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- PDB-8g91: LaM domain of human LARP1 in complex with Rp phosphorothioate iso... -

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Basic information

Entry
Database: PDB / ID: 8g91
TitleLaM domain of human LARP1 in complex with Rp phosphorothioate isomer of AAAAA(SRA) RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*AP*AP*(SRA))-3')
KeywordsRNA BINDING PROTEIN/RNA / Winged helix fold / RNA binding domain / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / 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: 1.2 Å
AuthorsKozlov, G. / Jiang, J. / Gehring, K.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Rna Biol. / Year: 2024
Title: Enhanced binding of guanylated poly(A) RNA by the LaM domain of LARP1.
Authors: Kozlov, G. / Jiang, J. / Rutherford, T. / Noronha, A.M. / Wilds, C.J. / Gehring, K.
History
DepositionFeb 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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*AP*AP*(SRA))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8453
Polymers13,7532
Non-polymers921
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint2 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.781, 53.781, 90.452
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-687-

HOH

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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*AP*AP*(SRA))-3')


Mass: 1946.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95371 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 41809 / % possible obs: 99.4 % / Redundancy: 20 % / Biso Wilson estimate: 13.23 Å2 / CC1/2: 0.999 / Net I/σ(I): 42.4
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 10.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3876 / CC1/2: 0.592 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→35.06 Å / SU ML: 0.1507 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.9635
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1893 2085 4.99 %
Rwork0.1782 39724 -
obs0.1788 41809 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.97 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 75 6 106 930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056854
X-RAY DIFFRACTIONf_angle_d1.17091168
X-RAY DIFFRACTIONf_chiral_restr0.0806132
X-RAY DIFFRACTIONf_plane_restr0.008138
X-RAY DIFFRACTIONf_dihedral_angle_d10.5402136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.230.44831090.4012407X-RAY DIFFRACTION90.8
1.23-1.260.35531380.30662573X-RAY DIFFRACTION98.69
1.26-1.290.25131230.22562613X-RAY DIFFRACTION99.17
1.29-1.330.21791460.20012615X-RAY DIFFRACTION99.32
1.33-1.370.18961430.1962611X-RAY DIFFRACTION99.53
1.37-1.420.18731490.1922621X-RAY DIFFRACTION99.64
1.42-1.480.21361470.1972616X-RAY DIFFRACTION99.71
1.48-1.550.18351530.18692626X-RAY DIFFRACTION99.78
1.55-1.630.20981340.16752655X-RAY DIFFRACTION99.93
1.63-1.730.18011510.17222667X-RAY DIFFRACTION100
1.73-1.870.19541490.17672644X-RAY DIFFRACTION99.96
1.87-2.050.15861320.16692700X-RAY DIFFRACTION100
2.05-2.350.15291480.15812705X-RAY DIFFRACTION100
2.35-2.960.19051160.17542772X-RAY DIFFRACTION100
2.96-35.060.18311470.16552899X-RAY DIFFRACTION99.44
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)
10.247033323632-0.198404344074-0.1740291793710.1963780965160.03830096607630.266976363244-0.0641790358487-0.00863693386779-0.0710973228157-0.03840075637330.07224549156050.1742969416580.25404184031-0.184663708292-0.003384458161790.160978985849-0.0538213564911-0.01069748265280.1097755096610.01761497813030.15203934515-23.388391135-11.9418610405-12.6842167698
20.1476414640590.023419651375-0.06312299648190.0457192248885-0.02382092166390.07887486801050.047915595731-0.0806493561929-0.03093442734280.110899943066-0.0207379487814-0.0835470178652-0.07494306830960.2215700290430.00353032016330.116045842293-0.0243393669769-0.007268899737930.1253147498190.006189223357340.104464500545-14.20950703881.65501848563-6.68954990874
30.0440072085341-0.0316524908429-0.1360054942650.710547880512-0.6777926943061.204690648950.04385810429170.009187690933310.0195780616907-0.203140757982-0.005317513798660.05817611565850.1049389155510.0651781134670.003805571308460.144449174345-0.00471734032345-0.02026899036870.0990260359874-1.95939636864E-50.115813597932-16.130793273-4.11190835384-19.3261968126
40.155639859986-0.1738985115980.3995539322430.479300467847-0.1440164442180.9262599428680.04770484294670.0495678799350.078263768231-0.0878139650437-0.0001933506352610.131278755167-0.258955880638-0.09787213758240.003546454918290.12969521417-0.00920717347591-0.001509495888420.1077605366370.008375447691850.115610011878-21.85819664394.45163169809-15.8184737887
50.036427519096-0.02804986275850.01907186480420.0620325148404-0.03831960978540.0142375479440.03189023017340.08981366972830.1090685314730.0893421713702-0.0212025392002-0.4145817713460.07149874121430.567479903676-0.0004428965991530.2649600170940.0508608392437-0.03934419979460.2386904152220.01343498457450.238402146654-7.86127198053-8.57178935623-10.4044762167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 322 through 337 )AA322 - 3371 - 16
22chain 'A' and (resid 338 through 345 )AA338 - 34517 - 24
33chain 'A' and (resid 346 through 384 )AA346 - 38425 - 63
44chain 'A' and (resid 385 through 410 )AA385 - 41064 - 89
55chain 'B' and (resid -4 through -2 )BB-4 - -2

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