BMRB: 10247

Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains

Authors

Sato, M., Tomizawa, T., Saito, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Assembly

NEDD9 interacting protein with calponin homology and LIM domains

Entity

1. LIM domain (polymer, Thiol state: free and other bound), 82 monomers, 8833.584 Da Detail

GSSGSSGQHQ EAGAGDLCAL CGEHLYVLER LCVNGHFFHR SCFRCHTCEA TLWPGGYEQH PGDGHFYCLQ HLPQTDSGPS SG

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

8964.402 Da

Max. entity weight

8833.584 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:HIS39:ND1	2:ZN1:ZN
4	na	sing	1:CYS42:SG	2:ZN1:ZN
5	na	sing	1:CYS45:SG	2:ZN1:ZN
6	na	sing	1:CYS48:SG	2:ZN1:ZN
7	na	sing	1:CYS68:SG	2:ZN1:ZN
8	na	sing	1:HIS71:ND1	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: 92.7 %, Completeness: 90.3 %, Completeness (bb): 88.2 % Detail

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Polymer type: polypeptide(L)

	Total	1H	13C	15N
All	90.3 % (791 of 876)	89.3 % (402 of 450)	92.1 % (314 of 341)	88.2 % (75 of 85)
Backbone	88.2 % (427 of 484)	85.0 % (147 of 173)	90.6 % (211 of 233)	88.5 % (69 of 78)
Sidechain	92.8 % (428 of 461)	92.1 % (255 of 277)	94.4 % (167 of 177)	85.7 % (6 of 7)
Aromatic	92.6 % (100 of 108)	92.6 % (50 of 54)	92.5 % (49 of 53)	100.0 % (1 of 1)
Methyl	100.0 % (54 of 54)	100.0 % (27 of 27)	100.0 % (27 of 27)

1. LIM domain

GSSGSSGQHQ EAGAGDLCAL CGEHLYVLER LCVNGHFFHR SCFRCHTCEA TLWPGGYEQH PGDGHFYCLQ HLPQTDSGPS SG

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)

#	Name	Isotope labeling	Type	Concentration
1	LIM domain	[U-13C; U-15N]	protein	1 mM
2	d-Tris HCl		buffer	20 mM
3	NaCl		salt	100 mM
4	d-DTT		salt	1 mM
5	NaN3		salt	0.02 %
6	ZnCl2		salt	0.01 mM
7	H2O		solvent	90 %
8	D2O		solvent	10 %

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LACS Plot; CA

Referencing offset: -0.22 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: -0.22 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: 0.02 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: 0.19 ppm, Outliers: 4 Detail

Show chemical shift referencing parameters

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: 2CO8, Strand ID: A Detail

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Release date

2009-11-02

Citation

Solution structures of the LIM domain of human NEDD9 interacting protein with calponin homology and LIM domains
Sato, M., Tomizawa, T., Saito, K., Koshiba, S., Inoue, M., Kigawa, T., Yokoyama, S.

Related entities 1. LIM domain, : 1 : 2 : 63 entities Detail

Interaction partners 1. LIM domain, : 8 interactors Detail

Experiments performed 2 experiments Detail