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- PDB-7sos: LaM domain of human LARP1 in complex with AAAA RNA -

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Basic information

Entry
Database: PDB / ID: 7sos
TitleLaM domain of human LARP1 in complex with AAAA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*A)-3')
KeywordsRNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology: / RNA / 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: 1.25 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)13,1173
Polymers13,0782
Non-polymers391
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-4 kcal/mol
Surface area5430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.194, 46.799, 58.742
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(*AP*AP*AP*A)-3')


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 1.95 Å3/Da / Density % sol: 37.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.08M magnesium acetate, 1.344M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. obs: 28289 / % possible obs: 97.7 % / Redundancy: 7 % / Biso Wilson estimate: 16.28 Å2 / Rsym value: 0.039 / Net I/σ(I): 50.4
Reflection shellResolution: 1.25→1.27 Å / Num. unique obs: 2236 / Rsym value: 0.464

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Processing

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

7soo


Resolution: 1.25→36.6 Å / SU ML: 0.1478 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 20.121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 1455 5.14 %
Rwork0.1744 26834 -
obs0.1756 28289 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.18 Å2
Refinement stepCycle: LAST / Resolution: 1.25→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms727 76 1 100 904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161828
X-RAY DIFFRACTIONf_angle_d1.66721138
X-RAY DIFFRACTIONf_chiral_restr0.126132
X-RAY DIFFRACTIONf_plane_restr0.0139133
X-RAY DIFFRACTIONf_dihedral_angle_d10.051142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.30.44691070.39222129X-RAY DIFFRACTION78.48
1.3-1.350.26361330.23362633X-RAY DIFFRACTION97.29
1.35-1.410.21661280.15192729X-RAY DIFFRACTION100
1.41-1.480.19141470.1542733X-RAY DIFFRACTION99.97
1.48-1.580.22121510.17162718X-RAY DIFFRACTION100
1.58-1.70.19531480.14552721X-RAY DIFFRACTION100
1.7-1.870.17751560.14722744X-RAY DIFFRACTION100
1.87-2.140.18981470.16022753X-RAY DIFFRACTION100
2.14-2.690.19331600.1772790X-RAY DIFFRACTION99.97
2.7-36.60.1851780.18072884X-RAY DIFFRACTION99.67

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