Solution NMR structure ov the chromobox protein Cbx7 with H3K27me3
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 83.2 % (715 of 859) | 89.7 % (408 of 455) | 76.6 % (256 of 334) | 72.9 % (51 of 70) |
Backbone | 76.3 % (313 of 410) | 82.7 % (115 of 139) | 73.3 % (151 of 206) | 72.3 % (47 of 65) |
Sidechain | 85.2 % (439 of 515) | 90.2 % (285 of 316) | 77.3 % (150 of 194) | 80.0 % (4 of 5) |
Aromatic | 83.8 % (62 of 74) | 94.6 % (35 of 37) | 70.6 % (24 of 34) | 100.0 % (3 of 3) |
Methyl | 82.4 % (56 of 68) | 91.2 % (31 of 34) | 73.5 % (25 of 34) |
1. Cbx7
GEQVFAVESI RKKRVRKGKV EYLVKWKGWP PKYSTWEPEE HILDPRLVMA YEEKEE2. H3K27me3
QLATKAARXS APATGSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methylene protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methylene protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methylene protons | 0.0 ppm | na | indirect | 0.1013291 |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl carbons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methylene protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Varian INOVA - 500 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Bruker Avance - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Cbx7 | [U-13C; U-15N] | 0.5 mM | |
2 | H3K27me3 | natural abundance | 2.7 mM | |
3 | sodium phosphate | natural abundance | 10 mM | |
4 | sodium chloride | natural abundance | 300 mM | |
5 | PMSF | natural abundance | 0.5 mM | |
6 | TCEP | natural abundance | 0.5 mM | |
7 | Benzamidine | natural abundance | 1 mM | |
8 | H2O | natural abundance | 90 % | |
9 | D2O | natural abundance | 10 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints | combined_17079_2l1b.nef |
Input source #2: Coordindates | 2l1b.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) |
---|---|---|---|---|
2:8:ARG:C | 2:9:M3L:N | unknown | unknown | n/a |
2:9:M3L:C | 2:10:SER:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 27 | M3L | N-TRIMETHYLLYSINE | Assigned chemical shifts, Coordinates |
Sequence alignments
--------10--------20--------30--------40--------50------ GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE |||||||||||||||||||||||||||||||||||||||||||||||||||||||| GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
-20-------30--- QLATKAARXSAPATG ||||||||||||||| QLATKAARXSAPATG --------10-----
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 56 | 0 | 0 | 100.0 |
B | B | 15 | 0 | 0 | 100.0 |
Content subtype: combined_17079_2l1b.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50------ GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE |||||||||||||||||||||||||||||||||||||||||||||||||||||| ..QVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE
-20-------30--- QLATKAARXSAPATG || ||||||| || QL.TKAARXS.PA -20-------30-
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 384 | 363 | 94.5 |
13C chemical shifts | 280 | 254 | 90.7 |
15N chemical shifts | 60 | 50 | 83.3 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 111 | 102 | 91.9 |
13C chemical shifts | 112 | 100 | 89.3 |
15N chemical shifts | 52 | 46 | 88.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 273 | 261 | 95.6 |
13C chemical shifts | 168 | 154 | 91.7 |
15N chemical shifts | 8 | 4 | 50.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 26 | 25 | 96.2 |
13C chemical shifts | 26 | 25 | 96.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 37 | 35 | 94.6 |
13C chemical shifts | 34 | 24 | 70.6 |
15N chemical shifts | 3 | 3 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 84 | 48 | 57.1 |
13C chemical shifts | 54 | 0 | 0.0 |
15N chemical shifts | 15 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 30 | 12 | 40.0 |
13C chemical shifts | 28 | 0 | 0.0 |
15N chemical shifts | 13 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 54 | 36 | 66.7 |
13C chemical shifts | 26 | 0 | 0.0 |
15N chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 12 | 6 | 50.0 |
13C chemical shifts | 12 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50------ GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE ||||||||||||||||||||||||| |||||||||||||||||||||||||||| ..QVFAVESIRKKRVRKGKVEYLVKWK.WPPKYSTWEPEEHILDPRLVMAYEEKEE