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- PDB-1u1m: Crystal Structure of UP1 Complexed With d(TTAGGGTTA 7GU GG); A Hu... -

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Basic information

Entry
Database: PDB / ID: 1u1m
TitleCrystal Structure of UP1 Complexed With d(TTAGGGTTA 7GU GG); A Human Telomeric Repeat Containing 7-deaza-guanine
Components
  • 5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(7GU)P*GP*G)-3'
  • Heterogeneous nuclear ribonucleoprotein A1
KeywordsTRANSPORT PROTEIN/DNA / protein-DNA complex / UP1 / human telomeric repeat / hTR / TR2-G(10)7GU / RRM / RNA Recognition Motif / 7GU / 7-deaza-guanine / hnRNP A1 / TRANSPORT PROTEIN-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 / alternative mRNA splicing, via spliceosome / G-rich strand telomeric DNA binding / pre-mRNA binding / nuclear export / RNA export from nucleus / miRNA binding ...cellular response to sodium arsenite / SARS-CoV-1-host interactions / import into nucleus / telomeric repeat-containing RNA binding / alternative mRNA splicing, via spliceosome / 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 / ribonucleoprotein complex / protein domain specific binding / synapse / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm / cytosol
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 / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMyers, J.C. / Shamoo, Y.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Human UP1 as a Model for Understanding Purine Recognition in the Family of Proteins Containing the RNA Recognition Motif (RRM).
Authors: Myers, J.C. / Shamoo, Y.
History
DepositionJul 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(7GU)P*GP*G)-3'
A: Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)25,7712
Polymers25,7712
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.840, 50.840, 172.427
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 5'-D(*TP*AP*GP*GP*GP*TP*TP*AP*(7GU)P*GP*G)-3'


Mass: 3468.281 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Oligonucleotide d(TTAGGGTTA(7GU)GG) based on human telomeric repeat d(TTAGGG)n
#2: Protein Heterogeneous nuclear ribonucleoprotein A1 / Helix-destabilizing protein / Single-strand binding protein / hnRNP core protein A1


Mass: 22303.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNRPA1 / Plasmid: pYS45 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P09651
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.258 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: ammonium phosphate, glycerol, Tris, sodium chloride, MES, EDTA, beta-mercaptoethanol , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 283.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1ammonium phosphate11
2Tris11
3sodium chloride11
4MES11
5EDTA11
6H2O11
7ammonium phosphate12
8glycerol12
9Tris12
10sodium chloride12
11MES12
12EDTA12
13beta-mercaptoethanol12
14H2O12

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Jan 4, 2002 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 16125 / Num. obs: 15551 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.08 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 7.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.41 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1328 / % possible all: 89.4

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Processing

Software
NameVersionClassification
CNS1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UP1

2up1


Resolution: 2→19.84 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 496017.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 766 4.9 %RANDOM
Rwork0.241 ---
obs0.241 15551 96.4 %-
all-16125 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.403 Å2 / ksol: 0.360285 e/Å3
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.98 Å20 Å20 Å2
2--4.98 Å20 Å2
3----9.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.3 Å
Luzzati d res low-20 Å
Luzzati sigma a0.38 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1466 231 0 114 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.981.5
X-RAY DIFFRACTIONc_mcangle_it7.762
X-RAY DIFFRACTIONc_scbond_it8.332
X-RAY DIFFRACTIONc_scangle_it11.922.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.423 68 4.9 %
Rwork0.349 1328 -
obs--89.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2010404.PARAM010404.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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