BMRB Entry 30074

Name: Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB
Published: 2016-08-11

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PDB ID: 5jpw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30074
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB PubMed: 27502274

Deposition date: 2016-05-04 Original release date: 2016-08-11

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

Citation: Rodriguez-Crespo, I.; Merino-Gracia, J.; Bruix, M.; Zamora-Carreras, H.. "Molecular basis for protein recognition specificity of the DYNLT1/Tctex1 canonical binding groove. Characterization of the interaction with activin receptor IIB" J. Biol. Chem. 291, 20962-20975 (2016).

Assembly members:
Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2, polymer, 143 residues, 15431.400 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
Dynein light chain Tctex-type 1,Cytoplasmic dynein 1 intermediate chain 2: GSMEDYQAAEETAFVVDEVS NIVKEAIESAIGGNAYQHSK VNQWTTNVVEQTLSQLTKLG KPFKYIVTCVIMQKNGAGLH TASSCFWDSSTDGSCTVRWE NKTMYCIVSAFGLSIGGGSG QSGPIKLGMAKITQVDFPPR EIV

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	808
15N chemical shifts	268
1H chemical shifts	1672

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1

Entities:

Entity 1, entity_1, chain 1 143 residues - 15431.400 Da.

1

GLY

SER

MET

GLU

ASP

TYR

GLN

ALA

GLU

2

GLU

THR

ALA

PHE

VAL

ASP

GLU

VAL

SER

3

ASN

ILE

VAL

LYS

GLU

ALA

ILE

GLU

SER

ALA

4

ILE

GLY

ASN

ALA

TYR

GLN

HIS

SER

LYS

5

VAL

ASN

GLN

TRP

THR

ASN

VAL

GLU

6

GLN

THR

LEU

SER

GLN

LEU

THR

LYS

LEU

GLY

7

LYS

PRO

PHE

LYS

TYR

ILE

VAL

THR

CYS

VAL

8

ILE

MET

GLN

LYS

ASN

GLY

ALA

GLY

LEU

HIS

9

THR

ALA

SER

CYS

PHE

TRP

ASP

SER

10

THR

ASP

GLY

SER

CYS

THR

VAL

ARG

TRP

GLU

11

ASN

LYS

THR

MET

TYR

CYS

ILE

VAL

SER

ALA

12

PHE

GLY

LEU

SER

ILE

GLY

SER

GLY

13

GLN

SER

GLY

PRO

ILE

LYS

LEU

GLY

MET

ALA

14

LYS

ILE

THR

GLN

VAL

ASP

PHE

PRO

ARG

15

GLU

ILE

VAL

Samples:

sample_1: DSS 50 uM; DTT 1 mM; DYNLT1/Tctex1-DIC chimera 100 uM; potassium phosphate 100 mM; H2O 90%; D2O 10%

sample_2: DSS 50 uM; DTT 1 mM; DYNLT1/Tctex1-DIC chimera, [U-99% 15N], 100 uM; potassium phosphate 100 mM; H2O 90%; D2O 10%

sample_3: DSS 50 uM; DTT 1 mM; DYNLT1/Tctex1-DIC chimera, [U-99% 13C; U-99% 15N], 100 uM; potassium phosphate 100 mM; H2O 90%; D2O 10%

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_3	isotropic	sample_conditions_1
3D HNCACB	sample_3	isotropic	sample_conditions_1
3D HNCA	sample_3	isotropic	sample_conditions_1
3D HN(CO)CA	sample_3	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

AMBER, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection, processing

NMR spectrometers:

Bruker Avance 800 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts