BMRB: 11309

Solution structure of the N-terminal zinc finger domain of mouse cell growth regulating nucleolar protein LYAR

Authors

Muto, Y., Yoneyama, M., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

Cell growth regulating nucleolar protein LYAR

Entity

1. Zinc finger DNA binding domain (polymer, Thiol state: free and other bound), 79 monomers, 8398.311 Da Detail

GSSGSSGMVF FTCNACGESV KKIQVEKHVS NCRNCECLSC IDCGKDFWGD DYKSHVKCIS EGQKYGGKGY EAKSGPSSG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8529.129 Da

Max. entity weight

8398.311 Da

Entity Connection

na 8 Detail

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ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS13:SG	2:ZN1:ZN
2	na	sing	1:CYS16:SG	2:ZN1:ZN
3	na	sing	1:HIS28:NE2	2:ZN1:ZN
4	na	sing	1:CYS32:SG	2:ZN1:ZN
5	na	sing	1:CYS40:SG	2:ZN1:ZN
6	na	sing	1:CYS43:SG	2:ZN1:ZN
7	na	sing	1:HIS55:NE2	2:ZN1:ZN
8	na	sing	1:CYS58:SG	2:ZN1:ZN

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.4 %, Completeness: 93.0 %, Completeness (bb): 90.9 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	93.0 % (793 of 853)	93.3 % (415 of 445)	93.8 % (304 of 324)	88.1 % (74 of 84)
Backbone	90.9 % (429 of 472)	89.9 % (152 of 169)	92.0 % (207 of 225)	89.7 % (70 of 78)
Sidechain	95.5 % (428 of 448)	95.3 % (263 of 276)	97.0 % (161 of 166)	66.7 % (4 of 6)
Aromatic	94.6 % (70 of 74)	94.6 % (35 of 37)	94.4 % (34 of 36)	100.0 % (1 of 1)
Methyl	100.0 % (42 of 42)	100.0 % (21 of 21)	100.0 % (21 of 21)

1. Zinc finger DNA binding domain

GSSGSSGMVF FTCNACGESV KKIQVEKHVS NCRNCECLSC IDCGKDFWGD DYKSHVKCIS EGQKYGGKGY EAKSGPSSG

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 1mM zinc finger DNA binding domain U-15N, {13C;} 20mM {d-Tris-HCl;} 200mM {NaCl;} 1mM {d-DTT;} 0.02% {NaN3;} 100uM {ZnCl2;} 10% D2O

#	Name	Isotope labeling	Type	Concentration
1	zinc finger DNA binding domain	[U-13C; U-15N]	protein	1 mM
2	d-Tris-HCl	natural abundance	buffer	20 mM
3	NaCl	natural abundance	salt	200 mM
4	d-DTT	natural abundance	salt	1 mM
5	NaN3	natural abundance	salt	0.02 %
6	ZnCl2	natural abundance	salt	100 uM
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.16 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: -0.16 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: -0.03 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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LACS Plot; CO

Referencing offset: 0.08 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: 1WJV, Strand ID: A Detail

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Release date

2011-08-18

Citation

Solution structure of the N-terminal zinc finger domain of mouse cell growth regulating nucleolar protein LYAR
Yoneyama, M., Tochio, N., Koshiba, S., Inoue, M., Kigawa, T., Muto, Y., Yokoyama, S.

Related entities 1. Zinc finger DNA binding domain, : 1 : 30 entities Detail

Interaction partners 1. Zinc finger DNA binding domain, : 4 interactors Detail

Experiments performed 2 experiments Detail