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BMRB: 30074

5JPW

Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB

Authors

Rodriguez-Crespo, I., Merino-Gracia, J., Bruix, M., Zamora-Carreras, H.

Assembly

Dynein light chain Tctex-type 1

Entity

1. Dynein light chain Tctex-type 1 (polymer, Thiol state: not reported), 143 monomers, 15418.28 × 2 Da Detail

GSMEDYQAAE ETAFVVDEVS NIVKEAIESA IGGNAYQHSK VNQWTTNVVE QTLSQLTKLG KPFKYIVTCV IMQKNGAGLH TASSCFWDSS TDGSCTVRWE NKTMYCIVSA FGLSIGGGSG QSGPIKLGMA KITQVDFPPR EIV

Total weight

30836.56 Da

Max. entity weight

15418.28 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 80.6 %, Completeness (bb): 84.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.6 % (1292 of 1602)	85.3 % (701 of 822)	72.6 % (453 of 624)	88.5 % (138 of 156)
Backbone	84.9 % (722 of 850)	95.9 % (284 of 296)	73.3 % (304 of 415)	96.4 % (134 of 139)
Sidechain	78.8 % (694 of 881)	79.3 % (417 of 526)	80.8 % (273 of 338)	23.5 % (4 of 17)
Aromatic	40.5 % (51 of 126)	49.2 % (31 of 63)	28.3 % (17 of 60)	100.0 % (3 of 3)
Methyl	99.4 % (157 of 158)	100.0 % (79 of 79)	98.7 % (78 of 79)

1. Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2

GSMEDYQAAE ETAFVVDEVS NIVKEAIESA IGGNAYQHSK VNQWTTNVVE QTLSQLTKLG KPFKYIVTCV IMQKNGAGLH TASSCFWDSS TDGSCTVRWE NKTMYCIVSA FGLSIGGGSG QSGPIKLGMA KITQVDFPPR EIV

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 100 uM DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	DSS	natural abundance	50 uM
2	DTT	natural abundance	1 mM
3	DYNLT1/Tctex1-DIC chimera	natural abundance	100 uM
4	potassium phosphate	natural abundance	100 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 100 uM [U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
7	DSS	natural abundance	50 uM
8	DTT	natural abundance	1 mM
9	DYNLT1/Tctex1-DIC chimera	[U-99% 15N]	100 uM
10	potassium phosphate	natural abundance	100 mM
11	H2O	natural abundance	90 %
12	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7, Details 100 uM [U-99% 13C; U-99% 15N] DYNLT1/Tctex1-DIC chimera, 100 mM potassium phosphate, 1 mM DTT, 50 uM DSS, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
13	DSS	natural abundance	50 uM
14	DTT	natural abundance	1 mM
15	DYNLT1/Tctex1-DIC chimera	[U-99% 13C; U-99% 15N]	100 uM
16	potassium phosphate	natural abundance	100 mM
17	H2O	natural abundance	90 %
18	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: -0.02 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5JPW, Strand ID: A, B Detail

Release date

2016-08-10

Citation

Molecular Basis for the Protein Recognition Specificity of the dynein light chain DYNLT1/Tctex1. Characterization of the Interaction with Activin Receptor IIB
Rodriguez-Crespo, I., Merino-Gracia, J., Bruix, M., Zamora-Carreras, H.
J. Biol. Chem. (2016), 291, 20962-20975, PubMed 27502274 , DOI 10.1074/jbc.M116.736884 , Abstract