BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17883

Title: The solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA   PubMed: 22157959

Authors: Allain, F.; Loughlin, F.

Citation: Loughlin, Fionna; Gebert, Luca; Towbin, Harry; Brunschweiger, Andreas; Hall, Jonathan; Allain, Frederic H-T. "Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28."  Nat. Struct. Mol. Biol. 19, 84-89 (2012).

Assembly members:
Lin28-ZnF, polymer, 74 residues, 8033.417 Da.
AGGAGAU, polymer, 7 residues, 2284.459 Da.
ZN, non-polymer, 65.409 Da.

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

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

Entity Sequences (FASTA):
Lin28-ZnF: SSGLVPRGSHMPKGKSMQKR RSKGDRCYNCGGLDHHAKEC KLPPQPKKCHFCQSISHMVA SCPLKAQQGPSAQG
AGGAGAU: AGGAGAU

Data sets:
Data typeCount
13C chemical shifts191
15N chemical shifts64
1H chemical shifts450

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1Lin-28 homolog A1
2hsa-pre-let-7g miRNA2
3ZINC ION3

Entities:

Entity 1, Lin-28 homolog A 74 residues - 8033.417 Da.

Residues 1-11 a non native expression tag

1   SERSERGLYLEUVALPROARGGLYSERHIS
2   METPROLYSGLYLYSSERMETGLNLYSARG
3   ARGSERLYSGLYASPARGCYSTYRASNCYS
4   GLYGLYLEUASPHISHISALALYSGLUCYS
5   LYSLEUPROPROGLNPROLYSLYSCYSHIS
6   PHECYSGLNSERILESERHISMETVALALA
7   SERCYSPROLEULYSALAGLNGLNGLYPRO
8   SERALAGLNGLY

Entity 2, hsa-pre-let-7g miRNA 7 residues - 2284.459 Da.

1   AGGAGAU

Entity 3, ZINC ION - Zn - 65.409 Da.

1   ZN

Samples:

sample_1: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; H2O 90%; D2O 10%

sample_2: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; D2O 100%

Sample_3: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; H2O 90%; D2O 10%

Sample_4: sodium acetate, [U-99% 2H], 10 ± 1 mM; beta-mercaptoethanol 1.5 ± .2 mM; ZnCl2 1.6 ± 0.1 mM; Lin28-ZnF, [U-10% 13C; U-99% 15N], 0.8 ± 0.1 mM; AGGAGAU 0.8 ± 0.1 mM; D2O 100%

sample_conditions_1: ionic strength: 10 mM; pH: 5.6; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 10 mM; pH: 5.6; pressure: 1 atm; temperature: 283 K

Experiments:

NameSampleSample stateSample conditions
3D_15N-separated_NOESY 3D_13C-separated_NOESYSample_3isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
2D 1H-1H TOCSYsample_2isotropicsample_conditions_1
2D-F1f-F2f-NOESYsample_2isotropicsample_conditions_1
2D-F2f-NOESYsample_2isotropicsample_conditions_1
3D-F3f-NOESYsample_2isotropicsample_conditions_1
2D 1H-15N HMQCSample_3isotropicsample_conditions_1
2D 1H-1H NOESYSample_3isotropicsample_conditions_1
2D 1H-1H NOESYSample_3isotropicsample_conditions_2
2D 1H-13C HSQCSample_4isotropicsample_conditions_1
3D-F3fe-NOESYsample_1isotropicsample_conditions_2
3D 1H-15N NOESYSample_3isotropicsample_conditions_2

Software:

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection, processing

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - structure solution

AMBER, Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm - refinement

NMR spectrometers:

  • Bruker AV-III 500 MHz
  • Bruker AV-III 600 MHz
  • Bruker AV-III 700 MHz
  • Bruker Avance 900 MHz

Related Database Links:

PDB
DBJ BAB14075 BAI46599
GB AAH28566 AAM77751 ABM84324 ABM87718 AIC52303
REF NP_001102739 NP_078950 XP_001114640 XP_002716148 XP_002720890
SP Q9H9Z2