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- PDB-8g90: LaM domain of human LARP1 in complex with Sp phosphorothioate iso... -

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Basic information

Entry
Database: PDB / ID: 8g90
TitleLaM domain of human LARP1 in complex with Sp phosphorothioate isomer of AAAAA(SRA) RNA
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(*AP*AP*AP*AP*AP*(SRA))-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: 1.2 Å
AuthorsKozlov, G. / Jiang, J. / 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
DepositionFeb 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: 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

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*AP*(SRA))-3')


Theoretical massNumber of molelcules
Total (without water)13,7532
Polymers13,7532
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-0 kcal/mol
Surface area5260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.951, 46.646, 59.276
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*(SRA))-3')


Mass: 1946.343 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.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 1.86 Å3/Da / Density % sol: 33.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.5, 28% (w/v) PEG 2000 MME

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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: 1.2→50 Å / Num. obs: 31018 / % possible obs: 95.2 % / Redundancy: 8.6 % / Biso Wilson estimate: 12.52 Å2 / CC1/2: 0.993 / Net I/σ(I): 35.6
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2236 / CC1/2: 0.825 / % possible all: 67.7

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→26.02 Å / SU ML: 0.1228 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 20.7747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1550 5 %
Rwork0.1919 29468 -
obs0.1928 31018 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.54 Å2
Refinement stepCycle: LAST / Resolution: 1.2→26.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms725 75 0 115 915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039838
X-RAY DIFFRACTIONf_angle_d0.93711149
X-RAY DIFFRACTIONf_chiral_restr0.0771132
X-RAY DIFFRACTIONf_plane_restr0.0062134
X-RAY DIFFRACTIONf_dihedral_angle_d9.2076135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.240.3011080.27481932X-RAY DIFFRACTION69.51
1.24-1.280.25281340.26682409X-RAY DIFFRACTION87.93
1.28-1.340.29551230.23442740X-RAY DIFFRACTION97.78
1.34-1.40.22751570.20362782X-RAY DIFFRACTION99.9
1.4-1.470.20581560.19742763X-RAY DIFFRACTION100
1.47-1.560.20081220.18732849X-RAY DIFFRACTION100
1.56-1.680.18021470.17572808X-RAY DIFFRACTION100
1.68-1.850.1881480.17912829X-RAY DIFFRACTION100
1.85-2.120.2071630.17912809X-RAY DIFFRACTION100
2.12-2.670.19011580.18452859X-RAY DIFFRACTION100
2.67-26.020.22241340.19382688X-RAY DIFFRACTION89.08
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)
10.431258916244-0.1302985485770.128053737050.332725940369-0.03307941325620.50835268948-0.01584383121470.0652046097176-0.00758714618112-0.142298580676-0.08802550143720.0533037059102-0.18110165203-0.0980595707516-0.02829486125740.1053837312670.0185477646358-0.008565653038780.131332812498-0.01003192508710.0938593389159-6.9019324465-5.41013873185-3.37831099107
20.0355735935140.0342601906920.02533904749780.206164790586-0.02195041252320.09178218074440.1889704522240.09592739497120.234656121049-0.316068025928-0.201850711092-0.141257737434-0.361119507699-0.154066382978-0.0129898467140.2063587695790.0413672209895-0.0133282468310.136106035989-0.01341737909330.137037944478-7.624865599546.615804916215.90519085521
30.1284039743450.01144658487810.002263310154690.1614216283630.07887451851930.08307582295790.0467735454542-0.146545493790.09860409958330.118188547475-0.1125529246780.0173997583976-0.0506594377042-0.153967557519-0.01439787487040.1393443621090.007899822213110.0009187011008750.128193264277-0.03947322458220.118890211248-7.031732762444.2874013379714.4162489502
40.0855570219678-0.1451245529140.0404364498830.0829454765412-0.03293393624010.187681958423-0.0228921167603-0.2875042936690.2384825094280.1056779405780.223023768249-0.507448836559-0.02211471413270.194532503920.03694394802440.147183823961-0.001745061892070.008845089101580.133327321019-0.04697767513920.2183576581873.987028544452.1903692417812.0448896493
50.272561989730.1976123327550.5238390977470.3530548090570.06059744861820.3157935083210.05603773425770.0300952548342-0.0926184042850.0774757311186-0.0526352477242-0.00295859089230.0885471976112-0.0260981676176-0.0001045266470450.09107104752190.00120314185913-2.97329259606E-50.125412282851-0.01504776428370.108519744939-5.8111938281-10.15161385386.09678297677
60.1491014124890.2306321762550.06734714142050.6684772397940.5582819032940.9745640976020.1673491594220.1080801365940.1002019580780.152564053897-0.0222601686367-0.1335770545450.2723931251830.08651890378930.0132605590940.08061062290830.00667927165834-0.01063845401980.128070342584-0.01161203963310.1394652735441.88332449844-8.99339873061-1.53056353519
70.151237066367-0.0577427238720.006387940518490.108572078-0.04505403876630.02723678974410.5757545683670.6991201803910.129861290185-0.627040411814-0.348853456199-0.3851378810430.0689011775730.547310332717-0.0002131435821860.2608573581880.04351297392780.05008618605990.2259144849530.004532336221280.1979122856713.302627185211.58789786261-0.961681037191
80.0760235195574-0.000996637325047-0.1642142332230.02185949129780.07330362306290.2690750555520.07575971585540.1113501864380.143154132482-0.0597326180745-0.0102228293736-0.232173003969-0.2828127442580.3616441070010.01133619175940.149966842279-0.0007665160805220.01292055131220.138692318746-0.02388613557690.1859328180255.509393722270.3291545293365.55744127019
90.006494843330810.05373292862540.03338737597280.1600248198550.4846004805021.89746249089-0.079420164762-0.09771676658530.255190328867-0.152437018613-0.270523504320.166128298744-0.3910437972280.459569745796-0.03293803999860.351116523991-0.06927590537620.0694123432240.155559249042-0.02935857130070.2402114344921.9083544468610.482391875.02959252191
100.4522713152880.263161995943-0.1640377292550.378073749804-0.2275669347360.2488251828220.053354050969-0.285399342794-0.1295564384480.254109449535-0.149520754455-0.310747232203-0.2159072709660.1439802891020.007061546350720.156140664409-0.00799152331752-0.01253663214040.116145902067-0.03522850166980.159542933712-1.294618127177.8376267520616.6228563525
110.05231260673510.1581375499960.05472334927090.8884075654610.3946438340890.198357120954-0.0523948880465-0.375478251785-0.07152806416350.541879006696-0.113799409820.73647509165-0.173617303364-0.7385885912250.00467054400460.1703608360370.04769447376370.0393753965940.294637533501-0.06819467144790.254941312345-14.7006721379-2.6071443621110.4439721021
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 351 )AA344 - 35122 - 29
44chain 'A' and (resid 352 through 360 )AA352 - 36030 - 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 405 )AA400 - 40578 - 83
1010chain 'A' and (resid 406 through 410 )AA406 - 41084 - 88
1111chain 'B' and (resid -4 through -2 )BB-4 - -2

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