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- PDB-3ts2: Mouse Lin28A in complex with let-7g microRNA pre-element -

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Basic information

Entry
Database: PDB / ID: 3ts2
TitleMouse Lin28A in complex with let-7g microRNA pre-element
Components
  • Protein lin-28 homolog A
  • RNA (5'-R(*GP*GP*GP*GP*UP*CP*UP*AP*UP*GP*AP*UP*AP*CP*CP*AP*CP*CP*CP*CP*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: 2.01 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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*CP*UP*AP*UP*GP*AP*UP*AP*CP*CP*AP*CP*CP*CP*CP*GP*GP*AP*G)-3')
V: RNA (5'-R(*GP*GP*GP*GP*UP*CP*UP*AP*UP*GP*AP*UP*AP*CP*CP*AP*CP*CP*CP*CP*GP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6828
Polymers47,4214
Non-polymers2624
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-8 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.030, 109.210, 182.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-7-

HOH

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: 16066.592 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*CP*UP*AP*UP*GP*AP*UP*AP*CP*CP*AP*CP*CP*CP*CP*GP*GP*AP*G)-3')


Mass: 7643.673 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.1M Tris pH 8.0, 32% w/v PEG 4000, and 0.2M sodium acetate , VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979491
20.97951
ReflectionResolution: 2.007→42.41 Å / Num. all: 31393 / Num. obs: 30861 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 40.31 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 16.9
Reflection shellResolution: 2.007→2.014 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.433 / % possible all: 92.5

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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: 2.01→25.82 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9404 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1550 5.04 %RANDOM
Rwork0.1895 ---
all0.191 30726 --
obs0.191 30726 98.35 %-
Displacement parametersBiso max: 134.27 Å2 / Biso mean: 49.5786 Å2 / Biso min: 20.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.7887 Å20 Å20 Å2
2---3.0578 Å20 Å2
3---6.8466 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: LAST / Resolution: 2.01→25.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 1022 4 311 3419
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1313SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes368HARMONIC5
X-RAY DIFFRACTIONt_it3277HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion446SEMIHARMONIC5
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_contact3587SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3277HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4640HARMONIC21.25
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion19.58
LS refinement shellResolution: 2.01→2.08 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2824 120 4.14 %
Rwork0.2192 2782 -
all0.2217 2902 -
obs--98.35 %
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)
12.57860.017-0.3471.2874-0.53772.97950.1398-0.0860.1198-0.0126-0.0168-0.0192-0.0170.1654-0.1229-0.10250.00530.0162-0.068-0.0537-0.092515.572918.7223-34.6537
21.3118-0.5599-0.00331.878-0.27643.3012-0.1333-0.0467-0.0690.05640.2810.0970.3619-0.0564-0.14780.0038-0.01340.0281-0.1077-0.024-0.1347-9.539446.0213-7.5428
30-2.6251-1.42010.4476-0.57341.1772-0.0302-0.54420.04270.3650.4746-0.1499-0.0062-0.5442-0.4444-0.18340.0930.12490.1446-0.122-0.22065.832222.4333-11.1584
40.6914-1.6525-2.22252.4480.87410.6789-0.11680.16280.4679-0.30090.2237-0.49580.09260.0228-0.1069-0.0145-0.09340.08160.0109-0.152-0.14317.199844.5386-27.3299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A36 - 179
2X-RAY DIFFRACTION2{ B|* }B34 - 2
3X-RAY DIFFRACTION3{ U|* }U1 - 24
4X-RAY DIFFRACTION4{ V|* }V1 - 24

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