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- PDB-7soo: LaM domain of human LARP1 -

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Basic information

Entry
Database: PDB / ID: 7soo
TitleLaM domain of human LARP1
ComponentsIsoform 2 of La-related protein 1
KeywordsRNA BINDING PROTEIN / Winged helix fold / RNA binding domain
Function / homologyIsoform 2 of La-related protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.1Sep 7, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2146
Polymers11,8071
Non-polymers4075
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.572, 46.776, 57.098
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M Bis-Tris pH 6.5, 25% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.52154 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52154 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 12117 / % possible obs: 98.68 % / Redundancy: 7.4 % / Biso Wilson estimate: 34.67 Å2 / Rsym value: 0.049 / Net I/σ(I): 55.9
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1138 / Rsym value: 0.34

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Processing

Software
NameVersionClassification
MxDCdata collection
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZH5

1zh5


Resolution: 1.65→36.18 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.4708
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2244 1212 10 %
Rwork0.2052 10905 -
obs0.2072 12117 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.51 Å2
Refinement stepCycle: LAST / Resolution: 1.65→36.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms724 0 21 48 793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052756
X-RAY DIFFRACTIONf_angle_d0.79431029
X-RAY DIFFRACTIONf_chiral_restr0.0488114
X-RAY DIFFRACTIONf_plane_restr0.0077130
X-RAY DIFFRACTIONf_dihedral_angle_d5.212199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.39831270.35751143X-RAY DIFFRACTION96.21
1.72-1.790.26061340.26351209X-RAY DIFFRACTION99.7
1.79-1.890.29571330.24191200X-RAY DIFFRACTION99.85
1.89-2.010.26961340.22421199X-RAY DIFFRACTION99.78
2.01-2.160.25751350.19451214X-RAY DIFFRACTION99.19
2.16-2.380.23611310.19961177X-RAY DIFFRACTION96.67
2.38-2.720.20931340.21791209X-RAY DIFFRACTION97.96
2.72-3.430.21591380.2071244X-RAY DIFFRACTION99.42
3.43-36.180.21071460.19181310X-RAY DIFFRACTION99.25
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)
12.25840309425-0.7814012653191.381124703863.34709758661-0.7632687262774.551728273820.163766870235-0.130978815063-0.3119531024960.212088982132-0.1534625206920.300527158539-0.09701219192060.0121516693669-0.08692322347460.272455294964-0.03821798642750.003876795420140.3308044692270.002357426773620.3119922574216.6512436079417.493360710932.3517044095
23.50802677532-0.342303359028-1.354195295153.41277574278-1.323602487514.852672669510.1279666086520.0368067070524-0.0540990501917-0.082396875171-0.296391701926-0.0663300059831-0.2660027288630.538166028690.1125807267940.356985135541-0.0222371289076-0.01398182889020.3386420449370.03229273579180.3482304363596.9195314517628.899114533918.3220335298
31.128797953960.0681522818284-0.555299477283.10210401255-1.028249050691.942406515790.02142863447410.09692690730730.575013192358-0.003962142479860.135240402343-0.0136607274901-0.3813202207650.0356971233587-0.09133257867820.2882734373940.02081775009870.002343477003450.3525927098050.01266981627380.368922812839-2.3121342351922.213450195418.6929060182
48.03158367621-0.00666392036922.822005533787.50370691092-2.846651136344.1868398365-0.08427156965580.590707715011-0.37341169145-0.101739703717-0.188445596945-0.6383892194550.2571930322470.1333559136570.1868390647650.2724713828080.01472542099240.01302803252060.369619052428-0.02114116343280.3177376593397.7939975959712.166015909723.8956161814
56.01376779356-1.293779885820.4497816927054.280111533560.1711704394045.821196640870.333242467013-0.30742640465-0.177251424268-0.0081950625575-0.4172413253840.5536553671-0.02035606211410.0208841779486-0.01287332786740.274878489610.01293211010020.0002580808564260.348611148721-0.01489000764940.284383934036-1.6758564414113.929437483229.6331117511
64.956857172110.8175566016690.5027296645833.13904674166-0.8195572403632.789441470470.239096220978-0.423740289543-0.05618607490780.194151445361-0.02223508269870.473451536919-0.0926075106482-0.44772962509-0.3505062036440.412382913276-0.003776721926790.04562037553660.3476312821470.02319722860250.425715671321-5.3674217564523.395900605527.2555891752
73.54664611554-0.193460174697-1.541443923822.33238621074-1.719172185036.303628047480.458305590942-0.3987472213610.3996960810230.4323359640890.1514227434940.299429844039-1.032073020490.0612040440859-0.5529142404840.4419607256920.01514409013130.06010329712140.3121668147810.01391956701250.365294448033-0.7150877302132.86136887620.1724429497
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 322 through 337 )322 - 3371 - 16
22chain 'A' and (resid 338 through 352 )338 - 35217 - 31
33chain 'A' and (resid 353 through 366 )353 - 36632 - 45
44chain 'A' and (resid 367 through 376 )367 - 37646 - 55
55chain 'A' and (resid 377 through 384 )377 - 38456 - 63
66chain 'A' and (resid 385 through 398 )385 - 39864 - 77
77chain 'A' and (resid 399 through 410 )399 - 41078 - 89

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