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- PDB-9gpj: Structure of UP1 S4DS6D phosphomimetic mutant in complex with hum... -

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Basic information

Entry
Database: PDB / ID: 9gpj
TitleStructure of UP1 S4DS6D phosphomimetic mutant in complex with human telomeric repeat DNA
Components
  • DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
  • Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed
KeywordsRNA BINDING PROTEIN / hnRNP A1 / RNA/DNA BINDING PROTEIN / RNA-DNA BINDING PROTEIN phosphomimetic mutant / RRM
Function / homology
Function and homology information


cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / SARS-CoV-1 modulates host translation machinery / regulation of RNA splicing / negative regulation of telomere maintenance via telomerase / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / cellular response to glucose starvation / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
hnRNP A3, RNA recognition motif 2 / hnRNP A1, RNA recognition motif 1 / Heterogeneous nuclear ribonucleoprotein A1/A2, C-terminal / Heterogeneous nuclear ribonucleoprotein A1, LC domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsDunnett, L. / Prischi, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of UP1 S4DS6D phosphomimetic mutant in complex with human telomeric repeat DNA
Authors: Dunnett, L. / Prischi, F.
History
DepositionSep 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed
B: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)26,1872
Polymers26,1872
Non-polymers00
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint1 kcal/mol
Surface area12610 Å2
Unit cell
Length a, b, c (Å)51.425, 51.425, 172.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-248-

HOH

21A-344-

HOH

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Components

#1: Protein Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed


Mass: 22413.129 Da / Num. of mol.: 1 / Mutation: S4D, S6D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPA1, HNRPA1 / Plasmid: pETM-14 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09651
#2: DNA chain DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 3773.462 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris, pH 8.50, 1.7 M Ammonium Phosphate Dibasic, 15 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.53→57.36 Å / Num. obs: 36066 / % possible obs: 100 % / Redundancy: 14.07 % / Biso Wilson estimate: 20.32 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.4
Reflection shellResolution: 1.53→1.56 Å / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1755 / CC1/2: 0.907 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→44.14 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3125
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2056 1771 4.93 %
Rwork0.1844 34176 -
obs0.1855 35947 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.19 Å2
Refinement stepCycle: LAST / Resolution: 1.53→44.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 234 0 223 1930
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751826
X-RAY DIFFRACTIONf_angle_d0.93772517
X-RAY DIFFRACTIONf_chiral_restr0.0594267
X-RAY DIFFRACTIONf_plane_restr0.0108292
X-RAY DIFFRACTIONf_dihedral_angle_d19.9208325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.570.25241360.22392568X-RAY DIFFRACTION99.82
1.57-1.620.2321030.21582602X-RAY DIFFRACTION99.89
1.62-1.670.24821470.20912558X-RAY DIFFRACTION99.85
1.67-1.730.28121370.2372583X-RAY DIFFRACTION99.85
1.73-1.80.23841460.21512551X-RAY DIFFRACTION99.93
1.8-1.880.24581110.20172609X-RAY DIFFRACTION99.93
1.88-1.980.23781330.19562619X-RAY DIFFRACTION99.89
1.98-2.10.22191280.20552590X-RAY DIFFRACTION99.85
2.1-2.270.21931460.19132623X-RAY DIFFRACTION100
2.27-2.490.19371420.19442644X-RAY DIFFRACTION100
2.49-2.860.18491510.20052651X-RAY DIFFRACTION100
2.86-3.60.23291480.18232688X-RAY DIFFRACTION99.93
3.6-44.140.16561430.15322890X-RAY DIFFRACTION99.9

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