Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA
ANKRMKVKHD DHYELIVDGR VYYICIVCKR SYVCLTSLRR HFNIHSWEKK YPCRYCEKVF PLAEYRTKHE IHHTGERRYQ CLACGKSFIN YQFMSSHIKS VHSQDPSGDS KLYRLHPCRS LQIRQYAYLS DRS
ID | Type | Value order | Atom ID 1 | Atom ID 2 |
---|---|---|---|---|
1 | na | sing | 1:CYS25:SG | 4:ZN1:ZN |
2 | na | sing | 1:CYS28:SG | 4:ZN1:ZN |
3 | na | sing | 1:HIS41:ND1 | 4:ZN1:ZN |
4 | na | sing | 1:HIS45:ND1 | 4:ZN1:ZN |
5 | na | sing | 1:CYS53:SG | 4:ZN1:ZN |
6 | na | sing | 1:CYS56:SG | 4:ZN1:ZN |
7 | na | sing | 1:HIS69:ND1 | 4:ZN1:ZN |
8 | na | sing | 1:HIS73:ND1 | 4:ZN1:ZN |
9 | na | sing | 1:CYS81:SG | 4:ZN1:ZN |
10 | na | sing | 1:CYS84:SG | 4:ZN1:ZN |
11 | na | sing | 1:HIS97:ND1 | 4:ZN1:ZN |
12 | na | sing | 1:HIS102:ND1 | 4:ZN1:ZN |
Polymer type: polypeptide(L) polydeoxyribonucleotide
Total | 1H | 13C | 15N | |
---|---|---|---|---|
All | 94.4 % (1898 of 2010) | 93.4 % (1153 of 1234) | 95.6 % (610 of 638) | 97.8 % (135 of 138) |
Backbone | 93.3 % (985 of 1056) | 88.5 % (471 of 532) | 98.2 % (388 of 395) | 97.7 % (126 of 129) |
Sidechain | 96.1 % (1041 of 1083) | 97.2 % (682 of 702) | 94.1 % (350 of 372) | 100.0 % (9 of 9) |
Aromatic | 95.1 % (251 of 264) | 96.5 % (164 of 170) | 92.5 % (86 of 93) | 100.0 % (1 of 1) |
Methyl | 100.0 % (119 of 119) | 100.0 % (64 of 64) | 100.0 % (55 of 55) |
1. Kaiso
ANKRMKVKHD DHYELIVDGR VYYICIVCKR SYVCLTSLRR HFNIHSWEKK YPCRYCEKVF PLAEYRTKHE IHHTGERRYQ CLACGKSFIN YQFMSSHIKS VHSQDPSGDS KLYRLHPCRS LQIRQYAYLS DRS2. DNA strand 1
GTGCTTCCTG CCAATAACG3. DNA strand 2
CGTTATTGGC AGGAAGCACSolvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Kaiso | [U-13C; U-15N] | 500 uM | |
2 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
3 | Tris | natural abundance | 10 mM | |
4 | TCEP | natural abundance | 1 mM | |
5 | H2O | natural abundance | 95 % | |
6 | D2O | natural abundance | 5 % |
Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | Kaiso | [U-13C; U-15N] | 500 uM | |
14 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
15 | Tris | natural abundance | 10 mM | |
16 | TCEP | natural abundance | 1 mM | |
17 | D2O | natural abundance | 100 % |
Atom type | Mol. common name | Atom group | Value | Ref. method | Ref. type | Shift ratio |
---|---|---|---|---|---|---|
13C | DSS | methyl protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl 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 protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl 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 protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl 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 protons | 0.0 ppm | na | indirect | 0.2514495 |
1H | DSS | methyl protons | 0.0 ppm | internal | direct | 1.0 |
15N | DSS | methyl protons | 0.0 ppm | na | indirect | 0.1013291 |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Kaiso | [U-13C; U-15N] | 500 uM | |
2 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
3 | Tris | natural abundance | 10 mM | |
4 | TCEP | natural abundance | 1 mM | |
5 | H2O | natural abundance | 95 % | |
6 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | Kaiso | [U-13C; U-15N] | 500 uM | |
14 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
15 | Tris | natural abundance | 10 mM | |
16 | TCEP | natural abundance | 1 mM | |
17 | D2O | natural abundance | 100 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | Kaiso | [U-13C; U-15N] | 500 uM | |
14 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
15 | Tris | natural abundance | 10 mM | |
16 | TCEP | natural abundance | 1 mM | |
17 | D2O | natural abundance | 100 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | Kaiso | [U-13C; U-15N] | 500 uM | |
14 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
15 | Tris | natural abundance | 10 mM | |
16 | TCEP | natural abundance | 1 mM | |
17 | D2O | natural abundance | 100 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
1 | Kaiso | [U-13C; U-15N] | 500 uM | |
2 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
3 | Tris | natural abundance | 10 mM | |
4 | TCEP | natural abundance | 1 mM | |
5 | H2O | natural abundance | 95 % | |
6 | D2O | natural abundance | 5 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
13 | Kaiso | [U-13C; U-15N] | 500 uM | |
14 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
15 | Tris | natural abundance | 10 mM | |
16 | TCEP | natural abundance | 1 mM | |
17 | D2O | natural abundance | 100 % |
Bruker DMX - 500 MHz
State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0
# | Name | Isotope labeling | Type | Concentration |
---|---|---|---|---|
7 | Kaiso | [U-100% 13C; U-100% 15N; U-80% 2H] | 500 uM | |
8 | Kaiso binding sequence (KBS) | natural abundance | 500 uM | |
9 | Tris | natural abundance | 10 mM | |
10 | TCEP | natural abundance | 1 mM | |
11 | H2O | natural abundance | 95 % | |
12 | D2O | natural abundance | 5 % |
Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_18462_2lt7.nef |
Input source #2: Coordindates | 2lt7.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 (Ã…) |
---|---|---|---|---|
1:41:HIS:NE2 | 4:1:ZN:ZN | unknown | unknown | n/a |
1:45:HIS:NE2 | 4:1:ZN:ZN | unknown | unknown | n/a |
1:73:HIS:NE2 | 4:2:ZN:ZN | unknown | unknown | n/a |
1:97:HIS:NE2 | 4:3:ZN:ZN | unknown | unknown | n/a |
1:102:HIS:NE2 | 4:3:ZN:ZN | unknown | unknown | n/a |
1:69:HIS:NE2 | 4:2:ZN:ZN | unknown | unknown | n/a |
1:56:CYS:SG | 4:2:ZN:ZN | unknown | unknown | n/a |
1:25:CYS:SG | 4:1:ZN:ZN | unknown | unknown | n/a |
1:84:CYS:SG | 4:3:ZN:ZN | unknown | unknown | n/a |
1:28:CYS:SG | 4:1:ZN:ZN | unknown | unknown | n/a |
1:81:CYS:SG | 4:3:ZN:ZN | unknown | unknown | n/a |
1:53:CYS:SG | 4:2:ZN:ZN | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|---|---|---|---|
B | 1 | ZN | ZINC ION | None |
B | 2 | ZN | ZINC ION | None |
B | 3 | ZN | ZINC ION | None |
Sequence alignments
------480-------490-------500-------510-------520-------530-------540-------550-------560-------570- ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS --------10--------20--------30--------40--------50--------60--------70--------80--------90-------100 ------580-------590-------600---- VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS ||||||||||||||||||||||||||||||||| VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS -------110-------120-------130---
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|---|---|---|---|---|
A | A | 133 | 0 | 0 | 100.0 |
D | D | 19 | 0 | 0 | 100.0 |
E | E | 19 | 0 | 0 | 100.0 |
Content subtype: combined_18462_2lt7.nef
Assigned chemical shifts
------480-------490-------500-------510-------520-------530-------540-------550-------560-------570- ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS ------580-------590-------600---- VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS ||||||||||||||||||||||||||||||||| VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS
--------10--------- GTGCTTCCTGCCAATAACG ||||||||||||||||||| GTGCTTCCTGCCAATAACG
20-------30-------- CGTTATTGGCAGGAAGCAC ||||||||||||||||||| CGTTATTGGCAGGAAGCAC
Comp_index_ID | Comp_ID | Atom_ID | CS value (ppm) |
---|---|---|---|
480 | HIS | ND1 | 200.103 |
480 | HIS | NE2 | 177.428 |
483 | HIS | ND1 | 205.16 |
483 | HIS | NE2 | 180.13 |
512 | HIS | HD1 | 12.785 |
512 | HIS | ND1 | 175.97 |
512 | HIS | NE2 | 214.773 |
516 | HIS | ND1 | 169.208 |
516 | HIS | NE2 | 213.846 |
540 | HIS | ND1 | 173.489 |
540 | HIS | NE2 | 217.21 |
543 | HIS | ND1 | 190.035 |
543 | HIS | NE2 | 177.109 |
544 | HIS | ND1 | 172.212 |
544 | HIS | NE2 | 215.603 |
568 | HIS | ND1 | 174.478 |
568 | HIS | NE2 | 217.699 |
573 | HIS | ND1 | 171.233 |
573 | HIS | NE2 | 214.171 |
587 | HIS | ND1 | 235.363 |
587 | HIS | NE2 | 168.675 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 863 | 846 | 98.0 |
13C chemical shifts | 638 | 607 | 95.1 |
15N chemical shifts | 151 | 144 | 95.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 266 | 260 | 97.7 |
13C chemical shifts | 266 | 260 | 97.7 |
15N chemical shifts | 129 | 126 | 97.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 597 | 586 | 98.2 |
13C chemical shifts | 372 | 347 | 93.3 |
15N chemical shifts | 22 | 18 | 81.8 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 57 | 56 | 98.2 |
13C chemical shifts | 57 | 56 | 98.2 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 94 | 91 | 96.8 |
13C chemical shifts | 93 | 86 | 92.5 |
15N chemical shifts | 1 | 1 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 188 | 159 | 84.6 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 133 | 106 | 79.7 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 55 | 53 | 96.4 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 5 | 5 | 100.0 |
13C chemical shifts | 5 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 12 | 12 | 100.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 183 | 152 | 83.1 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 133 | 107 | 80.5 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 50 | 45 | 90.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 4 | 4 | 100.0 |
13C chemical shifts | 4 | 0 | 0.0 |
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|---|---|---|
1H chemical shifts | 16 | 15 | 93.8 |
Covalent bonds
Distance restraints
------480-------490-------500-------510-------520-------530-------540-------550-------560-------570- ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS ||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| .NKR.KVKH.DHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLAC.KSFINYQFMSSHIKS ------580-------590-------600---- VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS ||||||||||||||||||||||||||||||||| VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS
--------10--------- GTGCTTCCTGCCAATAACG ||||||||||||||||||| GTGCTTCCTGCCAATAACG
20-------30-------- CGTTATTGGCAGGAAGCAC ||||||||||||||||||| CGTTATTGGCAGGAAGCAC
Dihedral angle restraints
------480-------490-------500-------510-------520-------530-------540-------550-------560-------570- ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ANKRMKVKHDDHYELIVDGRVYYICIVCKRSYVCLTSLRRHFNIHSWEKKYPCRYCEKVFPLAEYRTKHEIHHTGERRYQCLACGKSFINYQFMSSHIKS ------580-------590-------600---- VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS ||||||||||||||||||||||||||||||||| VHSQDPSGDSKLYRLHPCRSLQIRQYAYLSDRS
--------10--------- GTGCTTCCTGCCAATAACG ||||||||||||||||||| GTGCTTCCTGCCAATAACG
20-------30-------- CGTTATTGGCAGGAAGCAC ||||||||||||||||||| CGTTATTGGCAGGAAGCAC