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- PDB-8ey8: LaM domain of human LARP1 in complex with AAAAGA RNA -

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Basic information

Entry
Database: PDB / ID: 8ey8
TitleLaM domain of human LARP1 in complex with AAAAGA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*AP*GP*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: 1.3 Å
AuthorsKozlov, G. / 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
DepositionOct 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: 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

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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*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,7532
Polymers13,7532
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-5 kcal/mol
Surface area5400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.683, 45.879, 58.861
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*AP*GP*A)-3')


Mass: 1946.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
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: 1.8 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 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: 0.95371 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95371 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 23947 / % possible obs: 95.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 15.56 Å2 / CC1/2: 0.996 / Rsym value: 0.106 / Net I/σ(I): 22.1
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 794 / CC1/2: 0.932 / Rsym value: 0.427 / % possible all: 65.5

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Processing

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

7soo


Resolution: 1.3→36.19 Å / SU ML: 0.1309 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.0571
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 1179 4.94 %
Rwork0.183 22706 -
obs0.1835 23885 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.75 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms737 77 0 62 876
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144849
X-RAY DIFFRACTIONf_angle_d1.58871166
X-RAY DIFFRACTIONf_chiral_restr0.1133133
X-RAY DIFFRACTIONf_plane_restr0.0138137
X-RAY DIFFRACTIONf_dihedral_angle_d9.8386144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.360.27891140.24272135X-RAY DIFFRACTION73.26
1.36-1.430.25641250.21922791X-RAY DIFFRACTION94.55
1.43-1.520.23551590.18842909X-RAY DIFFRACTION99.84
1.52-1.640.19291520.17172932X-RAY DIFFRACTION99.9
1.64-1.80.22681380.18032964X-RAY DIFFRACTION99.94
1.8-2.070.17491690.18042938X-RAY DIFFRACTION99.71
2.07-2.60.19671590.18113015X-RAY DIFFRACTION99.84
2.6-36.190.17861630.18023022X-RAY DIFFRACTION96.52
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)
10.389476637528-0.1294339648170.1623087328310.3223825581060.04358588413620.2939550030970.0636549139008-0.1136767743640.03676028749520.240186376066-0.08793197582570.0738792273961-0.1772364762010.09807156893610.0002589996355940.161367130858-0.0249647904324-0.005918602460370.1960296812070.01567856710880.1307000413456.8163604740817.589680709332.9187190335
20.102599444597-0.212793127271-0.07744941855470.6679463803920.0462886773980.1753470428870.115094093819-0.2697007955360.007606725257880.188882335123-0.367736574531-0.198932506741-0.5068228844850.433016669876-0.1701469398790.239692471027-0.0552217214282-0.03162644537770.1810771516390.03167477882160.17890059137.6073192960329.538920725423.610604102
31.28288674519-0.2056969063150.3709913020680.519938754605-0.04877041758930.1269637094240.1898363772970.195475266923-0.0552815050291-0.134345282419-0.219354612328-0.306196811627-0.02333276691490.518370788793-0.01937693232190.211263497855-0.01915442706270.004911203356120.1986746337860.05536732313180.1684153164066.4425841185827.201654689315.2216278487
40.1386744178880.05522162159990.169829140970.02200626400140.08959296969760.3817726704130.01765241009970.2903356396660.274345810382-0.1318651717380.293829227470.8190314562560.13301847664-0.4158083226430.01968851801550.1728342525950.003826648096550.004840120995590.1922057682110.06740088261970.305668227743-4.7533500832825.864613837618.271057093
50.277738661611-0.2536817749870.2611873093810.283134052038-0.1368920832760.1570881775570.0450662042566-0.0672709787498-0.127629042719-0.0796236692361-0.052728222983-0.02053484656930.1422741679920.0738613325796-0.0004948777492040.1403730416590.00398932923583-0.00142600442030.1885775898630.02346771919090.1701649774655.7170007902413.101156179223.3987333569
60.166272981518-0.3708413590820.259570353881.0817038074-0.7852117171591.032155745950.173210142474-0.1788432210420.171978630011-0.3061825444230.03784950469970.4474042196880.177334366936-0.154277101960.04681197819130.118838828371-0.00955363381326-0.008633160296680.1673314644650.004062654152590.193137969141-2.0441566369314.479038681530.7721515222
70.071422970473-0.0113420812677-0.05924209959920.04230576830550.05985046695130.07720852471650.39187563878-0.949942257497-0.3060512340310.790505494212-0.17019575810.4273337117130.0423911528088-0.4996907380190.0004765407416930.348382909381-0.03802931930730.03768613174110.3086374854910.003421176832280.274022919802-3.2686857958624.240203012230.9545475415
80.212955232248-0.0380455104482-0.2862653601060.02416389768430.003270976243480.4185433044350.116299380033-0.03609109859260.3030519452970.109964728326-0.04977708326020.610404839779-0.305869483266-0.5565574422020.0387194224010.189023037598-0.008880188717120.01573132220680.1826427055350.01248759539830.252157341626-5.5650933998423.47294312424.0178594627
91.1956117017-0.077123802504-1.378505243250.4572046495320.5252943948982.519274748020.1750552946570.3031616609180.2061641849320.15054104787-0.07226621718150.563891112536-0.239852242299-0.9376341833120.1582885048660.3131060739770.05230826384080.05806234685010.1109190594010.0282145536130.227320369394-0.87166990815632.547578006419.3902527542
100.0458667405645-0.2898595471610.05640399243172.54141113062-0.5504871866380.138745119227-0.09049231898030.4579883199820.00421693826751-0.784498867726-0.562455250531-0.743553499015-0.07421363302080.568480730383-0.6274557678020.1993779003720.03408549876050.0412279657230.4048208608330.1341652501880.26705084889913.120384759820.137019055118.4163013492
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 337 )AA323 - 3371 - 15
22chain 'A' and (resid 338 through 343 )AA338 - 34316 - 21
33chain 'A' and (resid 344 through 352 )AA344 - 35222 - 30
44chain 'A' and (resid 353 through 360 )AA353 - 36031 - 38
55chain 'A' and (resid 361 through 376 )AA361 - 37639 - 54
66chain 'A' and (resid 377 through 385 )AA377 - 38555 - 63
77chain 'A' and (resid 386 through 393 )AA386 - 39364 - 71
88chain 'A' and (resid 394 through 399 )AA394 - 39972 - 77
99chain 'A' and (resid 400 through 410 )AA400 - 41078 - 88
1010chain 'B' and (resid -4 through -1 )BB-4 - -1

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