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- PDB-2li8: The solution structure of the Lin28-ZnF domains bound to AGGAGAU ... -

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Basic information

Entry
Database: PDB / ID: 2li8
TitleThe solution structure of the Lin28-ZnF domains bound to AGGAGAU of pre-let-7 miRNA
Components
  • Protein lin-28 homolog A
  • RNA (5'-R(*AP*GP*GP*AP*GP*AP*U)-3')
KeywordsTRANSCRIPTION/RNA / zinc finger / micro RNA / TRANSCRIPTION-RNA complex
Function / homology
Function and homology information


negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding / Transcriptional regulation of pluripotent stem cells ...negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding / Transcriptional regulation of pluripotent stem cells / pre-miRNA processing / positive regulation of cytoplasmic translation / sequence-specific mRNA binding / miRNA binding / stem cell population maintenance / germ cell development / positive regulation of TOR signaling / rough endoplasmic reticulum / translation initiation factor binding / positive regulation of neuron differentiation / P-body / stem cell differentiation / cellular response to glucose stimulus / cytoplasmic stress granule / G-quadruplex RNA binding / negative regulation of translation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / mRNA binding / nucleolus / RNA binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Few Secondary Structures / Irregular / zinc finger ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold shock domain / Cold shock protein domain / Few Secondary Structures / Irregular / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
RNA / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsAllain, F.H.-T. / Loughlin, F.E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Structural basis of pre-let-7 miRNA recognition by the zinc knuckles of pluripotency factor Lin28.
Authors: Loughlin, F.E. / Gebert, L.F. / Towbin, H. / Brunschweiger, A. / Hall, J. / Allain, F.H.
History
DepositionAug 25, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein lin-28 homolog A
B: RNA (5'-R(*AP*GP*GP*AP*GP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4494
Polymers10,3182
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200lowest energy/fewest violation
RepresentativeModel #1fewest violations

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Components

#1: Protein Protein lin-28 homolog A / Lin-28A / Zinc finger CCHC domain-containing protein 1


Mass: 8033.377 Da / Num. of mol.: 1
Fragment: CCHC-type 1 and CCHC-type 1 zinc finger domain residues 124-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSDD1, Lin-28a, LIN28, LIN28A, ZCCHC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon Plus / References: UniProt: Q9H9Z2
#2: RNA chain RNA (5'-R(*AP*GP*GP*AP*GP*AP*U)-3')


Mass: 2284.443 Da / Num. of mol.: 1 / Fragment: hsa-pre-let-7g terminal loop / Source method: obtained synthetically
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1123D 15N-separated NOESY 3D 13C-separated NOESY
1213D 1H-13C NOESY
1312D 1H-15N HSQC
1432D 1H-13C HSQC aliphatic
1532D 1H-13C HSQC aromatic
1613D CBCA(CO)NH
1733D HN(CA)CB
1813D HNCO
1913D H(CCO)NH
11033D (H)CCH-TOCSY
11132D 1H-1H TOCSY
11232D-F1f-F2f-NOESY
11332D-F2f-NOESY
11433D-F3f-NOESY
11522D 1H-15N HMQC
11622D 1H-1H NOESY
21722D 1H-1H NOESY
11842D 1H-13C HSQC
21913D-F3fe-NOESY
22023D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM [U-99% 2H] sodium acetate, 1.5 mM beta-mercaptoethanol, 1.6 mM ZnCl2, 0.8 mM [U-99% 13C; U-99% 15N] Lin28-ZnF, 0.8 mM AGGAGAU, 90% H2O, 10% D2O90% H2O/10% D2O
210 mM [U-99% 2H] sodium acetate, 1.5 mM beta-mercaptoethanol, 1.6 mM ZnCl2, 0.8 mM [U-99% 15N] Lin28-ZnF, 0.8 mM AGGAGAU, 90% H2O, 10% D2O90% H2O/10% D2O
310 mM [U-99% 2H] sodium acetate, 1.5 mM beta-mercaptoethanol, 1.6 mM ZnCl2, 0.8 mM [U-99% 13C; U-99% 15N] Lin28-ZnF, 0.8 mM AGGAGAU, 100% D2O100% D2O
410 mM [U-99% 2H] sodium acetate, 1.5 mM beta-mercaptoethanol, 1.6 mM ZnCl2, 0.8 mM [U-10% 13C; U-99% 15N] Lin28-ZnF, 0.8 mM AGGAGAU, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium acetate-1[U-99% 2H]1
1.5 mMbeta-mercaptoethanol-21
1.6 mMZnCl2-31
0.8 mMLin28-ZnF-4[U-99% 13C; U-99% 15N]1
0.8 mMAGGAGAU-51
10 mMsodium acetate-6[U-99% 2H]2
1.5 mMbeta-mercaptoethanol-72
1.6 mMZnCl2-82
0.8 mMLin28-ZnF-9[U-99% 15N]2
0.8 mMAGGAGAU-102
10 mMsodium acetate-11[U-99% 2H]3
1.5 mMbeta-mercaptoethanol-123
1.6 mMZnCl2-133
0.8 mMLin28-ZnF-14[U-99% 13C; U-99% 15N]3
0.8 mMAGGAGAU-153
10 mMsodium acetate-16[U-99% 2H]4
1.5 mMbeta-mercaptoethanol-174
1.6 mMZnCl2-184
0.8 mMLin28-ZnF-19[U-10% 13C; U-99% 15N]4
0.8 mMAGGAGAU-204
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 5.6 1 atm303 K
210 5.6 1 atm283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AV IIIBrukerAV III5001
Bruker AV IIIBrukerAV III6002
Bruker AV IIIBrukerAV III7003
Bruker AvanceBrukerAvance9004

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Processing

NMR software
NameVersionDeveloperClassification
SPARKYGoddardchemical shift assignment
TOPSPINBruker Biospincollection
TOPSPINBruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Explicit water AMBER ff99 25 ps
NMR constraintsNOE constraints total: 1624 / NOE intraresidue total count: 438 / NOE long range total count: 304 / NOE medium range total count: 353 / NOE sequential total count: 461 / Hydrogen bond constraints total count: 4 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 61 / Protein phi angle constraints total count: 25 / Protein psi angle constraints total count: 24
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: lowest energy/fewest violation
Conformers calculated total number: 200 / Conformers submitted total number: 20

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