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- PDB-1pgz: Crystal Structure of UP1 Complexed With d(TTAGGGTTAG(6-MI)G); A H... -

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Basic information

Entry
Database: PDB / ID: 1pgz
TitleCrystal Structure of UP1 Complexed With d(TTAGGGTTAG(6-MI)G); A Human Telomeric Repeat Containing 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine (6-MI)
Components
  • 5'-D(*T*TP*AP*GP*GP*GP*TP*TP*AP*GP*(6MI)P*G)-3'
  • Heterogeneous nuclear ribonucleoprotein A1
KeywordsDNA BINDING PROTEIN/DNA / protein-DNA complex / UP1 / human telomeric repeat / hTR / TR2-11F / RRM / RNA Recognition Motif / 6-MI / 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine / hnRNP A1 / DNA BINDING 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 / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMyers, J.C. / Moore, S.A. / Shamoo, Y.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure-based incorporation of 6-methyl-8-(2-deoxy-beta-ribofuranosyl)isoxanthopteridine into the human telomeric repeat DNA as a probe for UP1 binding and destabilization of G-tetrad structures
Authors: Myers, J.C. / Moore, S.A. / Shamoo, Y.
History
DepositionMay 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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(*T*TP*AP*GP*GP*GP*TP*TP*AP*GP*(6MI)P*G)-3'
A: Heterogeneous nuclear ribonucleoprotein A1


Theoretical massNumber of molelcules
Total (without water)25,9872
Polymers25,9872
Non-polymers00
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.622, 51.622, 171.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*T*TP*AP*GP*GP*GP*TP*TP*AP*GP*(6MI)P*G)-3'


Mass: 3815.499 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: sequence based on human telomeric repeat d(TTAGGG)n
#2: Protein Heterogeneous nuclear ribonucleoprotein A1 / Helix-destabilizing protein / hnRNP A1 / Single-strand binding protein / hnRNP core protein A1 / ...Helix-destabilizing protein / hnRNP A1 / Single-strand binding protein / hnRNP core protein A1 / Unwinding protein 1 / UP1


Mass: 22171.887 Da / Num. of mol.: 1 / Fragment: Residues 1-195
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 / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.37 Å3/Da / Density % sol: 47.6 %
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
1(NH4)3PO411
2glycerol11
3Tris HCl11
4NaClSodium chloride11
5MES11
6EDTAEthylenediaminetetraacetic acid11
7beta-mercaptoethanol2-Mercaptoethanol11
8(NH4)3PO412
9glycerol12
10NaClSodium chloride12
11EDTAEthylenediaminetetraacetic acid12
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMTris1reservoirpH8.5
215 %(v/v)1reservoir
31.8-2.2 Mdibasic ammonium phosphate1reservoir
41
51
61
71
81
91
101
111

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2003 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 13747 / Num. obs: 13747 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 15.2
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.4 / Num. unique all: 357 / Rsym value: 0.325 / % possible all: 96.1
Reflection
*PLUS
Highest resolution: 2.6 Å / Redundancy: 5.4 %

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UP1

2up1


Resolution: 2.6→19.8 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 607 5.1 %Random
Rwork0.235 ---
all0.237 13747 --
obs0.237 11985 83.6 %-
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-3.74 Å20 Å20 Å2
2--3.74 Å20 Å2
3----7.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 212 0 46 1725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg1.02
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.036
RfactorNum. reflection% reflection
Rfree0.302 69 -
Rwork0.324 --
obs--96.1 %
Refinement
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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