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- PDB-7soq: LaM domain of human LARP1 in complex with AAA RNA -

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Basic information

Entry
Database: PDB / ID: 7soq
TitleLaM domain of human LARP1 in complex with AAA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*A)-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: 1.15 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*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7492
Polymers12,7492
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.915, 46.474, 59.135
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*A)-3')


Mass: 942.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.056M sodium phosphate, 50mM sodium cacodylate, 30% PEG4000

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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 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 35581 / % possible obs: 96.8 % / Redundancy: 8 % / Biso Wilson estimate: 10.5 Å2 / Rsym value: 0.061 / Net I/σ(I): 32.2
Reflection shellResolution: 1.15→1.17 Å / Num. unique obs: 2885 / Rsym value: 0.431

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Processing

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

7soo


Resolution: 1.15→36.54 Å / SU ML: 0.0958 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.0628
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1877 1787 5.02 %
Rwork0.1756 33794 -
obs0.1762 35581 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.04 Å2
Refinement stepCycle: LAST / Resolution: 1.15→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms750 63 0 115 928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139855
X-RAY DIFFRACTIONf_angle_d1.43051173
X-RAY DIFFRACTIONf_chiral_restr0.1149132
X-RAY DIFFRACTIONf_plane_restr0.0125141
X-RAY DIFFRACTIONf_dihedral_angle_d11.9236139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.180.22581030.20722073X-RAY DIFFRACTION77.52
1.18-1.220.19211410.1932380X-RAY DIFFRACTION91.57
1.22-1.260.23181340.20582568X-RAY DIFFRACTION96.67
1.26-1.30.21771300.1872604X-RAY DIFFRACTION98.42
1.3-1.350.19371470.16492608X-RAY DIFFRACTION98.29
1.35-1.420.17921310.16892638X-RAY DIFFRACTION98.75
1.42-1.490.20021260.16932633X-RAY DIFFRACTION98.4
1.49-1.580.16031230.17232648X-RAY DIFFRACTION99.39
1.58-1.710.15771540.16352668X-RAY DIFFRACTION99.65
1.71-1.880.17271190.1642709X-RAY DIFFRACTION99.93
1.88-2.150.16761380.16962708X-RAY DIFFRACTION99.61
2.15-2.710.18631700.18012725X-RAY DIFFRACTION100
2.71-36.540.20021710.17792832X-RAY DIFFRACTION99.8
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)
12.00565135615-0.1650559461620.1804940860232.89589226073-1.126913038142.631574407670.0293863987811-0.139414766327-0.02366541414820.228185969896-0.06175154361050.0515015839047-0.1834315006710.09904061666490.0381139834250.0588206612917-0.00778188333855-0.009438090313790.1044725433680.000776132117740.05473494615076.68641840541-6.372014191553.98638775685
21.14974186912-0.852290418814-2.350058842567.16659670867-0.6701589625195.777176940540.149187052674-0.1818531291180.259945423460.317384579686-0.137260256267-0.231522854971-0.520978131460.295833583168-0.01040250533150.142868038243-0.0326143967751-0.02230600082960.1016656420050.006189368469170.112164212687.763302583286.47524258633-5.86984202289
31.454681480220.09573210571590.08380671019941.96448676544-0.8352487115541.116820025550.03472295525520.06192968745990.0291132285449-0.0839305318033-0.008711225283850.0843506634603-0.02076036253180.0470551743598-0.02115697400130.0692017126398-0.004915757971710.00370874365890.07400532624270.002989202598310.06272592171483.62705444025-2.62437517916-9.87751295772
41.220060082070.216165945154-0.1489894959362.16420140822-0.8227495406081.511875498160.116901878241-0.1545077046870.03803631017060.1814954607480.01901244211860.184332329381-0.201515162812-0.00513844140513-0.1305384732190.111872437829-0.008846192090410.0185952687720.103594025692-0.003594481365470.127165231327-3.73798432523-2.70914077529-0.777264538015
54.407853104890.294056272097-2.53611940281.53338050952-0.5331814010991.546511679770.1367753932910.04641912486340.3001358767270.2627036289620.01387121691460.373121873909-0.184605221193-0.177331015207-0.02628857035110.1859849889280.0129940786920.03353206163550.06730398062840.01366573935240.154899179707-0.7685814889749.65435285275-9.95414617069
65.21207735587-2.00509288028-0.1232454470184.76266399506-1.357013259340.497521004440.06216036737910.7407757146650.36083639152-0.292242507669-0.329672981387-0.393382633698-0.1808888752610.6698820998610.1372308916850.106442617698-0.00139513828550.006196091071610.2187007178610.06425458364950.16660772962412.5278432426-2.901125971-11.1127495908
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 321 through 337 )AA321 - 3371 - 17
22chain 'A' and (resid 338 through 343 )AA338 - 34318 - 23
33chain 'A' and (resid 344 through 376 )AA344 - 37624 - 56
44chain 'A' and (resid 377 through 399 )AA377 - 39957 - 79
55chain 'A' and (resid 400 through 410 )AA400 - 41080 - 90
66chain 'B' and (resid -3 through -1 )BB-3 - -1

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