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- PDB-8chw: Crystal structure of human PURA (fragment Pro216-Lys280, PUR repe... -

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Basic information

Entry
Database: PDB / ID: 8chw
TitleCrystal structure of human PURA (fragment Pro216-Lys280, PUR repeat III)
ComponentsTranscriptional activator protein Pur-alpha
KeywordsRNA BINDING PROTEIN / RNA/DNA binding / PUR repeat / PC4-like fold
Function / homology
Function and homology information


dendritic transport of messenger ribonucleoprotein complex / purine-rich negative regulatory element binding / lymphocyte proliferation / double-stranded telomeric DNA binding / transcription regulator inhibitor activity / DNA unwinding involved in DNA replication / SMAD binding / DNA replication initiation / dendrite cytoplasm / mRNA regulatory element binding translation repressor activity ...dendritic transport of messenger ribonucleoprotein complex / purine-rich negative regulatory element binding / lymphocyte proliferation / double-stranded telomeric DNA binding / transcription regulator inhibitor activity / DNA unwinding involved in DNA replication / SMAD binding / DNA replication initiation / dendrite cytoplasm / mRNA regulatory element binding translation repressor activity / epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / single-stranded DNA binding / nervous system development / DNA-binding transcription factor binding / postsynapse / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / neuronal cell body / glutamatergic synapse / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / RNA binding / nucleus
Similarity search - Function
PurA ssDNA and RNA-binding protein / Purine-rich element binding protein family / DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Similarity search - Domain/homology
Transcriptional activator protein Pur-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJanowski, R. / Niessing, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Elife / Year: 2024
Title: PURA syndrome-causing mutations impair PUR-domain integrity and affect P-body association.
Authors: Proske, M. / Janowski, R. / Bacher, S. / Kang, H.S. / Monecke, T. / Koehler, T. / Hutten, S. / Tretter, J. / Crois, A. / Molitor, L. / Varela-Rial, A. / Fino, R. / Donati, E. / De Fabritiis, ...Authors: Proske, M. / Janowski, R. / Bacher, S. / Kang, H.S. / Monecke, T. / Koehler, T. / Hutten, S. / Tretter, J. / Crois, A. / Molitor, L. / Varela-Rial, A. / Fino, R. / Donati, E. / De Fabritiis, G. / Dormann, D. / Sattler, M. / Niessing, D.
History
DepositionFeb 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional activator protein Pur-alpha
B: Transcriptional activator protein Pur-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,42315
Polymers15,7762
Non-polymers64713
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-68 kcal/mol
Surface area8580 Å2
Unit cell
Length a, b, c (Å)56.760, 75.640, 31.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-417-

HOH

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Components

#1: Protein Transcriptional activator protein Pur-alpha / Purine-rich single-stranded DNA-binding protein alpha


Mass: 7888.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PURA, PUR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00577
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris pH 8.5, 12% (v/v) glycerol, 1.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 15494 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 1 / Net I/σ(I): 19.5
Reflection shellResolution: 1.7→1.74 Å / Mean I/σ(I) obs: 6.7 / Num. unique obs: 1142 / CC1/2: 0.887

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→37.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.866 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 731 4.7 %RANDOM
Rwork0.1761 ---
obs0.1783 14763 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.08 Å2 / Biso mean: 31.919 Å2 / Biso min: 19.31 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å2-0 Å2
2---2.4 Å20 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 1.7→37.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 34 132 1258
Biso mean--47.79 43.18 -
Num. residues----135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131163
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171077
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.6751554
X-RAY DIFFRACTIONr_angle_other_deg1.3031.5832502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35521.57957
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05815198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.348156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02267
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 48 -
Rwork0.337 1092 -
all-1140 -
obs--100 %

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