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- PDB-2up1: STRUCTURE OF UP1-TELOMERIC DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2up1
TitleSTRUCTURE OF UP1-TELOMERIC DNA COMPLEX
Components
  • DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
  • PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1)
KeywordsGENE REGULATION/DNA / COMPLEX (RIBONUCLEOPROTEIN-DNA) / HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1 / GENE REGULATION-DNA 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 / RNA export from nucleus / nuclear export / negative regulation of telomere maintenance via telomerase / miRNA binding ...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 / RNA export from nucleus / nuclear export / negative regulation of telomere maintenance via telomerase / miRNA binding / FGFR2 alternative splicing / regulation of alternative mRNA splicing, via spliceosome / intracellular non-membrane-bounded organelle / regulation of RNA splicing / SARS-CoV-1 modulates host translation machinery / Processing of Capped Intron-Containing Pre-mRNA / mRNA transport / localization / cellular response to glucose starvation / 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
DNA / DNA (> 10) / Heterogeneous nuclear ribonucleoprotein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsDing, J. / Hayashi, M.K. / Krainer, A.R. / Xu, R.-M.
CitationJournal: Genes Dev. / Year: 1999
Title: Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA.
Authors: Ding, J. / Hayashi, M.K. / Zhang, Y. / Manche, L. / Krainer, A.R. / Xu, R.M.
History
DepositionJul 10, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')
A: PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1)


Theoretical massNumber of molelcules
Total (without water)24,3512
Polymers24,3512
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.200, 51.200, 171.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(P*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')


Mass: 3469.269 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN A1) / HNRNP A1 / UP1 / HELIX-DESTABILIZING PROTEIN / SINGLE-STRAND BINDING PROTEIN / HNRNP CORE PROTEIN A1


Mass: 20881.520 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
315 %glycerol1reservoir
42.0 M1reservoirNH42HPO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: BRANDEIS / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 14247 / % possible obs: 96.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 10 / % possible all: 86.5
Reflection shell
*PLUS
% possible obs: 86.5 %

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Processing

Software
NameVersionClassification
PHASERphasing
AMoREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIRAS
Starting model: PDB ENTRY 1UP1

1up1


Resolution: 2.1→47.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high rms absF: 436222.08 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1214 10.3 %RANDOM
Rwork0.195 ---
obs0.195 11767 83.4 %-
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.34 Å20 Å20 Å2
2---6.34 Å20 Å2
3---12.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 234 0 144 1844
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.991.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it2.942
X-RAY DIFFRACTIONc_scangle_it4.062.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 143 9.9 %
Rwork0.225 1303 -
obs--63.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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