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- PDB-7sow: LaM domain of human LARP1 in complex with UUUUUU -

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Basic information

Entry
Database: PDB / ID: 7sow
TitleLaM domain of human LARP1 in complex with UUUUUU
Components
  • Isoform 2 of La-related protein 1
  • RNA (5'-R(P*UP*UP*UP*UP*UP*U)-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
DepositionNov 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 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(P*UP*UP*UP*UP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8476
Polymers13,5992
Non-polymers2484
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-3 kcal/mol
Surface area6360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.804, 46.885, 57.904
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(P*UP*UP*UP*UP*UP*U)-3')


Mass: 1792.037 Da / Num. of mol.: 1 / 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.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.84 Å3/Da / Density % sol: 33.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium acetate, 0.1 M 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: 1.3→50 Å / Num. obs: 24922 / % possible obs: 98.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.26 Å2 / Rsym value: 0.06 / Net I/σ(I): 24.7
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 2179 / Rsym value: 0.431

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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: 1.3→36.44 Å / SU ML: 0.1337 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.73
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1921 1283 5.15 %
Rwork0.1824 23639 -
obs0.1829 24922 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.05 Å2
Refinement stepCycle: LAST / Resolution: 1.3→36.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 69 16 66 940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139906
X-RAY DIFFRACTIONf_angle_d1.48581236
X-RAY DIFFRACTIONf_chiral_restr0.1093142
X-RAY DIFFRACTIONf_plane_restr0.0118147
X-RAY DIFFRACTIONf_dihedral_angle_d15.5438154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.350.33711260.30442323X-RAY DIFFRACTION89.51
1.35-1.420.251360.21672640X-RAY DIFFRACTION99.93
1.42-1.490.20811230.19132637X-RAY DIFFRACTION99.96
1.49-1.580.21141580.19662594X-RAY DIFFRACTION100
1.58-1.710.21141440.17312648X-RAY DIFFRACTION99.96
1.71-1.880.17051210.16892659X-RAY DIFFRACTION99.93
1.88-2.150.18461660.16422636X-RAY DIFFRACTION99.82
2.15-2.710.21591600.17882675X-RAY DIFFRACTION99.93
2.71-36.440.16791490.18262827X-RAY DIFFRACTION99.73
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)
12.32442111301-0.9229572568040.8403900944481.95624456198-0.3708127710272.663576359870.081640052668-0.0720422557639-0.4127214403690.2407404860310.02773194259450.2818007291760.115904224302-0.0987559596248-0.05446343185740.125472983011-0.00913138194388-0.001874334688890.1482243787050.001687050744880.1561131673235.7993171366513.591166071233.9418312364
20.831124037276-0.377524166819-1.477895391815.1048503239-0.9112875934273.53308187760.088784706299-0.1537097272090.1788106082570.422420385203-0.22215627855-0.359075434659-0.4992042333990.3474988131550.04997545247980.21674227195-0.0390244210844-0.0313021318430.1484894731040.01361322518080.1701332461797.7171452864730.133990370623.8348132267
33.465711523830.865081466597-0.5518730709282.59455339369-1.022789346612.081514095570.1008693016450.2210756697630.239879655183-0.204052635653-0.06006375319960.220570329581-0.01866689692870.116355993407-0.04130056254910.1746632011380.0106343232203-0.02179303345120.1322042252560.02797904241420.1647265602272.1411779768227.587575397216.3026583543
41.03438394584-0.2758974269960.7692932325650.979599648824-0.5212453912580.6806897043860.0610605151935-0.05604347657630.03108508777530.0173783166317-0.0759071610732-0.01185631780380.002039248893590.09134577797020.01549706877380.116992632744-0.003949638598390.002896805435350.1444531751360.01042756693220.1258102951385.753636620513.519218917722.846588842
55.15706051665-0.04342413871130.7250410377453.49338118016-0.924341200414.958612359710.1876274684720.0350876908790.29191069491-0.1659306848440.06286236875120.3230293265130.0927021361026-0.211200011358-0.3177578023810.1139510946040.00339024250167-0.006160879105120.1480198318390.01591911918190.153525050667-1.6693737996314.124638384730.4842033844
62.683350771130.974296143725-0.1214598231111.624405117650.2005423394272.247263188050.209326285182-0.251642686095-0.00595428640430.247211206866-0.09677192582580.327171723433-0.0874589892861-0.222327579343-0.08144809533240.1735464363234.06677257021E-50.03384578260250.1386219598110.007278905635090.189671251106-4.5256428201724.056440913127.1446039156
72.44501628492-0.0286699165595-1.149387981821.97954668532-1.00319136955.771825408530.1458453411250.02748401737480.06148553177820.245890452103-0.04633763970650.35568890105-0.224118879034-0.2439404537-0.2388915344320.2379192927660.01361166748010.02537873947240.1382048863340.01979669602580.210931807526-0.76147754079433.404394254119.6034658147
88.300580017281.21266550451.0753265276.3050533509-2.564467904871.35053832855-0.01064697115930.571040476058-0.0286432931629-0.766978465245-0.318038420393-0.4488143806720.08976257649050.6655539738890.1577905200780.234247367970.03984064953470.03164607341040.2765808227620.0616987364340.20738243651712.839480938919.88079492117.0918042133
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 317 through 337 )AA317 - 3372 - 22
22chain 'A' and (resid 338 through 343 )AA338 - 34323 - 28
33chain 'A' and (resid 344 through 360 )AA344 - 36029 - 45
44chain 'A' and (resid 361 through 376 )AA361 - 37646 - 61
55chain 'A' and (resid 377 through 385 )AA377 - 38562 - 70
66chain 'A' and (resid 386 through 399 )AA386 - 39971 - 84
77chain 'A' and (resid 400 through 410 )AA400 - 41085 - 95
88chain 'B' and (resid -4 through -1 )BB-4 - -1

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