BMRB Entry 25082

Name: Fyn SH2 domain in complex with the natural inhibitory phosphotyrosine peptide
Published: 2015-07-13

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PDB ID: 2mrk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25082
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Fyn SH2 domain in complex with the natural inhibitory phosphotyrosine peptide

Deposition date:

2014-07-09

Original release date:

2015-07-13

Authors:

Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico

Citation:

Citation: Huculeci, Radu; Cilia, Elisa; Buts, Lieven; Houben, Klaartje; van Nuland, Nico; Lenaerts, Tom. "Dynamically coupled residues within the SH2 domain of FYN are key to unlock its activity" .

Assembly members:

Assembly members:
entity_1, polymer, 122 residues, 11690.439 Da.
entity_2, polymer, 10 residues, 1254.209 Da.

Natural source:

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

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MGSSHHHHHHSSGLVPRGSH MEWYFGKLGRKDAERQLLSF GNPRGTFLIRESETTKGAYS LSIRDWDDMKGDHVKHYKIR KLDNGGYYITTRAQFETLQQ LVQHYSERAAGLCCRLVVPC HK
entity_2: EPQYQPGENL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	57

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Fyn SH2 domain	1
2	natural inhibitory phosphotyrosine peptide	2

Entities:

Entity 1, Fyn SH2 domain 122 residues - 11690.439 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

3

MET

GLU

TRP

TYR

PHE

GLY

LYS

LEU

GLY

ARG

4

LYS

ASP

ALA

GLU

ARG

GLN

LEU

SER

PHE

5

GLY

ASN

PRO

ARG

GLY

THR

PHE

LEU

ILE

ARG

6

GLU

SER

GLU

THR

LYS

GLY

ALA

TYR

SER

7

LEU

SER

ILE

ARG

ASP

TRP

ASP

MET

LYS

8

GLY

ASP

HIS

VAL

LYS

HIS

TYR

LYS

ILE

ARG

9

LYS

LEU

ASP

ASN

GLY

TYR

ILE

THR

10

THR

ARG

ALA

GLN

PHE

GLU

THR

LEU

GLN

11

LEU

VAL

GLN

HIS

TYR

SER

GLU

ARG

ALA

12

GLY

LEU

CYS

ARG

LEU

VAL

PRO

CYS

13

HIS

LYS

Entity 2, natural inhibitory phosphotyrosine peptide 10 residues - 1254.209 Da.

1

GLU

PRO

GLN

PTR

GLN

PRO

GLY

GLU

ASN

LEU

Samples:

sample_1: entity_1, [U-99% 13C; U-99% 15N], 0.93 mM; entity_2 1.2 mM

sample_conditions_1: ionic strength: 0 M; pH: 6.50; 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-1H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CCPNMR, CCPN - chemical shift assignment, peak picking

HADDOCK, Alexandre Bonvin - refinement, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

Varian Varian NMR Systems 600 MHz
Varian Varian NMR Systems 800 MHz

BMRB	25081
PDB	1AOT 1AOU 1G83 2MQI 2MRJ 2MRK 4U17 4U1P
DBJ	BAE33766 BAG70107 BAG70240 BAI46902
EMBL	CAA36435
GB	AAA36615 AAA49719 AAA82942 AAC08285 AAH32496
REF	NP_001071440 NP_001073675 NP_001079077 NP_001080120 NP_001116365
SP	A0JNB0 A1Y2K1 P06241 P13406 P39688
TPG	DAA26259
AlphaFold	A0JNB0 A1Y2K1 P06241 P13406 P39688 Q8N5D7