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- PDB-5v7c: Crystal structure of LARP1-unique domain DM15 bound 5'TOP RNA sequence -

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Basic information

Entry
Database: PDB / ID: 5v7c
TitleCrystal structure of LARP1-unique domain DM15 bound 5'TOP RNA sequence
Components
  • La-related protein 1
  • RNA (5'-R(*CP*UP*UP*UP*UP*CP*CP*G)-3')
KeywordsRNA BINDING PROTEIN / Cap-binding / RNA-binding / DM15 / 5'TOP
Function / homology
Function and homology information


cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling / positive regulation of translational initiation / positive regulation of macroautophagy / ribosomal small subunit binding / positive regulation of viral genome replication / translation initiation factor binding / negative regulation of translational initiation / positive regulation of translation / mRNA 3'-UTR binding / translational initiation / mRNA 5'-UTR binding / cytoplasmic stress granule / cell population proliferation / negative regulation of translation / cadherin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / membrane / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DM15 / LARP1 HEAT repeat region / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
RNA / La-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBerman, A.J. / Lahr, R.M. / Al-Ashtal, H.A.
CitationJournal: Elife / Year: 2017
Title: La-related protein 1 (LARP1) binds the mRNA cap, blocking eIF4F assembly on TOP mRNAs.
Authors: Lahr, R.M. / Fonseca, B.D. / Ciotti, G.E. / Al-Ashtal, H.A. / Jia, J.J. / Niklaus, M.R. / Blagden, S.P. / Alain, T. / Berman, A.J.
History
DepositionMar 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: La-related protein 1
C: RNA (5'-R(*CP*UP*UP*UP*UP*CP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)22,0572
Polymers22,0572
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area9260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.095, 107.095, 29.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 19616.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DM15 / Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6PKG0
#2: RNA chain RNA (5'-R(*CP*UP*UP*UP*UP*CP*CP*G)-3')


Mass: 2440.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 1.97 Å3/Da / Density % sol: 37.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5 mM MgCl2, 50 mM HEPES, pH 7.0, 25 % PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.59→37.864 Å / Num. obs: 5272 / % possible obs: 98.5 % / Redundancy: 4.3 % / Net I/σ(I): 8.8
Reflection shellHighest resolution: 2.59 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.36 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHENIX(dev_2006: ???)refinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C0V

5c0v


Resolution: 2.59→37.864 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 822 15.6 %
Rwork0.2069 --
obs0.2112 5269 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→37.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1224 160 0 7 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151435
X-RAY DIFFRACTIONf_angle_d1.1861956
X-RAY DIFFRACTIONf_dihedral_angle_d21.424553
X-RAY DIFFRACTIONf_chiral_restr0.107200
X-RAY DIFFRACTIONf_plane_restr0.004222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5904-2.75270.25231180.2422676X-RAY DIFFRACTION89
2.7527-2.96510.31581280.2554741X-RAY DIFFRACTION99
2.9651-3.26340.29761710.2409711X-RAY DIFFRACTION100
3.2634-3.73520.23791210.1905765X-RAY DIFFRACTION100
3.7352-4.70460.19961250.1758780X-RAY DIFFRACTION100
4.7046-37.86780.19531590.2044774X-RAY DIFFRACTION100

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