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- PDB-5c0v: Structure of the LARP1-unique domain DM15 -

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Basic information

Entry
Database: PDB / ID: 5c0v
TitleStructure of the LARP1-unique domain DM15
ComponentsLa-related protein 1
KeywordsRNA BINDING PROTEIN / RNA-binding / Heat-like / mRNA / helical repeat
Function / homology
Function and homology information


cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / TORC1 signaling / response to amino acid starvation / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / positive regulation of macroautophagy ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / TORC1 signaling / response to amino acid starvation / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / positive regulation of macroautophagy / ribosomal small subunit binding / TOR signaling / positive regulation of translational initiation / positive regulation of viral genome replication / negative regulation of translational initiation / translational initiation / translation initiation factor binding / mRNA 3'-UTR binding / positive regulation of translation / mRNA 5'-UTR binding / cytoplasmic stress granule / cell population proliferation / negative regulation of translation / cadherin binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
LARP1 HEAT repeat region / Protein of unknown function DM15 / Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. / La domain containing protein / La domain / Domain in the RNA-binding Lupus La protein; unknown function / La-type HTH domain / La-type HTH domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
La-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsLahr, R.M. / Berman, A.J.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: The La-related protein 1-specific domain repurposes HEAT-like repeats to directly bind a 5'TOP sequence.
Authors: Lahr, R.M. / Mack, S.M. / Heroux, A. / Blagden, S.P. / Bousquet-Antonelli, C. / Deragon, J.M. / Berman, A.J.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: La-related protein 1
B: La-related protein 1
C: La-related protein 1
D: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2206
Polymers79,0284
Non-polymers1922
Water3,495194
1
A: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8532
Polymers19,7571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8532
Polymers19,7571
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: La-related protein 1


Theoretical massNumber of molelcules
Total (without water)19,7571
Polymers19,7571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: La-related protein 1


Theoretical massNumber of molelcules
Total (without water)19,7571
Polymers19,7571
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.730, 61.461, 83.202
Angle α, β, γ (deg.)90.00, 115.53, 90.00
Int Tables number4
Space group name H-MP1211
Detailsmonomer by gel filtration

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Components

#1: Protein
La-related protein 1 / La ribonucleoprotein domain family member 1


Mass: 19756.967 Da / Num. of mol.: 4
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
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.2 M Ammonium nitrate, 20% PEG 3350 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.976 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35696 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 34.2
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 2.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
PHENIX1.8.2_1309phasing
Coot1model building
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→42.567 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1082 3.03 %Random selection
Rwork0.1756 ---
obs0.177 35688 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5013 0 10 194 5217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085196
X-RAY DIFFRACTIONf_angle_d1.0056942
X-RAY DIFFRACTIONf_dihedral_angle_d15.1091973
X-RAY DIFFRACTIONf_chiral_restr0.067644
X-RAY DIFFRACTIONf_plane_restr0.004890
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30010.28431290.19214268X-RAY DIFFRACTION100
2.3001-2.42140.23441350.18964284X-RAY DIFFRACTION100
2.4214-2.57310.27961340.1964323X-RAY DIFFRACTION100
2.5731-2.77170.24241390.19464314X-RAY DIFFRACTION100
2.7717-3.05060.25521290.20024311X-RAY DIFFRACTION100
3.0506-3.49180.23861400.18114320X-RAY DIFFRACTION100
3.4918-4.39860.19451360.15324360X-RAY DIFFRACTION100
4.3986-42.57460.16731400.15414426X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 0.0837 Å / Origin y: -3.4879 Å / Origin z: -47.9555 Å
111213212223313233
T0.1224 Å2-0.0371 Å2-0.0263 Å2-0.1272 Å20.0413 Å2--0.1433 Å2
L0.529 °2-0.5818 °2-0.5162 °2-1.3246 °21.0846 °2--1.4915 °2
S0.0028 Å °-0.0519 Å °0.0147 Å °0.009 Å °0.0884 Å °-0.1202 Å °-0.0315 Å °0.1581 Å °-0.099 Å °
Refinement TLS groupSelection details: all

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