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- PDB-1up1: UP1, THE TWO RNA-RECOGNITION MOTIF DOMAIN OF HNRNP A1 -

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Basic information

Entry
Database: PDB / ID: 1up1
TitleUP1, THE TWO RNA-RECOGNITION MOTIF DOMAIN OF HNRNP A1
ComponentsHETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1
KeywordsNUCLEAR PROTEIN / NUCLEAR PROTEINHNRNP A1 / RNA-RECOGNITION MOTIF / RNA-BINDING / UP1
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 / intracellular non-membrane-bounded organelle / 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 / localization / positive regulation of telomere maintenance via telomerase / catalytic step 2 spliceosome / molecular condensate scaffold activity / mRNA Splicing - Major Pathway / mRNA 3'-UTR binding / spliceosomal complex / mRNA splicing, via spliceosome / single-stranded DNA binding / amyloid fibril formation / single-stranded RNA binding / ribonucleoprotein complex / protein domain specific binding / DNA binding / RNA binding / extracellular exosome / nucleoplasm / membrane / identical protein binding / 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 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily ...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 / RRM (RNA recognition motif) 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 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR WITH ANOMALOUS SCATTERING / Resolution: 1.9 Å
AuthorsXu, R.-M. / Jokhan, L. / Cheng, X. / Mayeda, A. / Krainer, A.R.
CitationJournal: Structure / Year: 1997
Title: Crystal structure of human UP1, the domain of hnRNP A1 that contains two RNA-recognition motifs.
Authors: Xu, R.M. / Jokhan, L. / Cheng, X. / Mayeda, A. / Krainer, A.R.
History
DepositionMar 12, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1


Theoretical massNumber of molelcules
Total (without water)20,8341
Polymers20,8341
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.990, 43.940, 55.750
Angle α, β, γ (deg.)90.00, 94.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 / HNRNP A1 / UP1


Mass: 20834.461 Da / Num. of mol.: 1 / Fragment: THE TWO RNA-RECOGNITION MOTIF DOMAIN, 1 - 196 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09651
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.5
Details: 25% PEG 4000, 20% MPD OR 10-15% GLYCEROL, 100MM TRIS, PH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1967
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Apr 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1967 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 14637 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 23.6
Reflection
*PLUS
Num. measured all: 123655

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR WITH ANOMALOUS SCATTERING
Resolution: 1.9→6 Å / Data cutoff high absF: 12500 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 2
Details: AMINO ACIDS 93 - 98 ARE DISORDERED IN THE CRYSTAL STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10.1 %RANDOM
Rwork0.197 ---
obs0.197 14055 99.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 0 130 1496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.29
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.23
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.06
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.23
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.06

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