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- PDB-5udz: Human LIN28A in complex with let-7f-1 microRNA pre-element -

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Basic information

Entry
Database: PDB / ID: 5udz
TitleHuman LIN28A in complex with let-7f-1 microRNA pre-element
Components
  • Protein lin-28 homolog A
  • let-7f-1 pre-element
KeywordsRNA Binding Protein/RNA / microRNA / let-7 / LIN28 / RNA Binding Protein-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 / Nucleic acid-binding proteins / Few Secondary Structures / Irregular ...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 / Nucleic acid-binding proteins / Few Secondary Structures / Irregular / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein lin-28 homolog A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNam, Y. / Wang, L. / Sliz, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA163647 United States
Citation
Journal: Cell Rep / Year: 2017
Title: LIN28 Zinc Knuckle Domain Is Required and Sufficient to Induce let-7 Oligouridylation.
Authors: Wang, L. / Nam, Y. / Lee, A.K. / Yu, C. / Roth, K. / Chen, C. / Ransey, E.M. / Sliz, P.
#1: Journal: Cell / Year: 2011
Title: Molecular basis for interaction of let-7 microRNAs with Lin28.
Authors: Nam, Y. / Chen, C. / Gregory, R.I. / Chou, J.J. / Sliz, P.
History
DepositionDec 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein lin-28 homolog A
B: Protein lin-28 homolog A
V: let-7f-1 pre-element
W: let-7f-1 pre-element
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4548
Polymers48,1934
Non-polymers2624
Water9,314517
1
A: Protein lin-28 homolog A
V: let-7f-1 pre-element
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2274
Polymers24,0962
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area11820 Å2
MethodPISA
2
B: Protein lin-28 homolog A
W: let-7f-1 pre-element
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2274
Polymers24,0962
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-12 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.429, 76.429, 105.615
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 16023.568 Da / Num. of mol.: 2 / Fragment: UNP residues 31-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIN28A, CSDD1, LIN28, ZCCHC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9Z2
#2: RNA chain let-7f-1 pre-element


Mass: 8072.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.1 M Citrate, pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→32.52 Å / Num. obs: 40547 / % possible obs: 99 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.09052 / Net I/σ(I): 10.79
Reflection shellResolution: 2→2.071 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.6189 / Mean I/σ(I) obs: 1.73 / % possible all: 96.96

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TS2

3ts2


Resolution: 2→32.52 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2003 1994 4.92 %Random selection
Rwork0.1642 ---
obs0.1659 40541 99.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 995 4 517 3644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113310
X-RAY DIFFRACTIONf_angle_d1.2774682
X-RAY DIFFRACTIONf_dihedral_angle_d14.2211375
X-RAY DIFFRACTIONf_chiral_restr0.07530
X-RAY DIFFRACTIONf_plane_restr0.007432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.31391390.25882635X-RAY DIFFRACTION96
2.05-2.10550.26361450.23012790X-RAY DIFFRACTION100
2.1055-2.16740.26171430.21052747X-RAY DIFFRACTION100
2.1674-2.23730.23261410.19532771X-RAY DIFFRACTION100
2.2373-2.31730.22711490.18522774X-RAY DIFFRACTION100
2.3173-2.410.24641430.17762758X-RAY DIFFRACTION100
2.41-2.51970.2151420.18532765X-RAY DIFFRACTION100
2.5197-2.65250.23241400.17122789X-RAY DIFFRACTION100
2.6525-2.81860.18761430.16812747X-RAY DIFFRACTION100
2.8186-3.0360.22441440.16352769X-RAY DIFFRACTION100
3.036-3.34130.16351410.14612778X-RAY DIFFRACTION99
3.3413-3.82410.18991490.132756X-RAY DIFFRACTION99
3.8241-4.81550.14441380.12772734X-RAY DIFFRACTION98
4.8155-32.52380.17721370.16722734X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 48.0106 Å / Origin y: 6.8764 Å / Origin z: 13.1883 Å
111213212223313233
T0.0491 Å20.0122 Å2-0.0116 Å2-0.139 Å2-0.0052 Å2--0.087 Å2
L0.0829 °2-0.0017 °20.117 °2--0.0367 °2-0.0434 °2---0.033 °2
S0.0094 Å °0.0372 Å °-0.0339 Å °0.0101 Å °0.0105 Å °-0.0067 Å °-0.0158 Å °-0.0285 Å °0.0084 Å °
Refinement TLS groupSelection details: all

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