BMRB Entry 17127

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

Data sets:
Data typeCount
13C chemical shifts768
15N chemical shifts215
1H chemical shifts1282

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1human domain 111
2IGF22

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   METLYSSERASNGLUHISASPASPCYSGLN
2   VALTHRASNPROSERTHRGLYHISLEUPHE
3   ASPLEUSERSERLEUSERGLYARGALAGLY
4   PHETHRALAALATYRSERLYSSERGLYVAL
5   VALTYRMETSERILECYSGLYGLUASNGLU
6   ASNCYSPROPROGLYVALGLYALACYSPHE
7   GLYGLNTHRARGILESERVALGLYLYSALA
8   ASNLYSARGLEUARGTYRVALASPGLNVAL
9   LEUGLNLEUVALTYRLYSASPGLYSERPRO
10   CYSPROSERLYSSERGLYLEUSERTYRLYS
11   SERVALILESERPHEVALCYSARGPROGLU
12   ALAGLYPROTHRASNARGPROMETLEUILE
13   SERLEUASPLYSGLNTHRCYSTHRLEUPHE
14   PHESERTRPHISTHRPROLEUALACYSGLU
15   PROGLU

Entity 2, IGF2 67 residues - 7484.514 Da.

1   ALATYRARGPROSERGLUTHRLEUCYSGLY
2   GLYGLULEUVALASPTHRLEUGLNPHEVAL
3   CYSGLYASPARGGLYPHETYRPHESERARG
4   PROALASERARGVALSERARGARGSERARG
5   GLYILEVALGLUGLUCYSCYSPHEARGSER
6   CYSASPLEUALALEULEUGLUTHRTYRCYS
7   ALATHRPROALALYSSERGLU

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:

NameSampleSample stateSample conditions
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
2D f2 filter noesysample_1isotropicsample_conditions_1
2D f2 filter noesysample_2isotropicsample_conditions_1
2D f2 filter noesysample_1isotropicsample_conditions_1
2D f2 filter noesysample_2isotropicsample_conditions_1
2D CN filtered noesysample_1isotropicsample_conditions_1
2D CN filtered noesysample_2isotropicsample_conditions_1
2D CN filtered noesysample_1isotropicsample_conditions_1
2D CN filtered noesysample_2isotropicsample_conditions_1
2D CN filtered tocsysample_1isotropicsample_conditions_1
2D CN filtered tocsysample_2isotropicsample_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

Related Database Links:

BMRB 17128 19117 19153
PDB
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 P51459 P01344 P23695 P41694 Q08279

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