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

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Basic information

Entry
Database: PDB / ID: 8cht
TitleCrystal structure of human PURA (fragment Glu57-Glu212, PUR repeat I and II)
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 / SMAD binding / DNA replication initiation / transcription regulator inhibitor activity / mRNA regulatory element binding translation repressor activity / epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...dendritic transport of messenger ribonucleoprotein complex / purine-rich negative regulatory element binding / lymphocyte proliferation / double-stranded telomeric DNA binding / SMAD binding / DNA replication initiation / transcription regulator inhibitor activity / 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 / nervous system development / single-stranded DNA binding / DNA-binding transcription factor binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / postsynapse / neuronal cell body / positive regulation of cell population proliferation / dendrite / regulation of transcription by RNA polymerase II / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / RNA binding / nucleus / cytoplasm
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
ACETATE ION / Transcriptional activator protein Pur-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2128
Polymers70,9724
Non-polymers2394
Water5,603311
1
A: Transcriptional activator protein Pur-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8022
Polymers17,7431
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcriptional activator protein Pur-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8022
Polymers17,7431
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcriptional activator protein Pur-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8052
Polymers17,7431
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Transcriptional activator protein Pur-alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8022
Polymers17,7431
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.920, 58.140, 81.940
Angle α, β, γ (deg.)90.000, 100.650, 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: 17743.092 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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 42.56 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8.2
Details: 0.1 M Tris buffer pH 8.2, 0.2 M sodium acetate, and 30% (w/v) PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0331 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0331 Å / Relative weight: 1
ReflectionResolution: 1.95→50.01 Å / Num. obs: 43138 / % possible obs: 98 % / Redundancy: 6.9 % / CC1/2: 0.998 / Net I/σ(I): 12.1
Reflection shellResolution: 1.95→2 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3147 / CC1/2: 0.743

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.155 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 2122 4.9 %RANDOM
Rwork0.1743 ---
obs0.1772 41016 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.48 Å2 / Biso mean: 32.4 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å20.17 Å2
2--0.63 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4581 0 16 314 4911
Biso mean--52.76 40.71 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0194746
X-RAY DIFFRACTIONr_bond_other_d0.0020.024580
X-RAY DIFFRACTIONr_angle_refined_deg2.3141.9736365
X-RAY DIFFRACTIONr_angle_other_deg1.157310569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0875592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.7922.903248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68215904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2051560
X-RAY DIFFRACTIONr_chiral_restr0.1420.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021050
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 153 -
Rwork0.242 2983 -
all-3136 -
obs--96.73 %
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)
10.51810.2096-0.27610.8020.13790.6912-0.00320.0304-0.0762-0.07120.050.043-0.0424-0.0068-0.04680.0181-0.0125-0.01520.0267-0.00250.0768-1.2717-3.4485-37.0732
20.4710.13970.0320.21850.1630.77240.02560.0307-0.0786-0.0036-0.00550.0693-0.0348-0.0032-0.02010.0092-0.0029-0.01680.0121-0.01530.121131.2461-3.5971-37.4256
30.09320.07130.31980.22320.34681.30940.0061-0.00620.00450.03340.0765-0.02370.00390.0161-0.08260.06240.01290.01160.0405-0.00680.04965.90565.4189-7.9945
40.3223-0.30270.46130.8381-0.28960.6975-0.0817-0.0567-0.03580.04280.151-0.0404-0.1303-0.0557-0.06930.0726-0.01740.06250.0404-0.03250.062239.30383.6326-8.4885
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 191
2X-RAY DIFFRACTION2B36 - 191
3X-RAY DIFFRACTION3C36 - 191
4X-RAY DIFFRACTION4D36 - 191

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