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- PDB-7cgg: Crystal Structure of PUF-8 in Complex with PBE-RNA -

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Basic information

Entry
Database: PDB / ID: 7cgg
TitleCrystal Structure of PUF-8 in Complex with PBE-RNA
Components
  • PBE-5A (5'-R(P*UP*GP*UP*AP*AP*AP*UP*A)-3')
  • PUM-HD domain-containing protein
KeywordsRNA BINDING PROTEIN / complex / PUF protein
Function / homology
Function and homology information


male meiotic nuclear division / P granule / post-transcriptional regulation of gene expression / negative regulation of MAPK cascade / nuclear periphery / mRNA 3'-UTR binding / regulation of translation / spermatogenesis / cell differentiation / nucleus / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / PUM-HD domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZheng, X. / Yunyu, S.
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans.
Authors: Xu, Z. / Zhao, J. / Hong, M. / Zeng, C. / Guang, S. / Shi, Y.
History
DepositionJul 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 19, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUM-HD domain-containing protein
B: PBE-5A (5'-R(P*UP*GP*UP*AP*AP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4683
Polymers44,4332
Non-polymers351
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-3 kcal/mol
Surface area16250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.146, 89.146, 117.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PUM-HD domain-containing protein


Mass: 41896.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: puf-8, C30G12.7, CELE_C30G12.7
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q09487
#2: RNA chain PBE-5A (5'-R(P*UP*GP*UP*AP*AP*AP*UP*A)-3')


Mass: 2535.569 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1M LiCl, 0.1M Citric acid (pH 5.0) and 15% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.977 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.695→40 Å / Num. obs: 13641 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 33.82 Å2 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.047 / Rrim(I) all: 0.158 / Χ2: 0.447 / Net I/σ(I): 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.7511.50.5486500.9310.1660.5730.418100
2.75-2.811.40.4786750.9380.1460.50.427100
2.8-2.8511.60.5246560.9210.1590.5480.412100
2.85-2.9111.60.456590.9490.1370.4710.425100
2.91-2.9711.40.3946820.9560.120.4120.428100
2.97-3.0411.40.3526510.9630.1080.3680.43100
3.04-3.12110.3216740.9730.10.3370.427100
3.12-3.210.10.2726660.970.090.2860.443100
3.2-3.310.60.2386730.9840.0760.250.46100
3.3-3.411.90.196730.9920.0570.1980.437100
3.4-3.52120.1756730.9920.0520.1830.454100
3.52-3.6611.90.1456680.9930.0430.1510.449100
3.66-3.8311.70.1296850.9950.0390.1350.475100
3.83-4.0311.60.1166850.9960.0350.1210.466100
4.03-4.2811.30.0996830.9960.030.1030.475100
4.28-4.6210.40.0916840.9970.0290.0950.491100
4.62-5.0810.40.0876960.9970.0280.0910.487100
5.08-5.8111.50.1016980.9960.0310.1060.46100
5.81-7.31110.0977230.9970.030.1010.455100
7.31-409.30.0517870.9990.0170.0530.42599.9

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Processing

Software
NameVersionClassification
PHENIX1.10-2155refinement
HKL-2000V716.1data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3q0q

3q0q


Resolution: 2.7→35.805 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 702 5.17 %
Rwork0.1896 12869 -
obs0.1922 13571 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.17 Å2 / Biso mean: 29.3835 Å2 / Biso min: 10.08 Å2
Refinement stepCycle: final / Resolution: 2.7→35.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2783 171 1 22 2977
Biso mean--28.29 24.16 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013034
X-RAY DIFFRACTIONf_angle_d0.964139
X-RAY DIFFRACTIONf_chiral_restr0.056466
X-RAY DIFFRACTIONf_plane_restr0.006509
X-RAY DIFFRACTIONf_dihedral_angle_d20.151826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7-2.90310.28411190.21942499100
2.9031-3.19510.27311390.21892538100
3.1951-3.65710.26181490.20232537100
3.6571-4.6060.21021380.16592591100
4.606-35.8050.21411570.1779270499

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