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Solution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA
Authors
Buck-Koehntop, B.A., Stanfield, R.L., Ekiert, D.C., Martinez-Yamout, M.A., Dyson, H., Wilson, I.A., Wright, P.E.
Assembly
Kaiso
Entity
1. Kaiso (polymer, Thiol state: free and other bound), 133 monomers, 16052.29 Da Detail

ANKRMKVKHD DHYELIVDGR VYYICIVCKR SYVCLTSLRR HFNIHSWEKK YPCRYCEKVF PLAEYRTKHE IHHTGERRYQ CLACGKSFIN YQFMSSHIKS VHSQDPSGDS KLYRLHPCRS LQIRQYAYLS DRS


2. DNA strand 1 (polymer, Thiol state: not present), 19 monomers, 5843.719 Da Detail

GTGCTTCCTG CCAATAACG


3. DNA strand 2 (polymer, Thiol state: not present), 19 monomers, 5932.781 Da Detail

CGTTATTGGC AGGAAGCAC


4. ZINC ION (non-polymer, Thiol state: not present), 65.409 × 3 Da
Total weight
28025.018 Da
Max. entity weight
16052.29 Da
Entity Connection
na 12 Detail

IDTypeValue orderAtom ID 1Atom ID 2
1nasing1:CYS25:SG4:ZN1:ZN
2nasing1:CYS28:SG4:ZN1:ZN
3nasing1:HIS41:ND14:ZN1:ZN
4nasing1:HIS45:ND14:ZN1:ZN
5nasing1:CYS53:SG4:ZN1:ZN
6nasing1:CYS56:SG4:ZN1:ZN
7nasing1:HIS69:ND14:ZN1:ZN
8nasing1:HIS73:ND14:ZN1:ZN
9nasing1:CYS81:SG4:ZN1:ZN
10nasing1:CYS84:SG4:ZN1:ZN
11nasing1:HIS97:ND14:ZN1:ZN
12nasing1:HIS102:ND14:ZN1:ZN

Source organism
Homo sapiens
Exptl. method
solution NMR
Refine. method
molecular dynamics
Data set
assigned_chemical_shifts
Chem. Shift Complete
Sequence coverage: 100.0 %, Completeness: 94.4 %, Completeness (bb): 93.3 % Detail

Polymer type: polypeptide(L) polydeoxyribonucleotide

Total1H13C15N
All94.4 % (1898 of 2010)93.4 % (1153 of 1234)95.6 % (610 of 638)97.8 % (135 of 138)
Backbone93.3 % (985 of 1056)88.5 % (471 of 532)98.2 % (388 of 395)97.7 % (126 of 129)
Sidechain96.1 % (1041 of 1083)97.2 % (682 of 702)94.1 % (350 of 372)100.0 % (9 of 9)
Aromatic95.1 % (251 of 264)96.5 % (164 of 170)92.5 % (86 of 93)100.0 % (1 of 1)
Methyl100.0 % (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 DRS

2. DNA strand 1

GTGCTTCCTG CCAATAACG

3. DNA strand 2

CGTTATTGGC AGGAAGCAC

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0


#NameIsotope labelingTypeConcentration
1Kaiso[U-13C; U-15N]500 uM
2Kaiso binding sequence (KBS)natural abundance500 uM
3Trisnatural abundance10 mM
4TCEPnatural abundance1 mM
5H2Onatural abundance95 %
6D2Onatural abundance5 %
Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0


#NameIsotope labelingTypeConcentration
7Kaiso[U-100% 13C; U-100% 15N; U-80% 2H]500 uM
8Kaiso binding sequence (KBS)natural abundance500 uM
9Trisnatural abundance10 mM
10TCEPnatural abundance1 mM
11H2Onatural abundance95 %
12D2Onatural abundance5 %
Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0


#NameIsotope labelingTypeConcentration
13Kaiso[U-13C; U-15N]500 uM
14Kaiso binding sequence (KBS)natural abundance500 uM
15Trisnatural abundance10 mM
16TCEPnatural abundance1 mM
17D2Onatural abundance100 %

LACS Plot; CA
Referencing offset: 0.42 ppm, Outliers: 1 Detail
LACS Plot; CB
Referencing offset: 0.42 ppm, Outliers: 1 Detail
LACS Plot; HA
Referencing offset: -0.04 ppm, Outliers: 2 Detail
LACS Plot; CO
Referencing offset: 0.24 ppm, Outliers: 2 Detail
Protein Blocks Logo
Calculated from 20 models in PDB: 2LT7, Strand ID: A Detail


Release date
2012-05-15
Citation
Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso
Buck-Koehntop, B.A., Stanfield, R.L., Ekiert, D.C., Martinez-Yamout, M.A., Dyson, H., Wilson, I.A., Wright, P.E.
Proc. Natl. Acad. Sci. U. S. A. (2012), 109, 15229-15234, PubMed 22949637 , DOI 10.1073/pnas.1213726109 ,
Related entities 1. Kaiso, : 1 : 13 : 2 : 2 : 160 entities Detail
Experiments performed 12 experiments Detail
NMR combined restraints 4 contents Detail
Keywords double helix, protein-DNA complex, zinc finger