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- PDB-8dhu: Crystal structure of LARP-DM15 from Drosophila melanogaster bound... -

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Basic information

Entry
Database: PDB / ID: 8dhu
TitleCrystal structure of LARP-DM15 from Drosophila melanogaster bound to m7GpppC
ComponentsLa-related protein 1
KeywordsRNA BINDING PROTEIN / LARP / DM15
Function / homology
Function and homology information


spindle assembly involved in male meiosis / extrinsic component of mitochondrial outer membrane / syncytial blastoderm mitotic cell cycle / mitochondrion inheritance / positive regulation of mitochondrial DNA replication / poly-pyrimidine tract binding / male meiotic nuclear division / RNA cap binding / positive regulation of cytoplasmic translation / mRNA stabilization ...spindle assembly involved in male meiosis / extrinsic component of mitochondrial outer membrane / syncytial blastoderm mitotic cell cycle / mitochondrion inheritance / positive regulation of mitochondrial DNA replication / poly-pyrimidine tract binding / male meiotic nuclear division / RNA cap binding / positive regulation of cytoplasmic translation / mRNA stabilization / positive regulation of protein targeting to mitochondrion / negative regulation of cytoplasmic translation / positive regulation of translation / mRNA 5'-UTR binding / cytoplasmic stress granule / RNA binding / 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
Chem-91P / La-related protein 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å
AuthorsNguyen, E. / Berman, A.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
American Cancer Society United States
CitationJournal: Plos One / Year: 2024
Title: Comparative analysis of the LARP1 C-terminal DM15 region through Coelomate evolution.
Authors: Nguyen, E. / Sosa, J.A. / Cassidy, K.C. / Berman, A.J.
History
DepositionJun 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9154
Polymers37,1282
Non-polymers7882
Water91951
1
A: La-related protein 1


Theoretical massNumber of molelcules
Total (without water)18,5641
Polymers18,5641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: La-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3523
Polymers18,5641
Non-polymers7882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.808, 60.737, 129.199
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 La-related protein 1 / dLarp


Mass: 18563.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: larp, CG42551 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VAW5
#2: Chemical ChemComp-91P / [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-9-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate / dinucleotide triphosphate cap analog m7GpppC


Mass: 763.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H30N8O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.27 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / Details: 0.05 M Bicine, pH 9, 2.5% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.295→44.01 Å / Num. obs: 17090 / % possible obs: 99.65 % / Redundancy: 2 % / Biso Wilson estimate: 49.52 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01978 / Rrim(I) all: 0.02797 / Net I/σ(I): 17.01
Reflection shellResolution: 2.295→2.377 Å / Rmerge(I) obs: 0.2632 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 1695 / CC1/2: 0.8 / Rrim(I) all: 0.3722

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V87

5v87


Resolution: 2.295→44.01 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 1709 10 %
Rwork0.2196 15379 -
obs-17088 99.65 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.34 Å2
Refinement stepCycle: LAST / Resolution: 2.295→44.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2570 0 50 51 2671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812697
X-RAY DIFFRACTIONf_angle_d1.22063626
X-RAY DIFFRACTIONf_chiral_restr0.0522340
X-RAY DIFFRACTIONf_plane_restr0.0062461
X-RAY DIFFRACTIONf_dihedral_angle_d14.7354342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.34231400.29191260X-RAY DIFFRACTION99.72
2.36-2.440.31291410.27111263X-RAY DIFFRACTION99.93
2.44-2.530.31511390.2711257X-RAY DIFFRACTION100
2.53-2.630.31181400.2521269X-RAY DIFFRACTION99.93
2.63-2.750.28061420.23131271X-RAY DIFFRACTION99.44
2.75-2.890.34111390.23811257X-RAY DIFFRACTION99.64
2.89-3.070.3191410.23731259X-RAY DIFFRACTION99.72
3.07-3.310.31581410.23761273X-RAY DIFFRACTION99.86
3.31-3.640.28441430.21831290X-RAY DIFFRACTION99.44
3.64-4.170.27831440.19011289X-RAY DIFFRACTION99.79
4.17-5.250.18561450.16941304X-RAY DIFFRACTION99.45

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