BMRB Entry 16462

Name: Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling
Published: 2010-03-08

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR16462

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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling PubMed: 12717021

Deposition date: 2009-08-19 Original release date: 2010-03-08

Authors: Ferreon, Josephine; Hilser, Vincent

Citation: Ferreon, Josephine; Hilser, Vincent. "Ligand-induced changes in dynamics in the RT loop of the C-terminal SH3 domain of Sem-5 indicate cooperative conformational coupling" Protein Sci. 12, 982-996 (2003).

Assembly members:
Sem-5, polymer, 58 residues, Formula weight is not available
Sos_peptide, polymer, 10 residues, Formula weight is not available

Natural source: Common Name: Caenorhabditis elegans Taxonomy ID: 6239 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Caenorhabditis elegans

Experimental source: Production method: purified from the natural source Host organism: Escherichia coli

Entity Sequences (FASTA):
Sem-5: ETKFVQALFDFNPQESGELA FKRGDVITLINKDDPNWWEG QLNNRRGIFPSNYVAPYN
Sos_peptide: XPPPVPPRRR

Data sets:

assigned_chemical_shifts
binding_constants

Data type	Count
binding constants	1

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Sem-5	1
2	Sos peptide	2

Entities:

Entity 1, Sem-5 58 residues - Formula weight is not available

1

GLU

THR

LYS

PHE

VAL

GLN

ALA

LEU

PHE

ASP

2

PHE

ASN

PRO

GLN

GLU

SER

GLY

GLU

LEU

ALA

3

PHE

LYS

ARG

GLY

ASP

VAL

ILE

THR

LEU

ILE

4

ASN

LYS

ASP

PRO

ASN

TRP

GLU

GLY

5

GLN

LEU

ASN

ARG

GLY

ILE

PHE

PRO

6

SER

ASN

TYR

VAL

ALA

PRO

TYR

ASN

Entity 2, Sos peptide 10 residues - Formula weight is not available

1

ACE

PRO

VAL

PRO

ARG

Samples:

sample_1: Sem-5, [U-15N], 0.66 mM; NaOAc 50 mM; sodium chloride 100 mM; calcium chloride 10 mM; Sos peptide0 – 1.32 mM; D2O 10%; H2O 90%

sample_2: Sem-5, [U-15N], 0.66 mM; NaOAc 50 mM; sodium chloride 100 mM; calcium chloride 10 mM; Sos peptide 1.32 mM; D2O 10%; H2O 90%

sample_3: Sem-5, [U-15N], 0.66 mM; NaOAc 50 mM; sodium chloride 100 mM; calcium chloride 10 mM; D2O 10%; H2O 90%

sample_conditions_1: pH: 4.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1

Software:

FELIX v98, Accelrys Software Inc. - processing

Modelfree_4.01, (Columbia University. http://cpmcnet.columbia.edu/dept/gsas/biochem/labs/palmer) - statistical tests

Molmol v2K.1, Koradi, Billeter and Wuthrich - visualization

NMR spectrometers:

Varian UnityPlus 400 MHz

Biological Magnetic Resonance Data Bank