 95.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 72 | 71 | 98.6 |
13C chemical shifts | 72 | 71 | 98.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 57 | 57 | 100.0 |
13C chemical shifts | 57 | 35 | 61.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 91 | 89 | 97.8 |
13C chemical shifts | 62 | 0 | 0.0 |
15N chemical shifts | 19 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 35 | 34 | 97.1 |
13C chemical shifts | 29 | 0 | 0.0 |
15N chemical shifts | 17 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 56 | 55 | 98.2 |
13C chemical shifts | 33 | 0 | 0.0 |
15N chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 6 | 6 | 100.0 |
13C chemical shifts | 6 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 5 | 100.0 |
13C chemical shifts | 5 | 0 | 0.0 |
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .AMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE -------110--------- SEKDEDGFLYMVYASQETF ||||||||||||||||||| SEKDEDGFLYMVYASQETF
-170-----180----- NXXGXXEDXFVEIRMAE | |||||||| N........FVEIRMAE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE | |||||||||||||||||| |||||| | ||||| ||||||||||||| | | ||||||| .....T...RRTFEQRVEDVRLIREQH...IPVIIE.Y...........TKFLV....NMSELIKIIRRRL........F.L...........PISEVYE --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 -------110--------- SEKDEDGFLYMVYASQETF ||| | |||| SEK.....L.MVYA -------110----
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GAMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| .AMGKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYE -------110--------- SEKDEDGFLYMVYASQETF ||||||||||||||||||| SEKDEDGFLYMVYASQETF
-170-----180----- NXXGXXEDXFVEIRMAE || |||||||| ......ED.FVEIRMAE