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- PDB-3ts0: Mouse Lin28A in complex with let-7f-1 microRNA pre-element -

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Basic information

Entry
Database: PDB / ID: 3ts0
TitleMouse Lin28A in complex with let-7f-1 microRNA pre-element
Components
  • Protein lin-28 homolog A
  • RNA (5'-R(*GP*GP*GP*GP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*AP*CP*CP*CP*UP*GP*GP*AP*G)-3')
KeywordsRNA BINDING PROTEIN/RNA / microRNA biogenesis / Protein-RNA complex / pre-element / CCHC zinc knuckle / cold shock domain / 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 / regulation of miRNA-mediated gene silencing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding ...negative regulation of glial cell differentiation / positive regulation of cell proliferation involved in kidney development / negative regulation of pre-miRNA processing / regulation of miRNA-mediated gene silencing / protein-RNA adaptor activity / : / miRNA catabolic process / RNA 3' uridylation / RNA 3'-end processing / pre-miRNA binding / miRNA metabolic process / : / 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 / positive regulation of translation / 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 / ribonucleoprotein complex / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.763 Å
AuthorsNam, Y. / Sliz, P.
CitationJournal: Cell(Cambridge,Mass.) / 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
DepositionSep 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,8258
Polymers46,5644
Non-polymers2624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-26 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.880, 139.880, 85.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsIn the crystal forms, the authors observe a domain swap in which the Lin28 CSD interacts with the loop of one microRNA molecule, and the CCHCx2 interacts with the GGAG of a second microRNA.

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Components

#1: Protein Protein lin-28 homolog A / Lin-28A / Testis-expressed protein 17


Mass: 15924.437 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lin28, Lin28a, Tex17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3Y3
#2: RNA chain RNA (5'-R(*GP*GP*GP*GP*UP*AP*GP*UP*GP*AP*UP*UP*UP*UP*AP*CP*CP*CP*UP*GP*GP*AP*G)-3')


Mass: 7357.444 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: RNA oligonucleotide
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 4.48 Å3/Da / Density % sol: 72.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 0.6M NaH2PO4, 1.4M K2HPO4, pH 7, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
211
ReflectionResolution: 2.763→72.98 Å / Num. all: 22328 / Num. obs: 22328 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 78.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 28.2
Reflection shellResolution: 2.763→2.772 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.629 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSdata reduction
autoPROCdata scaling
SCALAdata scaling
PHASERphasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TRZ

3trz


Resolution: 2.763→72.98 Å / Cor.coef. Fo:Fc: 0.9069 / Cor.coef. Fo:Fc free: 0.8901 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.292 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 1148 5.15 %RANDOM
Rwork0.193 ---
all0.1941 22279 --
obs0.1941 22279 99.6 %-
Displacement parametersBiso max: 165.79 Å2 / Biso mean: 74.7989 Å2 / Biso min: 38.45 Å2
Refine analyzeLuzzati coordinate error obs: 0.447 Å
Refinement stepCycle: LAST / Resolution: 2.763→72.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 984 4 0 3068
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1286SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes38HARMONIC2
X-RAY DIFFRACTIONt_gen_planes366HARMONIC5
X-RAY DIFFRACTIONt_it3234HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion438SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3197SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3234HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4574HARMONIC21.36
LS refinement shellResolution: 2.763→2.9 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.244 172 6.06 %
Rwork0.2311 2666 -
all0.2319 2838 -
obs--99.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2195-0.76230.59421.4692-1.0893.1297-0.3293-0.06210.06040.44540.0091-0.1584-0.6005-0.36880.32020.03840.0761-0.2571-0.0891-0.07260.1046-15.165732.2552-12.3152
21.0928-1.14551.55742.5974-1.48713.9896-0.00420.23750.13950.0214-0.3738-0.0890.4350.59430.378-0.06440.0520.07330.0050.25550.0537-39.991864.0283-25.0023
31.6114-2.73890.45712.6921-2.90750.303-0.0640.38140.09631.0302-0.16790.0237-0.4669-0.05490.23190.1210.29-0.1284-0.00890.0207-0.0928-26.920648.9467-5.0912
410.5088-5.02532.71023.5438-1.26240.14170.18810.85670.05320.2538-0.2996-0.22880.11470.37880.11150.11990.2539-0.0115-0.05390.1303-0.0506-26.621648.6159-32.4273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A35 - 179
2X-RAY DIFFRACTION2{ B|* }B35 - 179
3X-RAY DIFFRACTION3{ U|* }U1 - 23
4X-RAY DIFFRACTION4{ V|* }V1 - 23

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