BMRB Entry 17883

Name: The solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA
Published: 2011-12-08

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PDB ID: 2li8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17883
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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:

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

Deposition date:

2011-08-25

Original release date:

2011-12-08

Authors:

Allain, F.; Loughlin, F.

Citation:

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).
PubMed: 22157959

Assembly members:

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:

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: pET28a

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	191
15N chemical shifts	64
1H chemical shifts	450

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Lin-28 homolog A	1
2	hsa-pre-let-7g miRNA	2
3	ZINC ION	3

Entities:

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

Residues 1-11 a non native expression tag

1

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

HIS

2

MET

PRO

LYS

GLY

LYS

SER

MET

GLN

LYS

ARG

3

ARG

SER

LYS

GLY

ASP

ARG

CYS

TYR

ASN

CYS

4

GLY

LEU

ASP

HIS

ALA

LYS

GLU

CYS

5

LYS

LEU

PRO

GLN

PRO

LYS

CYS

HIS

6

PHE

CYS

GLN

SER

ILE

SER

HIS

MET

VAL

ALA

7

SER

CYS

PRO

LEU

LYS

ALA

GLN

GLY

PRO

8

SER

ALA

GLN

GLY

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

1

A

G

A

G

A

U

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:

Name	Sample	Sample state	Sample conditions
3D_15N-separated_NOESY 3D_13C-separated_NOESY	Sample_3	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D-F1f-F2f-NOESY	sample_2	isotropic	sample_conditions_1
2D-F2f-NOESY	sample_2	isotropic	sample_conditions_1
3D-F3f-NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HMQC	Sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	Sample_3	isotropic	sample_conditions_1
2D 1H-1H NOESY	Sample_3	isotropic	sample_conditions_2
2D 1H-13C HSQC	Sample_4	isotropic	sample_conditions_1
3D-F3fe-NOESY	sample_1	isotropic	sample_conditions_2
3D 1H-15N NOESY	Sample_3	isotropic	sample_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

PDB	2CQF 2LI8
DBJ	BAB14075 BAI46599
GB	AAH28566 AAM77751 ABM84324 ABM87718 AIC52303
REF	NP_001102739 NP_078950 XP_001114640 XP_002716148 XP_002720890
SP	Q9H9Z2
AlphaFold	Q9H9Z2