Solution structure of JARID1A C-terminal PHD finger in complex with H3(1-9)K4me3
Polymer type: polypeptide(L)
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 85.3 % (561 of 658) | 87.1 % (298 of 342) | 82.3 % (204 of 248) | 86.8 % (59 of 68) |
Backbone | 88.2 % (314 of 356) | 95.0 % (115 of 121) | 84.2 % (149 of 177) | 86.2 % (50 of 58) |
Sidechain | 82.5 % (296 of 359) | 82.8 % (183 of 221) | 81.3 % (104 of 128) | 90.0 % (9 of 10) |
Aromatic | 78.3 % (36 of 46) | 78.3 % (18 of 23) | 76.2 % (16 of 21) | 100.0 % (2 of 2) |
Methyl | 91.7 % (44 of 48) | 95.8 % (23 of 24) | 87.5 % (21 of 24) |
1. JARID1A PHD finger 3
SVCAAQNCQR PCKDKVDWVQ CDGGCDEWFH QVCVGVSPEM AENEDYICIN CA3. H3(1-9)K4me3
ARTXQTARKSolvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details This sample was used to measure N-H RDCs of JARID1A PHD finger 3
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | JARID1A PHD finger 3 | [U-100% 15N] | 0.2 ~ 0.5 mM | |
7 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
8 | DTT | natural abundance | 5 mM | |
9 | ZINC ION | natural abundance | 1 mM | |
10 | MOPS | natural abundance | 10 mM | |
11 | bacteriophage Pf1 | natural abundance | 12 mg/mL |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 293.2 K, pH 7.0, Details 20 mM sodium phosphate, 1 mM ZnCl2, 5 mM DTT, 90%H2O, 10% D2O
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | JARID1A PHD finger 3 | [U-100% 13C; U-100% 15N] | 0.2 ~ 0.5 mM | |
2 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
3 | DTT | natural abundance | 0.5 mM | |
4 | ZINC ION | natural abundance | 1 mM | |
5 | sodium phosphate | natural abundance | 20 mM |
Bruker DMX - 800 MHz
State anisotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 7.0, Details This sample was used to measure N-H RDCs of JARID1A PHD finger 3
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
6 | JARID1A PHD finger 3 | [U-100% 15N] | 0.2 ~ 0.5 mM | |
7 | H3(1-9)K4Me3 | natural abundance | 0.2 ~ 0.5 mM | |
8 | DTT | natural abundance | 5 mM | |
9 | ZINC ION | natural abundance | 1 mM | |
10 | MOPS | natural abundance | 10 mM | |
11 | bacteriophage Pf1 | natural abundance | 12 mg/mL |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints | combined_16210_2kgi.nef |
Input source #2: Coordindates | 2kgi.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) |
---|---|---|---|---|
2:3:THR:C | 2:4:M3L:N | unknown | unknown | n/a |
2:4:M3L:C | 2:5:GLN:N | unknown | unknown | n/a |
1:3:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:8:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:21:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:25:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:30:HIS:ND1 | 3:2:ZN:ZN | unknown | unknown | n/a |
1:33:CYS:SG | 3:2:ZN:ZN | unknown | unknown | n/a |
1:48:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
1:51:CYS:SG | 3:1:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 304 | M3L | N-TRIMETHYLLYSINE | Assigned chemical shifts, Coordinates |
C | 1 | ZN | ZINC ION | None |
C | 2 | ZN | ZINC ION | None |
Sequence alignments
--------10--------20--------30--------40--------50-- SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA |||||||||||||||||||||||||||||||||||||||||||||||||||| SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA
--------- ARTXQTARK ||||||||| ARTXQTARK
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 52 | 0 | 0 | 100.0 |
B | B | 9 | 0 | 0 | 100.0 |
Content subtype: combined_16210_2kgi.nef
Assigned chemical shifts
--------10--------20--------30--------40--------50-- SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA |||||||||||||||||||||||||||||||||||||||||||||||||||| SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA
--------- ARTXQTARK ||||||||| ARTXQTARK
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 214 | 203 | 94.9 |
1H chemical shifts | 292 | 273 | 93.5 |
15N chemical shifts | 60 | 58 | 96.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 104 | 99 | 95.2 |
1H chemical shifts | 105 | 103 | 98.1 |
15N chemical shifts | 50 | 49 | 98.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 110 | 104 | 94.5 |
1H chemical shifts | 187 | 170 | 90.9 |
15N chemical shifts | 10 | 9 | 90.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 21 | 20 | 95.2 |
1H chemical shifts | 21 | 20 | 95.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 21 | 16 | 76.2 |
1H chemical shifts | 23 | 18 | 78.3 |
15N chemical shifts | 2 | 2 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 34 | 0 | 0.0 |
1H chemical shifts | 63 | 42 | 66.7 |
15N chemical shifts | 11 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 16 | 0 | 0.0 |
1H chemical shifts | 18 | 16 | 88.9 |
15N chemical shifts | 8 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 18 | 0 | 0.0 |
1H chemical shifts | 45 | 26 | 57.8 |
15N chemical shifts | 3 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
13C chemical shifts | 7 | 0 | 0.0 |
1H chemical shifts | 7 | 4 | 57.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
Covalent bonds
Distance restraints
--------10--------20--------30--------40--------50-- SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA ||||||||||||||||||||||||||||||||||||||||||||||||||| .VCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA
--------- ARTXQTARK || |||| .RT.QTAR --------
Dihedral angle restraints
--------10--------20--------30--------40--------50-- SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA ||||||||||| ||||||| ||||||||||||||||||||||||||| SVCAAQNCQRP...KVDWVQC..GCDEWFHQVCVGVSPEMAENEDYICIN --------10--------20--------30--------40--------50
RDC restraints
--------10--------20--------30--------40--------50-- SVCAAQNCQRPCKDKVDWVQCDGGCDEWFHQVCVGVSPEMAENEDYICINCA |||||||| ||||||||||||||||||||||||| |||||||||||||| ..CAAQNCQR..KDKVDWVQCDGGCDEWFHQVCVGVS.EMAENEDYICINCA