BMRB Entry 34384

Name: C-SH2 domain of SHP-2 in complex with phospho-ITSM of PD-1
Published: 2020-01-31

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PDB ID: 6r5g
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34384
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:

C-SH2 domain of SHP-2 in complex with phospho-ITSM of PD-1

Deposition date:

2019-03-25

Original release date:

2020-01-31

Authors:

Marasco, M.

Citation:

Citation: Marasco, Michelangelo; Kirkpatrick, John; Carlomagno, Teresa. "1H, 13C, 15N chemical shift assignments of SHP2 SH2 domains in complex with PD-1 immune-tyrosine motifs" Biomol. NMR Assign. 14, 179-188 (2020).
PubMed: 32236803

Assembly members:

Assembly members:
entity_1, polymer, 119 residues, 13301.950 Da.
entity_2, polymer, 11 residues, 1377.387 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 BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GPMADPTSERWFHGHLSGKE AEKLLTEKGKHGSFLVRESQ SHPGDFVLSVRTGDDKGESN DGKSKVTHVMIRCQELKYDV GGGERFDSLTDLVEHYKKNP MVETLGTVLQLKQPLNTTR
entity_2: EQTEXATIVFP

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	514
15N chemical shifts	125
1H chemical shifts	906

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 119 residues - 13301.950 Da.

1

GLY

PRO

MET

ALA

ASP

PRO

THR

SER

GLU

ARG

2

TRP

PHE

HIS

GLY

HIS

LEU

SER

GLY

LYS

GLU

3

ALA

GLU

LYS

LEU

THR

GLU

LYS

GLY

LYS

4

HIS

GLY

SER

PHE

LEU

VAL

ARG

GLU

SER

GLN

5

SER

HIS

PRO

GLY

ASP

PHE

VAL

LEU

SER

VAL

6

ARG

THR

GLY

ASP

LYS

GLY

GLU

SER

ASN

7

ASP

GLY

LYS

SER

LYS

VAL

THR

HIS

VAL

MET

8

ILE

ARG

CYS

GLN

GLU

LEU

LYS

TYR

ASP

VAL

9

GLY

GLU

ARG

PHE

ASP

SER

LEU

THR

10

ASP

LEU

VAL

GLU

HIS

TYR

LYS

ASN

PRO

11

MET

VAL

GLU

THR

LEU

GLY

THR

VAL

LEU

GLN

12

LEU

LYS

GLN

PRO

LEU

ASN

THR

ARG

Entity 2, entity_2 11 residues - 1377.387 Da.

1

GLU

GLN

THR

GLU

PTR

ALA

THR

ILE

VAL

PHE

2

PRO

Samples:

sample_1: C-SH2 domain of SHP-2, [U-13C; U-15N], 800 uM; ITSM 1000 uM; NaCl 150 mM; MES (2-(N-morpholino)ethanesulfonic acid) 10 mM; TCEP (tris(2-carboxyethyl)phosphine) 3 mM

sample_2: C-SH2 domain of SHP-2, [U-13C; U-15N], 800 uM; ITSM 640 uM; NaCl 150 mM; MES (2-(N-morpholino)ethanesulfonic acid) 10 mM; TCEP (tris(2-carboxyethyl)phosphine) 3 mM

sample_conditions_1: ionic strength: 150 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D NOESY-13C HSQC	sample_1	isotropic	sample_conditions_1
3D 13C/15N-filtered NOESY-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 13C/15N-filtered 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 13C/15N-filtered 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
3D NOESY-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

CcpNmr Analysis, CCPN - chemical shift assignment, peak picking

ARIA, Linge, O'Donoghue and Nilges - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

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

NMR spectrometers:

Bruker AVANCE III HD 850 MHz
Bruker AVANCE III HD 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks