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- PDB-9f4o: UP1 in complex with Z991506900 -

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Basic information

Entry
Database: PDB / ID: 9f4o
TitleUP1 in complex with Z991506900
ComponentsHeterogeneous nuclear ribonucleoprotein A1, N-terminally processed
KeywordsRNA BINDING PROTEIN / fragment screening / hnRNP A1 / UP1 / RNA/DNA BINDING PROTEIN / UP1-fragment complex
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
: / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDunnett, L. / Prischi, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Enhanced identification of small molecules binding to hnRNP A1 via in silico hotspot and cryptic pockets mapping coupled with X-Ray fragment screening
Authors: Dunnett, L. / Prischi, F.
History
DepositionApr 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heterogeneous nuclear ribonucleoprotein A1, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5482
Polymers22,3571
Non-polymers1911
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10070 Å2
Unit cell
Length a, b, c (Å)37.864, 43.968, 56.083
Angle α, β, γ (deg.)90.000, 94.640, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 22357.109 Da / Num. of mol.: 1
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: Chemical ChemComp-A1H95 / (3~{R})-3-methyl-1-(6-methylpyridin-2-yl)piperazine


Mass: 191.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.50, 25% PEG-4000, 8% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.4→37.74 Å / Num. obs: 35631 / % possible obs: 98.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 10.01 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.043 / Rrim(I) all: 0.06 / Χ2: 0.84 / Net I/σ(I): 11.9 / Num. measured all: 63383
Reflection shellResolution: 1.4→1.42 Å / % possible obs: 88.4 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.084 / Num. measured all: 2206 / Num. unique obs: 1558 / CC1/2: 0.969 / Rpim(I) all: 0.084 / Rrim(I) all: 0.118 / Χ2: 0.82 / Net I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.74 Å / SU ML: 0.1246 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 16.7583
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1808 1829 5.13 %
Rwork0.1677 33801 -
obs0.1683 35630 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.68 Å2
Refinement stepCycle: LAST / Resolution: 1.4→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 14 250 1674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691461
X-RAY DIFFRACTIONf_angle_d0.98551965
X-RAY DIFFRACTIONf_chiral_restr0.0967208
X-RAY DIFFRACTIONf_plane_restr0.0118258
X-RAY DIFFRACTIONf_dihedral_angle_d13.8597561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.19061300.17442327X-RAY DIFFRACTION89.18
1.44-1.480.20381500.17452457X-RAY DIFFRACTION93.07
1.48-1.530.20731370.16222518X-RAY DIFFRACTION95.95
1.53-1.580.1911400.16492572X-RAY DIFFRACTION97.41
1.58-1.650.17871560.16022618X-RAY DIFFRACTION99.5
1.65-1.720.18731650.1642606X-RAY DIFFRACTION99.75
1.72-1.810.18531420.16432648X-RAY DIFFRACTION99.82
1.81-1.920.18621390.16612636X-RAY DIFFRACTION99.75
1.93-2.070.17081440.15472652X-RAY DIFFRACTION99.93
2.07-2.280.17721270.16032647X-RAY DIFFRACTION99.75
2.28-2.610.2061320.1672676X-RAY DIFFRACTION99.93
2.61-3.290.17041260.17772698X-RAY DIFFRACTION99.96
3.29-37.740.16631410.1732746X-RAY DIFFRACTION99.86

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