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- PDB-8chv: Crystal structure of human PURA (fragment Glu57-Glu212, PUR repea... -

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Basic information

Entry
Database: PDB / ID: 8chv
TitleCrystal structure of human PURA (fragment Glu57-Glu212, PUR repeat I and II) R140P mutant
ComponentsTranscriptional activator protein Pur-alpha
KeywordsRNA BINDING PROTEIN / RNA/DNA binding / PUR repeat / PC4-like fold / PURA Syndrome
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 / nervous system development / single-stranded DNA binding / postsynapse / DNA-binding transcription factor binding / 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: 2.15 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
C: Transcriptional activator protein Pur-alpha
D: Transcriptional activator protein Pur-alpha


Theoretical massNumber of molelcules
Total (without water)70,7324
Polymers70,7324
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-5 kcal/mol
Surface area28730 Å2
Unit cell
Length a, b, c (Å)63.307, 57.573, 84.879
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17683.012 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 292 K / Method: small tubes / Details: 200 mM NaCl, 20 mM HEPES, 2 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 32410 / % possible obs: 99.4 % / Redundancy: 3.5 % / CC1/2: 0.997 / Net I/σ(I): 7.6
Reflection shellResolution: 2.15→2.28 Å / Num. unique obs: 5012 / CC1/2: 0.583 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.29 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.917 / SU B: 20.086 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.289 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2821 1621 5 %RANDOM
Rwork0.2048 ---
obs0.2087 30789 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.17 Å2 / Biso mean: 49.087 Å2 / Biso min: 20.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å2-0 Å2-0.85 Å2
2---0.37 Å2-0 Å2
3----1.43 Å2
Refinement stepCycle: final / Resolution: 2.15→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 0 197 4766
Biso mean---44.77 -
Num. residues----569
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124663
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164365
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.6516247
X-RAY DIFFRACTIONr_angle_other_deg0.4931.56310166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8675566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.28555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80710876
X-RAY DIFFRACTIONr_chiral_restr0.0690.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025424
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02960
LS refinement shellResolution: 2.153→2.209 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 115 -
Rwork0.346 2191 -
all-2306 -
obs--96.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7488-0.01740.60293.2358-0.5712.77680.0002-0.0356-0.0228-0.13860.04280.3859-0.1595-0.1653-0.0430.0390.0005-0.01010.0144-0.00680.118724.93270.46617.7234
21.03740.27330.85392.43560.22913.95850.123-0.1452-0.13240.27680.08-0.1773-0.01340.1085-0.20290.0517-0.0142-0.04320.04270.00890.068432.1034-8.983636.0093
32.2061-1.41861.731.6907-1.50284.35050.2235-0.1125-0.37710.24460.04950.15370.1669-0.112-0.2730.2304-0.0313-0.0970.0496-0.00120.19182.2005-8.453638.0906
42.6528-0.64571.232.2014-0.26195.7120.26460.5306-0.0221-0.05120.0173-0.0522-0.07490.5171-0.28190.03490.0407-0.00030.13890.00190.0883-6.2474-0.34628.3215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 212
2X-RAY DIFFRACTION2B57 - 212
3X-RAY DIFFRACTION3C57 - 211
4X-RAY DIFFRACTION4D58 - 212

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