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- PDB-7sov: LaM domain of human LARP1 in complex with AAAAAAAAAAA RNA polynuc... -

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Basic information

Entry
Database: PDB / ID: 7sov
TitleLaM domain of human LARP1 in complex with AAAAAAAAAAA RNA polynucleotide
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10) / Isoform 2 of La-related protein 1
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsKozlov, G. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural basis of 3'-end poly(A) RNA recognition by LARP1.
Authors: Kozlov, G. / Mattijssen, S. / Jiang, J. / Nyandwi, S. / Sprules, T. / Iben, J.R. / Coon, S.L. / Gaidamakov, S. / Noronha, A.M. / Wilds, C.J. / Maraia, R.J. / Gehring, K.
History
DepositionNov 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of La-related protein 1
B: RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5714
Polymers15,3832
Non-polymers1882
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-14 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.785, 46.307, 58.625
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Isoform 2 of La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 11806.507 Da / Num. of mol.: 1 / Fragment: Residues 323-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / References: UniProt: Q6PKG0-3
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3576.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.62 Å3/Da / Density % sol: 24.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BICINE pH 9.0, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 17326 / % possible obs: 95.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 20.56 Å2 / Rsym value: 0.086 / Net I/σ(I): 18.8
Reflection shellResolution: 1.45→1.48 Å / Num. unique obs: 1586 / Rsym value: 0.595

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7SOO

7soo


Resolution: 1.45→36.34 Å / SU ML: 0.1668 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.1981
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2231 906 5.23 %
Rwork0.1835 16420 -
obs0.1857 17326 94.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.31 Å2
Refinement stepCycle: LAST / Resolution: 1.45→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms732 79 11 63 885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093845
X-RAY DIFFRACTIONf_angle_d1.25821161
X-RAY DIFFRACTIONf_chiral_restr0.1019134
X-RAY DIFFRACTIONf_plane_restr0.0103135
X-RAY DIFFRACTIONf_dihedral_angle_d12.987146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.540.27671470.15282643X-RAY DIFFRACTION92.75
1.54-1.660.2591750.16572783X-RAY DIFFRACTION99.06
1.66-1.830.23331560.14322792X-RAY DIFFRACTION98.46
1.83-2.090.20481360.16232779X-RAY DIFFRACTION96.2
2.09-2.640.20561430.19122709X-RAY DIFFRACTION93.54
2.64-36.340.22581490.1972714X-RAY DIFFRACTION89.16

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