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- PDB-4zc4: Crystal structure of LARP1-unique domain DM15 -

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Basic information

Entry
Database: PDB / ID: 4zc4
TitleCrystal structure of 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 / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling ...cellular response to rapamycin / translation activator activity / eukaryotic initiation factor 4E binding / RNA cap binding / response to amino acid starvation / TORC1 signaling / RNA 7-methylguanosine cap binding / mRNA stabilization / post-transcriptional regulation of gene expression / TOR signaling / positive regulation of translational initiation / positive regulation of macroautophagy / ribosomal small subunit binding / positive regulation of viral genome replication / translation initiation factor binding / negative regulation of translational initiation / positive regulation of translation / mRNA 3'-UTR binding / translational initiation / 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 / cytoplasm / cytosol
Similarity search - Function
Protein of unknown function DM15 / LARP1 HEAT repeat region / 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 / MAD / Resolution: 1.86 Å
AuthorsLahr, R.M. / Berman, A.J.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: The LARP1-specific domain DM15 repurposes HEAT-like repeats to directly bind messenger RNA
Authors: Lahr, R.M. / Mack, S.M. / Heroux, A. / Blagden, S.P. / Bousquet-Antonelli, C. / Deragon, J.M. / Berman, A.J.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)78,6576
Polymers78,4654
Non-polymers1922
Water8,413467
1
A: La-related protein 1
D: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3293
Polymers39,2332
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-16 kcal/mol
Surface area15320 Å2
MethodPISA
2
B: La-related protein 1
C: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3293
Polymers39,2332
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-21 kcal/mol
Surface area15570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.906, 61.759, 85.336
Angle α, β, γ (deg.)90.00, 116.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19616.281 Da / Num. of mol.: 4 / Fragment: UNP residues 873-1023
Source method: isolated from a genetically manipulated source
Details: QHPSHELLKENGFTQHVYHKYRRRCLNERKRLGIGQSQEMNTLFRFWSFFLRDHFNKKMYEEFKQLALEDAKEGYRYGLECLFRYYSYGLEKKFRLDIFKDFQEETVKDYEAGQLYGLEKFWAFLKYSKAKNLDIDPKLQEYLGKFR
Source: (gene. exp.) Homo sapiens (human) / Gene: LARP1, KIAA0731, LARP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PKG0
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 304 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.225 M ammonium chloride, pH 6.3, 23% PEG 3350 / Temp details: Room Temp

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.62→76.57 Å / Num. obs: 87993 / % possible obs: 95 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 34.582
Reflection shellHighest resolution: 1.62 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.108 / Mean I/σ(I) obs: 1.4 / % possible all: 63.66

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Processing

Software
NameVersionClassification
PHENIXdev_2006refinement
CootCoot 0.7model building
HKL-20002.3.2data reduction
HKL-20002.3.2data scaling
PHENIX1.8.2phasing
RefinementMethod to determine structure: MAD / Resolution: 1.86→38.285 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1316 2.15 %Random selection
Rwork0.1815 ---
obs0.1822 61174 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→38.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5137 0 10 467 5614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015338
X-RAY DIFFRACTIONf_angle_d1.0527144
X-RAY DIFFRACTIONf_dihedral_angle_d15.722034
X-RAY DIFFRACTIONf_chiral_restr0.081668
X-RAY DIFFRACTIONf_plane_restr0.004916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.93450.35051430.30836565X-RAY DIFFRACTION99
1.9345-2.02250.28561450.24176608X-RAY DIFFRACTION100
2.0225-2.12910.23781440.22286619X-RAY DIFFRACTION100
2.1291-2.26250.24861440.20636636X-RAY DIFFRACTION100
2.2625-2.43720.23171440.18566629X-RAY DIFFRACTION100
2.4372-2.68240.22431490.18296650X-RAY DIFFRACTION100
2.6824-3.07040.22651490.18476656X-RAY DIFFRACTION100
3.0704-3.86780.20881450.16426697X-RAY DIFFRACTION100
3.8678-38.2930.16381530.15246798X-RAY DIFFRACTION100

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