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- PDB-9hql: UP1 in complex with Z1152242726 -

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Basic information

Entry
Database: PDB / ID: 9hql
TitleUP1 in complex with Z1152242726
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 / negative regulation of telomere maintenance via telomerase / regulation of RNA splicing / SARS-CoV-1 modulates host translation machinery / 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 / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / single-stranded RNA binding / protein domain specific binding / ribonucleoprotein complex / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / 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
N-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsDunnett, L. / Prischi, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Biol.Chem. / Year: 2025
Title: Enhanced identification of small molecules binding to hnRNPA1 via cryptic pockets mapping coupled with X-ray fragment screening.
Authors: Dunnett, L. / Das, S. / Venditti, V. / Prischi, F.
#1: Journal: Biorxiv / Year: 2024
Title: Enhanced identification of small molecules binding to hnRNPA1 via cryptic pockets mapping coupled with X-Ray fragment screening.
Authors: Dunnett, L. / Das, S. / Venditti, V. / Prischi, F.
History
DepositionDec 16, 2024Deposition site: PDBE / Processing site: PDBE
SupersessionDec 25, 2024ID: 9F4E
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 26, 2025Group: Database references / Category: citation / citation_author
Revision 1.3Apr 2, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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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)22,6062
Polymers22,3571
Non-polymers2491
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9360 Å2
Unit cell
Length a, b, c (Å)37.900, 43.920, 55.730
Angle α, β, γ (deg.)90.000, 94.050, 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09651
#2: Chemical ChemComp-VZM / N-(6-methoxypyridin-3-yl)-N'-thiophen-2-ylurea


Mass: 249.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.34 %
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: 1.75→55.59 Å / Num. obs: 17906 / % possible obs: 96.6 % / Redundancy: 1.8 % / Biso Wilson estimate: 18.38 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.092 / Net I/σ(I): 11.1
Reflection shellResolution: 1.75→1.78 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 950 / CC1/2: 0.767 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→55.59 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2121 890 4.97 %
Rwork0.1899 17011 -
obs0.191 17901 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→55.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1313 0 17 202 1532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631363
X-RAY DIFFRACTIONf_angle_d0.87631831
X-RAY DIFFRACTIONf_chiral_restr0.0573196
X-RAY DIFFRACTIONf_plane_restr0.0075238
X-RAY DIFFRACTIONf_dihedral_angle_d16.322518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.860.3291600.26972783X-RAY DIFFRACTION95.61
1.86-20.23931420.20232807X-RAY DIFFRACTION95.65
2-2.20.21761600.19492793X-RAY DIFFRACTION96.47
2.21-2.520.21971370.18312876X-RAY DIFFRACTION96.42
2.52-3.180.22181340.19192845X-RAY DIFFRACTION96.6
3.18-55.590.17851570.17482907X-RAY DIFFRACTION96.29

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