BMRB: 11316

Solution Structure of the zinc finger domain of Transcriptional repressor CTCF protein

Authors

Miyamoto, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Transcriptional repressor CTCF

Entity

1. zinc finger domain (polymer, Thiol state: all other bound), 77 monomers, 8484.439 Da Detail

GSSGSSGRTH SGEKPYECYI CHARFTQSGT MKMHILQKHT ENVAKFHCPH CDTVIARKSD LGVHLRKQHS YSGPSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8615.258 Da

Max. entity weight

8484.439 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS18:SG	2:ZN1:ZN
2	na	sing	1:CYS21:SG	2:ZN1:ZN
3	na	sing	1:HIS34:NE2	2:ZN1:ZN
4	na	sing	1:HIS39:NE2	2:ZN1:ZN
5	na	sing	1:CYS48:SG	2:ZN1:ZN
6	na	sing	1:CYS51:SG	2:ZN1:ZN
7	na	sing	1:HIS64:NE2	2:ZN1:ZN
8	na	sing	1:HIS69:NE2	2:ZN1:ZN

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.5 %, Completeness: 92.8 %, Completeness (bb): 88.8 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	92.8 % (795 of 857)	93.5 % (418 of 447)	93.4 % (310 of 332)	85.9 % (67 of 78)
Backbone	88.8 % (405 of 456)	88.7 % (141 of 159)	90.1 % (201 of 223)	85.1 % (63 of 74)
Sidechain	96.8 % (455 of 470)	96.2 % (277 of 288)	97.8 % (174 of 178)	100.0 % (4 of 4)
Aromatic	100.0 % (76 of 76)	100.0 % (38 of 38)	100.0 % (38 of 38)
Methyl	100.0 % (52 of 52)	100.0 % (26 of 26)	100.0 % (26 of 26)

1. zinc finger domain

GSSGSSGRTH SGEKPYECYI CHARFTQSGT MKMHILQKHT ENVAKFHCPH CDTVIARKSD LGVHLRKQHS YSGPSSG

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 (±0.001) atm, Temperature 298 (±0.1) K, pH 7.0 (±0.05), Details 2.46mM zinc finger domain U-13C, {15N;} 20mM {d-Tris-HCl(pH7.0);} 100mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 0.05mM {ZnCl2;} 90% H2O, 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	zinc finger domain	[U-13C; U-15N]	protein	2.46 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	100 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	0.05 mM
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.2 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CB

Referencing offset: -0.2 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; HA

Referencing offset: 0.04 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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LACS Plot; CO

Referencing offset: -0.03 ppm, Outliers: 1 Detail

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Chemical shift reference

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
13C	DSS	methyl protons	0.0 ppm	null	indirect	0.2514495
1H	DSS	methyl protons	0.0 ppm	null	indirect	1.0
15N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

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Protein Blocks Logo

Calculated from 20 models in PDB: 2CT1, Strand ID: A Detail

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Release date

2011-08-18

Citation

Solution Structure of the zinc finger domain of Transcriptional repressor CTCF protein
Miyamoto, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Related entities 1. zinc finger domain, : 1 : 26 : 260 entities Detail

Interaction partners 1. zinc finger domain, : 12 interactors Detail

Experiments performed 2 experiments Detail