BMRB Entry 19153

Name: NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R
Published: 2014-10-13

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PDB ID: 2m6t
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR19153
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R

Deposition date:

2013-04-09

Original release date:

2014-10-13

Authors:

Strickland, Madeleine; Williams, Chris; Richards, Emily; Minnall, Leanne; Crump, Matthew; Frago, Susana; Hughes, Jennifer; Garner, Lee; Hoppe, Hans-Jurgen; Rezgui, Dellel; Zaccheo, Oliver; Prince, Stuart; Hassan, Andrew; Whittaker, Sara

Citation:

Citation: Frago, Susana; Strickland, Madeleine; Hughes, Jennifer; Williams, Christopher; Garner, Lee; Hoppe, Hans-Jurgen; Rezgui, Dellel; Zaccheo, Oliver; Prince, Stuart; Crump, Matthew; Hassan, Andrew. "Directed evolution of structurally selected IGF2R domain 11 binding loop residues generates an IGF2 super-antagonist" EMBO J. ., .-..

Assembly members:

Assembly members:
IGF2R, polymer, 142 residues, 15433.671 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: pET26a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
IGF2R: MKSNEHDDCQVTNPSTGHLF DLSSLSGRAGFTAAYAKGWG VYMSICGENENCPPGVGACF GQTRISVGKANKRLRYVDQV LQLVYKDGSPCPSKSGLSYK SVISFVCRPEAGPTNRPMLI SLDKQTCTLFFSWHTPLACE LA

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
- Heteronuclear_noe_list_2
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
- heteronuclear_list_T1_2
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
- heteronuclear_T2_list_2

Data type	Count
1H chemical shifts	955
13C chemical shifts	597
15N chemical shifts	151
heteronuclear NOE values	266
T1 relaxation values	284
T2 relaxation values	284

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	IGF2R	1

Entities:

Entity 1, IGF2R 142 residues - 15433.671 Da.

1

MET

LYS

SER

ASN

GLU

HIS

ASP

CYS

GLN

2

VAL

THR

ASN

PRO

SER

THR

GLY

HIS

LEU

PHE

3

ASP

LEU

SER

LEU

SER

GLY

ARG

ALA

GLY

4

PHE

THR

ALA

TYR

ALA

LYS

GLY

TRP

GLY

5

VAL

TYR

MET

SER

ILE

CYS

GLY

GLU

ASN

GLU

6

ASN

CYS

PRO

GLY

VAL

GLY

ALA

CYS

PHE

7

GLY

GLN

THR

ARG

ILE

SER

VAL

GLY

LYS

ALA

8

ASN

LYS

ARG

LEU

ARG

TYR

VAL

ASP

GLN

VAL

9

LEU

GLN

LEU

VAL

TYR

LYS

ASP

GLY

SER

PRO

10

CYS

PRO

SER

LYS

SER

GLY

LEU

SER

TYR

LYS

11

SER

VAL

ILE

SER

PHE

VAL

CYS

ARG

PRO

GLU

12

ALA

GLY

PRO

THR

ASN

ARG

PRO

MET

LEU

ILE

13

SER

LEU

ASP

LYS

GLN

THR

CYS

THR

LEU

PHE

14

PHE

SER

TRP

HIS

THR

PRO

LEU

ALA

CYS

GLU

15

LEU

ALA

Samples:

sample_1: IGF2R, [U-95% 13C; U-95% 15N], 1 mM; D2O, [U-2H], 7%; H2O 93%; sodium azide 100 uM; EDTA 1 mM; sodium acetate 10 mM

sample_2: IGF2R, [U-95% 15N], 1 mM; D2O, [U-2H], 7%; H2O 93%; sodium azide 100 uM; EDTA 1 mM; sodium acetate 10 mM

sample_conditions_1: pH: 5.5; pressure: 1 atm; temperature: 273 K

sample_conditions_2: pH: 5.5; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
Heteronuclear NOE ratio	sample_2	isotropic	sample_conditions_2
Heteronuclear NOE ratio	sample_2	isotropic	sample_conditions_2
T1 experiments	sample_2	isotropic	sample_conditions_2
T1 experiments	sample_2	isotropic	sample_conditions_2
T2 experiments	sample_2	isotropic	sample_conditions_2
T2 experiments	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1

Software:

ARIA v2.2, Linge, O'Donoghue and Nilges - processing, refinement, structure solution

CING viCing, Doreleijers - refinement

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

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

Relax v1.3.9, Palmer - data analysis, processing

SPARKY v2.6, Goddard - data analysis

VNMRJ v0.4, Varian - collection

CCPN_Analysis v2.1, CCPN - chemical shift assignment, data analysis, peak picking

TALOS vTALOS+, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

Varian VNMRS 600 MHz
Varian VNMRS 900 MHz

EMBL	P11717
BMRB	17127 17128 19117
PDB	2L29 2L2A 2M68 2M6T