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- PDB-3trz: Mouse Lin28A in complex with let-7d microRNA pre-element -

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Basic information

Entry
Database: PDB / ID: 3trz
TitleMouse Lin28A in complex with let-7d microRNA pre-element
Components
  • Protein lin-28 homolog A
  • RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*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 / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / pre-miRNA binding / miRNA metabolic process / pre-miRNA processing ...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 / miRNA catabolic process / protein-RNA adaptor activity / RNA 3' uridylation / 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 / stem cell differentiation / cellular response to glucose stimulus / P-body / 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
: / : / Lin-28A-like, second zinc knuckle / Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / Cold shock domain / Cold shock protein domain ...: / : / Lin-28A-like, second zinc knuckle / Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / Cold-shock (CSD) domain profile. / 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)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.9 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 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_name_com / entity_src_gen / ndb_struct_conf_na / ndb_struct_na_base_pair / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref / 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 / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _ndb_struct_na_base_pair.buckle / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _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 / _struct_ref.pdbx_seq_one_letter_code / _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
C: Protein lin-28 homolog A
D: Protein lin-28 homolog A
E: Protein lin-28 homolog A
F: Protein lin-28 homolog A
U: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
V: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
W: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
X: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
Y: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
Z: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,74524
Polymers136,96012
Non-polymers78512
Water00
1
A: Protein lin-28 homolog A
B: Protein lin-28 homolog A
U: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
V: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9158
Polymers45,6534
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-14 kcal/mol
Surface area18830 Å2
MethodPISA
2
C: Protein lin-28 homolog A
D: Protein lin-28 homolog A
W: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
X: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9158
Polymers45,6534
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-13 kcal/mol
Surface area18730 Å2
MethodPISA
3
E: Protein lin-28 homolog A
F: Protein lin-28 homolog A
Y: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
Z: RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9158
Polymers45,6534
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8780 Å2
ΔGint-14 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.820, 143.820, 177.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
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.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lin28a, Lin28, Tex17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8K3Y3
#2: RNA chain
RNA (5'-R(*GP*GP*GP*CP*AP*GP*GP*GP*AP*UP*UP*UP*UP*GP*CP*CP*CP*GP*GP*AP*G)-3')


Mass: 6760.128 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: RNA oligonucleotide / Source: (synth.) Synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
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: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.9→66.66 Å / Num. all: 41278 / Num. obs: 41278 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 83.22 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 21.4
Reflection shellResolution: 2.9→2.91 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.586 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
XDSautoPROCdata reduction
SCALAdata scaling
BUSTER2.11.1phasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.9→66.66 Å / Cor.coef. Fo:Fc: 0.9459 / Cor.coef. Fo:Fc free: 0.9271 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.609 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 2086 5.06 %RANDOM
Rwork0.1833 ---
obs0.1847 41252 98.34 %-
all-41252 --
Displacement parametersBiso mean: 71.81 Å2
Baniso -1Baniso -2Baniso -3
1--1.6056 Å20 Å20 Å2
2---1.6056 Å20 Å2
3---3.2111 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: LAST / Resolution: 2.9→66.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 2718 12 0 8694
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099156HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.312942HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3588SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes114HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1032HARMONIC5
X-RAY DIFFRACTIONt_it9156HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
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_contact
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3083 155 5.15 %
Rwork0.2348 2852 -
all0.2387 3007 -
obs--98.34 %
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)
12.20820.10261.89591.1163-0.59915.3136-0.07810.04480.0213-0.186-0.03690.1301-0.0028-0.40210.115-0.04040.0506-0.102-0.0283-0.0561-0.036818.377836.57-18.3059
24.2725-0.40941.59041.00831.08955.02080.02830.0192-0.2028-0.090.01550.03550.21780.3826-0.0438-0.113-0.0265-0.0862-0.01370.0802-0.0677-21.293140.15-26.1773
32.5819-0.38561.44991.4855-0.50375.34050.03760.033-0.1221-0.18-0.13880.186-0.0198-0.50050.1011-0.12650.0861-0.1370.0388-0.0807-0.001718.150834.548740.9339
45.2698-1.05691.52270.75260.44684.07090.07680.0188-0.4849-0.0377-0.0879-0.07120.21180.37540.0111-0.1175-0.0556-0.0718-0.00130.0817-0.0553-21.55937.727333.1896
51.25230.22770.56782.53372.16014.85540.08780.2803-0.1603-0.07380.0018-0.17050.4850.2246-0.08960.01750.01630.0451-0.0435-0.1214-0.040635.53888.189356.2249
60.0519-0.0128-0.46625.48471.79654.932-0.17090.01340.0191-0.16070.1365-0.2694-0.42680.23570.0343-0.05640.0691-0.0791-0.0567-0.1107-0.027233.943848.59248.2746
710.6247-5.97312.4522.252-1.84791.7165-0.2929-0.4094-0.06590.31350.2273-0.00740.134-0.72510.0656-0.30430.0002-0.12540.3962-0.02650.0226-0.923439.2314-8.3083
816.55264.44883.13420.20621.20351.2901-0.2250.741-0.0407-0.15010.1161-0.01040.31720.60160.1089-0.24240.1797-0.14770.3799-0.1214-0.0471-1.903239.4647-36.3231
912.424-6.35092.69811.0782-0.97951.3994-0.2985-0.32520.17780.26360.1183-0.26460.152-0.72790.1802-0.3648-0.0103-0.08310.50920.04320.0731-0.889236.85350.8011
1017.32054.18222.529600.93811.5636-0.09180.8147-0.0491-0.15440.06580.03390.36130.54150.026-0.27730.2015-0.09540.3894-0.1527-0.0376-2.503536.803123.1644
111.90356.1460.435212.8132.25150.67030.2377-0.15420.12780.3518-0.2620.04820.71310.29160.02440.44520.0878-0.1413-0.3147-0.08290.029633.516768.994266.1747
120.6016-5.7194-0.668516.27831.83351.68150.08050.5112-0.2081-0.6265-0.3544-0.1719-0.70390.34680.27390.3783-0.11490.1367-0.2118-0.16260.010734.203167.928938.4254
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{ C|* }C35 - 179
4X-RAY DIFFRACTION4{ D|* }D35 - 179
5X-RAY DIFFRACTION5{ E|* }E35 - 179
6X-RAY DIFFRACTION6{ F|* }F35 - 179
7X-RAY DIFFRACTION7{ U|* }U1 - 21
8X-RAY DIFFRACTION8{ V|* }V1 - 21
9X-RAY DIFFRACTION9{ W|* }W1 - 21
10X-RAY DIFFRACTION10{ X|* }X1 - 21
11X-RAY DIFFRACTION11{ Y|* }Y1 - 21
12X-RAY DIFFRACTION12{ Z|* }Z1 - 21

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