BMRB Entry 17127

Name: COMPLEX STRUCTURE OF E4 mutant HUMAN IGF2R DOMAIN 11 BOUND TO IGF-II
Published: 2012-08-30

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PDB ID: 2l29
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR17127
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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:

COMPLEX STRUCTURE OF E4 mutant HUMAN IGF2R DOMAIN 11 BOUND TO IGF-II

Deposition date:

2010-08-13

Original release date:

2012-08-30

Authors:

Williams, Christopher; Hoppe, Hans; Rezgui, Dellel; Strickland, Madeline; Frago, Susana; Ellis, Rosamund; Wattana-Amorn, Pakorn; Prince, Stuart; Zaccheo, Oliver; Forbes, Briony; Jones, E.; Crump, Matthew; Hassan, A.

Citation:

Citation: Williams, Christopher; Hoppe, Hans; Rezgui, Dellel; Strickland, Madeline; Frago, Susana; Ellis, Rosamund; Wattana-Amorn, Pakorn; Prince, Stuart; Zaccheo, Oliver; Forbes, Briony; Jones, E.; Crump, Matthew; Hassan, A.; Grutzner, Frank; Nolan, Catherine; Mungall, Andrew. "An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution" Science 338, 1209-1213 (2012).
PubMed: 23197533

Assembly members:

Assembly members:
HD11, polymer, 142 residues, 15434.610 Da.
IGF2, polymer, 67 residues, 7484.514 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):
HD11: MKSNEHDDCQVTNPSTGHLF DLSSLSGRAGFTAAYSKSGV VYMSICGENENCPPGVGACF GQTRISVGKANKRLRYVDQV LQLVYKDGSPCPSKSGLSYK SVISFVCRPEAGPTNRPMLI SLDKQTCTLFFSWHTPLACE PE
IGF2: AYRPSETLCGGELVDTLQFV CGDRGFYFSRPASRVSRRSR GIVEECCFRSCDLALLETYC ATPAKSE

Data sets:

assigned_chemical_shifts
- assigned_bound_E4_chem_shift_list_1

Data type	Count
13C chemical shifts	768
15N chemical shifts	215
1H chemical shifts	1282

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human domain 11	1
2	IGF2	2

Entities:

Entity 1, human domain 11 142 residues - 15434.610 Da.

Mutated Domain 11 of the Cytoplasmic region of the Cation-independent mannose-6-phosphate receptor E4 IGF2R domain 11 in complex with IGF-II

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

SER

LYS

SER

GLY

VAL

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

PRO

GLU

Entity 2, IGF2 67 residues - 7484.514 Da.

1

ALA

TYR

ARG

PRO

SER

GLU

THR

LEU

CYS

GLY

2

GLY

GLU

LEU

VAL

ASP

THR

LEU

GLN

PHE

VAL

3

CYS

GLY

ASP

ARG

GLY

PHE

TYR

PHE

SER

ARG

4

PRO

ALA

SER

ARG

VAL

SER

ARG

SER

ARG

5

GLY

ILE

VAL

GLU

CYS

PHE

ARG

SER

6

CYS

ASP

LEU

ALA

LEU

GLU

THR

TYR

CYS

7

ALA

THR

PRO

ALA

LYS

SER

GLU

Samples:

sample_1: HD11, [U-98% 13C; U-98% 15N], 0.5 – 1 mM; IGF21 – 1.5 mM; D2O 5 ± 0.1 %; sodium azide 100 ± 0.1 uM; sodium acetate 5 ± 0.1 mM; EDTA 0.1 ± 0.1 mM

sample_2: IGF2, [U-98% 13C; U-98% 15N], 0.5 – 1 mM; HD111 – 1.5 mM; D2O 5 ± 0.1 %; sodium azide 100 ± 0.1 uM; sodium acetate 5 ± 0.1 mM; EDTA 0.1 ± 0.1 mM; H2O 95 ± 0.1 %

sample_3: IGF2, [U-98% 15N; U-95% 2H], 0.5 – 1 mM; HD111 – 1.5 mM; D2O 5 ± 0.1 %; sodium azide 100 ± 0.1 uM; sodium acetate 5 ± 0.1 mM; EDTA 0.1 ± 0.1 mM

sample_conditions_1: pH: 4.2; pressure: 1 atm; temperature: 273 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	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 HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_1
3D C(CO)NH	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
2D f2 filter noesy	sample_1	isotropic	sample_conditions_1
2D f2 filter noesy	sample_2	isotropic	sample_conditions_1
2D f2 filter noesy	sample_1	isotropic	sample_conditions_1
2D f2 filter noesy	sample_2	isotropic	sample_conditions_1
2D CN filtered noesy	sample_1	isotropic	sample_conditions_1
2D CN filtered noesy	sample_2	isotropic	sample_conditions_1
2D CN filtered noesy	sample_1	isotropic	sample_conditions_1
2D CN filtered noesy	sample_2	isotropic	sample_conditions_1
2D CN filtered tocsy	sample_1	isotropic	sample_conditions_1
2D CN filtered tocsy	sample_2	isotropic	sample_conditions_1

Software:

VNMRJ, Varian - collection

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

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

iCing vr765, Vuister, Doreleijers, Sousa da Silva - refinement

Analysis v2.13, CCPN - chemical shift assignment, data analysis

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

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

NMR spectrometers:

Varian INOVA 600 MHz
Varian VNMRS 600 MHz
Varian UnityPlus 900 MHz

BMRB	17128 19117 19153
PDB	1E6F 1GP0 1GP3 1GQB 2CNJ 2L29 2L2A 2M68 2M6T 1IGL 1IGL 2L29 2V5P 3E4Z 3KR3
DBJ	BAF84283 BAG36657 BAG54360 BAI46830 BAO53964
EMBL	CAA04657 CAA25426 CAA27156 CAA27249 CAA29516
GB	AAA52544 AAA52545 AAA60088 AAA73915 AAB26479
PRF	0407244A:PDB=1GF2 1009249A 1203258B 1707201B 1904317A
REF	NP_000603 NP_001007140 NP_001108011 NP_001121070 NP_001164877
SP	P01344 P23695 P41694 P51459 Q08279
AlphaFold	P01344 P23695 P41694 P51459 Q08279