Solution NMR structures of AF9 yeats domain in complex with histone H3 crotonylation at K18
GSHMASSCAV QVKLELGHRA QVRKKPTVEG FTHDWMVFVR GPEHSNIQHF VEKVVFHLHE SFPRPKRVCK DPPYKVEESG YAGFILPIEV YFKNKEEPRK VRFDYDLFLH LEGHPPVNHL RCEKLTFNNP TEDFRRKLLK A
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 88.8 % (1666 of 1877) | 87.1 % (862 of 990) | 91.2 % (671 of 736) | 88.1 % (133 of 151) |
Backbone | 90.2 % (806 of 894) | 92.1 % (279 of 303) | 89.6 % (403 of 450) | 87.9 % (124 of 141) |
Sidechain | 89.0 % (1003 of 1127) | 84.9 % (583 of 687) | 95.6 % (411 of 430) | 90.0 % (9 of 10) |
Aromatic | 85.1 % (165 of 194) | 83.5 % (81 of 97) | 86.5 % (83 of 96) | 100.0 % (1 of 1) |
Methyl | 100.0 % (142 of 142) | 100.0 % (71 of 71) | 100.0 % (71 of 71) |
1. entity 1
GSHMASSCAV QVKLELGHRA QVRKKPTVEG FTHDWMVFVR GPEHSNIQHF VEKVVFHLHE SFPRPKRVCK DPPYKVEESG YAGFILPIEV YFKNKEEPRK VRFDYDLFLH LEGHPPVNHL RCEKLTFNNP TEDFRRKLLK A2. entity 2
GGKAPRXQLA TKASolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | sodium phosphate | natural abundance | 10 mM | |
10 | sodium chloride | natural abundance | 500 mM | |
11 | EDTA | natural abundance | 2 mM | |
12 | DTT | [U-100% 2H] | 2 mM | |
13 | D2O | natural abundance | 100 % | |
14 | entity_1 | 13C/15N-labelled | 0.5 mM | |
15 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | sodium phosphate | natural abundance | 10 mM | |
2 | sodium chloride | natural abundance | 500 mM | |
3 | EDTA | natural abundance | 2 mM | |
4 | DTT | [U-100% 2H] | 2 mM | |
5 | H20 | natural abundance | 90 % | |
6 | D2O | natural abundance | 10 % | |
7 | entity_1 | 13C/15N-labelled | 0.5 mM | |
8 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | sodium phosphate | natural abundance | 10 mM | |
10 | sodium chloride | natural abundance | 500 mM | |
11 | EDTA | natural abundance | 2 mM | |
12 | DTT | [U-100% 2H] | 2 mM | |
13 | D2O | natural abundance | 100 % | |
14 | entity_1 | 13C/15N-labelled | 0.5 mM | |
15 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | sodium phosphate | natural abundance | 10 mM | |
10 | sodium chloride | natural abundance | 500 mM | |
11 | EDTA | natural abundance | 2 mM | |
12 | DTT | [U-100% 2H] | 2 mM | |
13 | D2O | natural abundance | 100 % | |
14 | entity_1 | 13C/15N-labelled | 0.5 mM | |
15 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | sodium phosphate | natural abundance | 10 mM | |
10 | sodium chloride | natural abundance | 500 mM | |
11 | EDTA | natural abundance | 2 mM | |
12 | DTT | [U-100% 2H] | 2 mM | |
13 | D2O | natural abundance | 100 % | |
14 | entity_1 | 13C/15N-labelled | 0.5 mM | |
15 | entity_2 | 13C/15N-labelled | 0.25 mM |
Bruker Avance - 800 MHz cryo-probe
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
9 | sodium phosphate | natural abundance | 10 mM | |
10 | sodium chloride | natural abundance | 500 mM | |
11 | EDTA | natural abundance | 2 mM | |
12 | DTT | [U-100% 2H] | 2 mM | |
13 | D2O | natural abundance | 100 % | |
14 | entity_1 | 13C/15N-labelled | 0.5 mM | |
15 | entity_2 | 13C/15N-labelled | 0.25 mM |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_26060_2ndg.nef |
Input source #2: Coordindates | 2ndg.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) |
---|---|---|---|---|
2:6:ARG:C | 2:7:KCR:N | unknown | unknown | n/a |
2:7:KCR:C | 2:8:GLN:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 218 | KCR | N-6-crotonyl-L-lysine | Assigned chemical shifts, Coordinates |
Sequence alignments
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK -------110-------120-------130-------140- VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA ||||||||||||||||||||||||||||||||||||||||| VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA
------220---- GGKAPRXQLATKA ||||||||||||| GGKAPRXQLATKA --------10---
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 141 | 0 | 0 | 100.0 |
B | B | 13 | 0 | 0 | 100.0 |
Content subtype: combined_26060_2ndg.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ...MASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK -------110-------120-------130-------140- VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA ||||||||| ||||||||||||||||||||||||||||||| VRFDYDLFL.LEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA
------220---- GGKAPRXQLATKA ||||||||||||| GGKAPRXQLATKA
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
27 | THR | HG1 | 5.57 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 687 | 633 | 92.1 |
1H chemical shifts | 920 | 809 | 87.9 |
15N chemical shifts | 149 | 123 | 82.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 282 | 246 | 87.2 |
1H chemical shifts | 278 | 255 | 91.7 |
15N chemical shifts | 130 | 115 | 88.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 405 | 387 | 95.6 |
1H chemical shifts | 642 | 554 | 86.3 |
15N chemical shifts | 19 | 8 | 42.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 67 | 66 | 98.5 |
1H chemical shifts | 67 | 66 | 98.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 96 | 83 | 86.5 |
1H chemical shifts | 97 | 85 | 87.6 |
15N chemical shifts | 1 | 1 | 100.0 |
Comp_index_ID | Comp_ID |
---|---|
218 | KCR |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 49 | 28 | 57.1 |
1H chemical shifts | 70 | 46 | 65.7 |
15N chemical shifts | 13 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 24 | 7 | 29.2 |
1H chemical shifts | 25 | 19 | 76.0 |
15N chemical shifts | 11 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 25 | 21 | 84.0 |
1H chemical shifts | 45 | 27 | 60.0 |
15N chemical shifts | 2 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 6 | 6 | 100.0 |
1H chemical shifts | 6 | 6 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK | | | |||||||| | | | ||||||||||| | | || |||||||||| | | | | | | ||| || |||||||| || .......C.V.V.LELGHRAQ.R.K.T..GFTHDWMVFVR.P..S.IQ.FVEKVVFHLH..F..P.R.C....Y.V.ESG..GF.LPIEVYFK.....RK -------110-------120-------130-------140- VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA | | | || || | | | | | | | | ||||||||||| V.F.Y.LF.HL..H..V.H.R.E.L.F.N.TEDFRRKLLKA
Dihedral angle restraints
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 GSHMASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ....ASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFPRPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRK -------110-------120-------130-------140- VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA ||||||||||||||||||||||||||||||||||||||||| VRFDYDLFLHLEGHPPVNHLRCEKLTFNNPTEDFRRKLLKA