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- PDB-8ey7: LaM domain of human LARP1 in complex with AAAGAA RNA -

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Basic information

Entry
Database: PDB / ID: 8ey7
TitleLaM domain of human LARP1 in complex with AAAGAA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*GP*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: 1.35 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*GP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,7532
Polymers13,7532
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-2 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.908, 45.338, 59.406
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*GP*AP*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.: 81 / 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: 1.81 Å3/Da / Density % sol: 31.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.056 M sodium phosphate, 1.344 M potassium phosphate

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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: 1.35→50 Å / Num. obs: 20906 / % possible obs: 93.3 % / Redundancy: 7.1 % / Biso Wilson estimate: 13.11 Å2 / CC1/2: 0.998 / Rsym value: 0.109 / Net I/σ(I): 17.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 636 / CC1/2: 0.967 / Rsym value: 0.498 / % possible all: 57.6

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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: 1.35→28.62 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.7838
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 1077 5.16 %
Rwork0.1859 19778 -
obs0.1879 20855 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.1 Å2
Refinement stepCycle: LAST / Resolution: 1.35→28.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms777 130 0 81 988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126952
X-RAY DIFFRACTIONf_angle_d1.46291321
X-RAY DIFFRACTIONf_chiral_restr0.1104148
X-RAY DIFFRACTIONf_plane_restr0.0154149
X-RAY DIFFRACTIONf_dihedral_angle_d10.4218174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.410.3169990.28061694X-RAY DIFFRACTION64.78
1.41-1.490.29011430.22342487X-RAY DIFFRACTION95.36
1.49-1.580.20831370.18512620X-RAY DIFFRACTION99.82
1.58-1.70.21951460.17382634X-RAY DIFFRACTION99.96
1.7-1.870.21571680.16972592X-RAY DIFFRACTION99.21
1.87-2.140.19641300.1692588X-RAY DIFFRACTION96.93
2.15-2.70.221340.18762655X-RAY DIFFRACTION98.1
2.7-28.620.231200.18682508X-RAY DIFFRACTION88.43
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)
10.353923794654-0.08831895471160.07629585595190.1703033918930.03375423188380.1512723903070.01169158231530.0224030815052-0.145156602256-0.109352472933-0.04579837007810.0269365087828-0.0354509900492-0.0679367979630.000169209856950.129864635226-0.011580623255-0.003745371061460.161819246947-0.01343053615470.118842008844-7.40209086723-8.01705022232-6.39531141987
20.03994264510050.0461697234622-0.03539200515950.214132261341-0.2058805969640.261328010582-0.0608138623980.01763016552020.049223795137-0.203257953012-0.1740927549840.115089116388-0.145675175992-0.130084254843-0.03905742824390.1540585252420.0260276167653-0.009212583951060.126387349016-0.03633156301940.139348791096-7.469922459956.463511558795.47477257744
30.4237049677840.01678404802570.2686314704060.5880772791060.2626707593470.5354639809160.0134353955765-0.0523761993330.01899159046340.00353730336301-0.0161932510116-0.001262478146380.00420675156701-0.1271949581340.007353366978830.1166924179250.00650339529470.003453230808060.107115950728-0.01629656517860.111103215894-3.76122828461-2.603525383919.91818553067
40.1422097467480.0511007524634-0.08123670694270.1421447039960.104900702620.1680050874010.03860315413570.2054581515880.0215164044756-0.1204332320470.0460682011896-0.276601063539-0.0537987190231-0.01302920175430.0002734029493850.126800413776-0.001011176957860.01185695241750.134188188584-0.005470114636260.13467457393.89219417546-2.903793284181.21463687506
51.5810222902-0.748053759508-0.2707348040490.3667362663820.1363623797720.1248000499990.1540122194320.3360354779030.120543975036-0.2209291971120.0406551384233-0.3729557645540.000727248999560.2792226587010.1128384546790.1963563638550.001240560418970.01068624943230.175413923489-0.05033862036530.1767498922491.105715771469.185724349659.86572192019
60.1072333377920.00672442011448-0.01853828843180.0589714441123-0.03797759820290.02707469387940.142838605852-0.4506159481270.06614383900370.2878478083460.007122647916750.318219851505-0.0999148963249-0.222507229643-0.0001156470542810.186892457391-0.02160547425490.02141680663980.298171463154-0.01439720518680.247364930087-16.4646206571-4.337361450513.0553098724
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 318 through 337 )AA318 - 3371 - 20
22chain 'A' and (resid 338 through 343 )AA338 - 34321 - 26
33chain 'A' and (resid 344 through 376 )AA344 - 37627 - 59
44chain 'A' and (resid 377 through 399 )AA377 - 39960 - 82
55chain 'A' and (resid 400 through 410 )AA400 - 41083 - 93
66chain 'B' and (resid -6 through -1 )BB-6 - -1

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