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- PDB-7sor: LaM domain of human LARP1 in complex with AAA RNA -

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Basic information

Entry
Database: PDB / ID: 7sor
TitleLaM domain of human LARP1 in complex with AAA RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*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: 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(*AP*AP*A)-3')
C: Isoform 2 of La-related protein 1
D: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6587
Polymers25,4984
Non-polymers1603
Water2,828157
1
A: Isoform 2 of La-related protein 1
B: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8474
Polymers12,7492
Non-polymers982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area5670 Å2
MethodPISA
2
C: Isoform 2 of La-related protein 1
D: RNA (5'-R(*AP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8113
Polymers12,7492
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint1 kcal/mol
Surface area5660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.562, 55.890, 70.172
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.: 2 / 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*A)-3')


Mass: 942.660 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium chloride, 0.1M Bis-Tris pH 5.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 42380 / % possible obs: 99.8 % / Redundancy: 8.3 % / Biso Wilson estimate: 16.27 Å2 / Rsym value: 0.039 / Net I/σ(I): 44.5
Reflection shellResolution: 1.35→1.37 Å / Num. unique obs: 4097 / Rsym value: 0.633

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Processing

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

7soo


Resolution: 1.35→43.72 Å / SU ML: 0.1471 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.7005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2045 2128 5.02 %
Rwork0.1807 40252 -
obs0.1819 42380 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 124 9 157 1762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01381650
X-RAY DIFFRACTIONf_angle_d1.5842255
X-RAY DIFFRACTIONf_chiral_restr0.0985256
X-RAY DIFFRACTIONf_plane_restr0.0137267
X-RAY DIFFRACTIONf_dihedral_angle_d12.9079263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.380.31651330.27462563X-RAY DIFFRACTION97.08
1.38-1.420.23941460.22982633X-RAY DIFFRACTION99.07
1.42-1.450.28311420.21942656X-RAY DIFFRACTION99.61
1.45-1.50.23911270.21462668X-RAY DIFFRACTION99.71
1.5-1.550.21961300.20112657X-RAY DIFFRACTION99.57
1.55-1.60.2231360.18242668X-RAY DIFFRACTION99.64
1.6-1.670.21391390.16162652X-RAY DIFFRACTION99.82
1.67-1.740.20381360.16732687X-RAY DIFFRACTION99.82
1.74-1.830.17591490.16732659X-RAY DIFFRACTION99.75
1.83-1.950.2141580.17742695X-RAY DIFFRACTION99.86
1.95-2.10.20231510.16182674X-RAY DIFFRACTION99.96
2.1-2.310.1891460.16342707X-RAY DIFFRACTION99.79
2.31-2.640.21251270.1832734X-RAY DIFFRACTION99.76
2.64-3.330.21331390.18692759X-RAY DIFFRACTION99.93
3.33-43.720.18421690.1792840X-RAY DIFFRACTION98.92
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)
10.24520208627-0.1145122891970.1748382259730.434972692598-0.4295249873070.438253979314-0.0166536888653-0.1437507087130.03416911407310.257798419667-0.07144700008010.36875910473-0.0928361158479-0.3132810926440.0004185628279020.1991992223610.02718114883350.04285695083660.184294607651-0.001077588882640.179871307219-16.83833354124.566177525598.17893204943
20.0815564805941-0.0163082765427-0.06735256335680.2419935228750.01679564635190.0553635865146-0.0445737252090.217056596181-0.188323344231-0.587656765298-0.05002018459710.228220298867-0.0273802139861-0.0782073079302-0.001012409223670.214600810356-0.00393560864314-0.02124321837790.16914219328-0.01269369994570.176678448429-16.2002533296-9.29189870135-1.30107818656
30.06105837758550.02420340438930.003389366301850.0838063636144-0.06240133033530.0649349155922-0.01632136305160.216022641109-0.00862204176938-0.36190026887-0.146040806933-0.4792071710030.01555168304610.290003398161-0.0001233083121670.1984077562830.004934532936670.04813636463240.1799520089524.80478108392E-50.218969838395-6.39059117808-11.1900573937-1.51042607479
40.5980650804410.01221155401190.0490791696761.17033656481-0.15548668830.3200924981520.0341588209388-0.0574831148563-0.0302192229690.100304994962-0.0427356012316-0.148976447922-0.0283442839148-0.004325520329166.50947482293E-50.129201460528-0.00586989299114-0.003338410289690.1437385852270.0154626180640.120344110328-8.83652970339-3.220392794110.1336095326
50.08630094104210.01333805864360.1358189622210.388846793171-0.2258287327160.5688949314240.129530331529-0.276174755955-0.0991581751355-0.07958867536830.0306411053104-0.2802341814020.1036388514040.1254669181840.01752365984160.137787399882-0.01312315969040.01040376496220.1740454717740.003612519275870.197275456509-12.6651188143-16.79954331814.67224385571
60.0497809267279-0.0323985873251-0.03148718712020.0825310830719-0.03185572464370.05533894790.3586920915220.454619515206-0.0676841853401-0.686853629828-0.3484132168460.042947066642-0.0572586886033-0.200074598095-0.001742614361760.3180549130540.04323814681070.03252758766260.2332092132030.04023419709230.207618630099-9.33266943335-1.13579768525-4.54710594018
70.198153129949-0.035982413487-0.1405464872160.3723081397970.2435271316520.2203998270780.0143034636307-0.130278241645-0.09669759787610.257834451334-0.024931629227-0.309973107010.1942102407810.2622051152094.61220625979E-50.2391773309740.0381039850525-0.05851672871980.1817331528280.001841764319580.20045995648616.5337776219-4.530605310468.3905998915
80.0467365102213-0.01714327626690.02801790131240.08907093290210.01798069622260.0528464320544-0.002328202279250.0965991955236-0.0793876390151-0.09244270333860.0416520150241-0.1043312380010.0298994256096-0.05418719614960.0002129101971040.140021461243-0.007227765693270.008648076068820.154676785856-6.6152226971E-50.13634269244715.91461334719.57697331263-0.768680260727
90.06046761270110.05664881239370.03831877106750.09168980718940.09294980085980.0935481290245-0.01354688100750.358866559308-0.0594028140936-0.322214135335-0.09385393320140.21918176951-0.0625538618004-0.1314420275380.000124527644080.134365437263-0.00019689572645-0.01618996996510.1642931286870.003100728949020.1558393300915.9357215723711.1992743118-1.20122712953
100.0700230093512-0.06079721731770.06046210769690.046380656875-0.04806601282180.0497204480412-0.003471823524960.0822334806041-0.08054039879630.016655529773-0.05820910602210.203390671658-0.128864744444-0.06065549152437.69555657008E-50.155939226762-0.01613926208530.02527119447770.162972949771-0.01302891672360.174858916876.3187921113613.5576908299.19851355915
110.1539074864650.0284315989617-0.006995755974110.215939360612-0.06078852374430.123846814979-0.03813461475610.153763639158-0.0368356534292-0.272745273352-0.1417517517980.417244276212-0.0361127891218-0.023441712081-0.0005368839381120.1629579846350.00941192073225-0.04441337239010.131465320071-0.01512991496160.1987538837375.53300499798-1.455883352994.3388606145
121.27831197509-0.8574332368780.1383558442161.471017654450.4119917600480.318205360942-0.101975295436-0.283107725577-0.188531402930.715562081720.28281668640.34856799993-0.232008068662-0.06753543436650.2616656346190.3550869941680.05446761567910.05637726830830.2053945706240.03726303961540.1758658429768.48871367867-4.840825481412.8062867917
131.09277757017-0.0287904549819-0.1402788029940.3309648047240.2460161907220.2740692210190.115841949197-0.1894798410240.1384807340120.346168596083-0.0667347638456-0.01560429070010.106308864826-0.00716018309498-0.00792604311180.185596720809-0.008651288185140.006976921137270.175863827479-0.02492711044960.1294057568112.20389380447.9219550890713.9687345861
140.0011234537686-0.0440167801516-0.05943284560630.8432125954521.232702734791.805262294870.113252278219-0.1442641554460.086281761448-0.08598766204190.14349647666-0.17511455976-0.2928963061050.3532170768630.1321949593760.0979015904824-0.03603210389850.002172429731480.221102964032-0.008048933631440.12235155932716.681512758616.37755624618.13461548007
150.07598096711090.0265796586173-0.03597165851460.06459842668080.003137343409130.08625725665070.0805470613491-0.1506317648890.209640790439-0.206417038514-0.05384370054180.4708387120840.0926494832221-0.367096097183-0.0001474883469230.1277199831630.00132490305936-0.01695887975140.1702165266610.004852917827610.2151942948497.2735435484117.08351332140.950727156643
160.0303904076526-0.00182273734422-0.0256709866720.07107191107750.03462402143590.03575105177270.398352447310.3983527214460.0242112498409-0.70740717106-0.2833588743190.03223697023590.1315960260110.1486601534-0.0005299062365560.2968119723250.0334856196339-0.0447388057380.213467380255-0.03590798170290.2356688645648.844512464411.16173356458-4.24111010426
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 345 )AA338 - 34517 - 24
33chain 'A' and (resid 346 through 352 )AA346 - 35225 - 31
44chain 'A' and (resid 353 through 399 )AA353 - 39932 - 78
55chain 'A' and (resid 400 through 410 )AA400 - 41079 - 89
66chain 'B' and (resid -3 through -1 )BB-3 - -1
77chain 'C' and (resid 322 through 337 )CC322 - 3371 - 16
88chain 'C' and (resid 338 through 345 )CC338 - 34517 - 24
99chain 'C' and (resid 346 through 352 )CC346 - 35225 - 31
1010chain 'C' and (resid 353 through 360 )CC353 - 36032 - 39
1111chain 'C' and (resid 361 through 371 )CC361 - 37140 - 50
1212chain 'C' and (resid 372 through 384 )CC372 - 38451 - 63
1313chain 'C' and (resid 385 through 399 )CC385 - 39964 - 78
1414chain 'C' and (resid 400 through 405 )CC400 - 40579 - 84
1515chain 'C' and (resid 406 through 410 )CC406 - 41085 - 89
1616chain 'D' and (resid -3 through -1 )DD-3 - -1

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