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- PDB-8ey6: LaM domain of human LARP1 in complex with AAAAAG RNA -

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Basic information

Entry
Database: PDB / ID: 8ey6
TitleLaM domain of human LARP1 in complex with AAAAAG RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*AP*AP*G)-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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 / _pdbx_entry_details.has_protein_modification

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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
B: RNA (5'-R(*AP*AP*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0415
Polymers13,7532
Non-polymers2883
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-43 kcal/mol
Surface area5430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.523, 46.187, 58.895
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*AP*G)-3')


Mass: 1946.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 31.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.5, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 12601 / % possible obs: 97.2 % / Redundancy: 6 % / Biso Wilson estimate: 26.76 Å2 / CC1/2: 1 / Rsym value: 0.091 / Net I/σ(I): 16.6
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 629 / CC1/2: 0.782 / Rsym value: 0.537 / % possible all: 96.3

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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: 1.63→36.34 Å / SU ML: 0.2232 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.1633
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2422 685 5.44 %
Rwork0.2086 11916 -
obs0.2105 12601 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.9 Å2
Refinement stepCycle: LAST / Resolution: 1.63→36.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 77 15 33 839
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069838
X-RAY DIFFRACTIONf_angle_d0.98211159
X-RAY DIFFRACTIONf_chiral_restr0.0616134
X-RAY DIFFRACTIONf_plane_restr0.0106134
X-RAY DIFFRACTIONf_dihedral_angle_d9.9827144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.760.31671510.26532330X-RAY DIFFRACTION98.34
1.76-1.930.2461390.2162415X-RAY DIFFRACTION99.88
1.93-2.210.28011330.19592405X-RAY DIFFRACTION99.3
2.21-2.790.26041320.22192410X-RAY DIFFRACTION97.77
2.79-36.340.21751300.20042356X-RAY DIFFRACTION91.36
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)
12.41006364434-0.6857751659171.090964995275.32227447555-2.410890353454.93765345320.0996518574045-0.0374784825889-0.2369195758620.592975659709-0.02708613704670.191099393396-0.3706341180840.1548299928550.02095191432450.23068987823-0.0473400225354-0.005726706432180.317744891091-0.007095741605890.2342212078957.1648277676917.395363912532.987084392
22.066252829160.65599889002-1.288036092951.91701042451-1.426735648331.996494185880.0728005872711-0.09180424677940.2770683515010.966854917847-0.451165163622-0.277547472023-0.8235481095690.2458837773160.3288015169630.352169838773-0.0575430831942-0.07575122437530.2510578550420.04071031305760.3043995511497.0473222680729.393028979923.5849824171
31.752234823670.6310886296-0.8102215738142.84993304568-0.7785654095582.224528084180.1366434052720.1190212926340.181218595062-0.104394410949-0.09198091526510.27762765332-0.2050705861360.0424216400923-0.01444973333420.19412719724-0.0165408457718-0.001483074249390.2169871667180.03424700388010.2348065216271.4082028562424.184651519717.3042812261
41.395341119880.0120003608879-0.2717450266622.09747380675-1.877452542311.858579544850.0282018497160.134069464462-0.141834720649-0.1264844668950.01157117534180.08286062197640.08013000467750.1159894721860.0003074995408170.2361376374210.00817941944877-0.004317406692150.3753578290490.01170831890450.2772696279747.9959290131711.856650658524.6576268248
57.33844011591-0.4490111047380.4640424773675.20016484661-0.03353256600557.356644874670.156540738346-0.379913289206-0.02502646873170.02905046307520.1676893161410.4162054470690.1610491216320.258770102492-0.2839970620740.184421798738-0.0189921529905-0.00634972007230.2321154996140.02214848354080.269656217267-1.6107465685514.178855141630.6682803818
67.915178249113.593991756614.181894776143.973920223811.978692759185.179530771920.735022975832-1.2581645060.3815245434420.744262778899-0.3498804442150.415961638886-0.195822891992-0.676475033284-0.3231335487870.381106442624-0.03157273145830.08483991233840.337660529411-0.01409103913030.326283176333-3.5131419033624.460860268930.375575259
72.65961710890.239478501603-0.6711894248543.94574355708-0.6860449695882.516725440170.128629745511-0.2291741102580.3762484479450.1212895111530.03844418069350.732978895873-0.136500512581-0.344913327524-0.1960690397510.2271469572410.003663068173870.0303946440110.2233690937190.03190024384830.326018490048-5.7213543149722.345456264223.7500852993
85.82572747459-0.214142148509-0.1657654460626.21104574555-2.733817259361.417639960060.484583836051-0.2552428154610.4581000308440.9953725849160.212345841351-0.414363169494-0.019232541491-0.148318333299-0.7261670473210.532818827310.03793159197080.0801208141360.230233028765-0.0100512077550.322964476997-2.5391036867733.146773515324.9834479497
96.27730299445-0.137418647878-0.1690506097944.32868531516-1.945183407964.965671517690.4314468729850.141946454601-0.240380207384-0.128373409398-0.09369249460750.4643823768810.339331602771-0.116277645733-0.4618392088750.3367807799260.0188198585313-0.02358629519670.190951005230.02928938872320.2956442136311.0300402447330.960921017513.2985152093
102.98957716431-2.040825528221.559359060023.13603759060.1686220401082.97684321735-0.1939129455030.731343122013-0.312860872033-0.755005119314-0.345987795808-0.747220293115-0.5908617443511.95837883650.1631962390150.356011393464-0.02066823616170.03657693640290.6491339648470.112044876710.46586678234813.092663431620.311207315318.1751464811
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 322 through 337 )AA322 - 3371 - 16
22chain 'A' and (resid 338 through 343 )AA338 - 34317 - 22
33chain 'A' and (resid 344 through 366 )AA344 - 36623 - 45
44chain 'A' and (resid 367 through 376 )AA367 - 37646 - 55
55chain 'A' and (resid 377 through 385 )AA377 - 38556 - 64
66chain 'A' and (resid 386 through 393 )AA386 - 39365 - 72
77chain 'A' and (resid 394 through 399 )AA394 - 39973 - 78
88chain 'A' and (resid 400 through 405 )AA400 - 40579 - 84
99chain 'A' and (resid 406 through 410 )AA406 - 41085 - 89
1010chain 'B' and (resid -4 through -1 )BB-4 - -1

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