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- PDB-7sop: LaM domain of human LARP1 in complex with AAAUAA RNA -

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Basic information

Entry
Database: PDB / ID: 7sop
TitleLaM domain of human LARP1 in complex with AAAUAA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(P*AP*AP*AP*UP*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: 1.55 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(P*AP*AP*AP*UP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,7142
Polymers13,7142
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-3 kcal/mol
Surface area5490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.521, 46.259, 57.374
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*UP*AP*A)-3')


Mass: 1907.237 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.: 60 / 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: 1.77 Å3/Da / Density % sol: 30.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 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: 1.55→50 Å / Num. obs: 14361 / % possible obs: 98.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.9 Å2 / Rsym value: 0.057 / Net I/σ(I): 29
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 1208 / Rsym value: 0.313

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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: 7SOO

7soo


Resolution: 1.55→36.01 Å / SU ML: 0.2458 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.9297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2202 1437 10.01 %
Rwork0.1943 12924 -
obs0.197 14361 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.72 Å2
Refinement stepCycle: LAST / Resolution: 1.55→36.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms723 69 0 60 852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131815
X-RAY DIFFRACTIONf_angle_d1.34331116
X-RAY DIFFRACTIONf_chiral_restr0.0806128
X-RAY DIFFRACTIONf_plane_restr0.0112133
X-RAY DIFFRACTIONf_dihedral_angle_d8.7521129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.610.45941210.37261087X-RAY DIFFRACTION85.86
1.61-1.670.43051430.35931289X-RAY DIFFRACTION99.24
1.67-1.750.33931440.30461294X-RAY DIFFRACTION99.93
1.75-1.840.27481430.22911292X-RAY DIFFRACTION99.79
1.84-1.960.26231440.21321291X-RAY DIFFRACTION100
1.96-2.110.2581440.18421298X-RAY DIFFRACTION100
2.11-2.320.23351450.17411302X-RAY DIFFRACTION100
2.32-2.650.21141480.18611326X-RAY DIFFRACTION99.93
2.65-3.340.21571480.18811339X-RAY DIFFRACTION100
3.34-36.010.18111570.18071406X-RAY DIFFRACTION99.68
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)
11.69777866819-0.6512077108381.272679961193.40368164837-1.702158036052.936230988790.01831901660860.04635961430790.1395171218250.0543299419757-0.143157348129-0.0170255096585-0.2880691207280.2448218329590.08002379625460.202898193321-0.0100215490971-0.0001021771250030.240436466692-0.004513559132420.1965456425067.133321734723.290159895425.5497536815
21.19064800431.171669749240.9550541666764.52526971592-1.845058215253.20819394610.07562204489760.04832628109230.0729593020818-0.4197994938490.0866075841930.6865153299860.012002468299-0.41239254346-0.1206381731830.258067142805-0.006575481586-0.05805945735140.2953577968379.33617839681E-50.385351665625-4.0128157462425.958017244217.2343183789
31.90968722797-0.008525547438080.5091490618951.55873147396-0.5858594182231.208868102520.06714074822240.2022996722550.0323781709379-0.217250773923-0.120091362444-0.109612996680.0893601782439-0.08746256580810.007605928420590.2244498404470.003428013855960.009379201436690.302549302634-0.01102641075390.2444536291855.830044080613.536899138122.687998449
45.28287383319-2.084042266331.603772005433.5227295677-0.8696240882656.835967601270.290010954126-0.2459230761670.0701833493983-0.417300885479-0.03160826911460.006758830722860.3358113234650.162619300144-0.2695478630230.19957947804-0.01177235798280.004120225239190.274532342181-0.00972874478270.251777408047-1.4106156564213.895598843429.6553950456
55.728400853971.889269042061.178527314323.961856172550.5559102844744.009022550010.0398715800549-0.377317787181-0.2427707334970.315136777035-0.1423700683780.722649542720.276160994312-0.608168813558-0.06759805575750.2808933191340.02167829371110.02374425570490.2206113637760.01568165477640.300487195476-5.0044959748622.891395135627.7470976718
62.711646582880.094192256726-0.02671629115922.494982297640.4114544512617.201974389390.325815639788-0.06158768648160.1485097999150.1074613206360.1622865339570.148627876716-0.46118491497-0.429280337272-0.2952778348060.3144702158670.02978338491340.03019540409220.235014064140.00472874103510.299148986402-0.71173288233332.765123471620.2252218382
75.52011985568-0.2115979071720.8469906637327.468958980571.016034362922.18379874325-0.05834435574681.0337769919-0.206550081687-1.15294629869-0.133799532245-1.67968247427-1.01818499221.063522283570.1581277645520.3897720766460.007134736295350.1127364781720.5418135467640.08458859604610.48090398660212.746399868520.52196973317.7233966547
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 323 through 351 )AA323 - 3511 - 29
22chain 'A' and (resid 352 through 360 )AA352 - 36030 - 38
33chain 'A' and (resid 361 through 376 )AA361 - 37639 - 54
44chain 'A' and (resid 377 through 384 )AA377 - 38455 - 62
55chain 'A' and (resid 385 through 398 )AA385 - 39863 - 76
66chain 'A' and (resid 399 through 410 )AA399 - 41077 - 88
77chain 'B' and (resid -4 through -1 )BB-4 - -1

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