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

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Basic information

Entry
Database: PDB / ID: 7cgf
TitleCrystal Structure of PUF-8 in Complex with PBE-RNA
Components
  • PBE-5G (5'-R(P*UP*GP*UP*AP*GP*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: 1.7 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-5G (5'-R(P*UP*GP*UP*AP*GP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4923
Polymers44,4572
Non-polymers351
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-3 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.564, 89.564, 117.205
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: 41905.070 Da / Num. of mol.: 1 / Mutation: N318C, H319R
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-5G (5'-R(P*UP*GP*UP*AP*GP*AP*UP*A)-3')


Mass: 2551.569 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.: 204 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
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: Dec 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 53127 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 21.61 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.029 / Rrim(I) all: 0.093 / Χ2: 0.674 / Net I/σ(I): 4.8 / Num. measured all: 535738
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.7310.20.56226220.9220.1820.5910.437100
1.73-1.7610.10.47426140.9390.1560.50.437100
1.76-1.799.60.41725970.950.1410.4410.443100
1.79-1.839.60.35626130.9570.120.3760.448100
1.83-1.8710.60.32126200.9690.1020.3370.464100
1.87-1.9110.50.27226240.9770.0870.2860.477100
1.91-1.9610.50.22226120.9840.0710.2330.485100
1.96-2.0210.30.18926160.9870.0610.1990.522100
2.02-2.0710.10.15926340.990.0520.1670.521100
2.07-2.149.70.14326280.9910.0480.1510.56100
2.14-2.229.60.12426190.9920.0420.1310.594100
2.22-2.3110.60.11526710.9940.0370.1210.643100
2.31-2.4110.50.10626230.9940.0340.1120.676100
2.41-2.5410.40.09626530.9950.0310.1010.69100
2.54-2.710.10.08726620.9950.0290.0920.749100
2.7-2.919.50.0826590.9960.0270.0840.8299.9
2.91-3.210.60.07826860.9960.0250.0820.93399.9
3.2-3.6610.30.0727040.9960.0230.0741.095100
3.66-4.619.50.06727430.9960.0230.0711.215100
4.61-409.40.06829270.9970.0230.0711.235100

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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: 1.7→35.81 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 2730 5.15 %
Rwork0.1984 50293 -
obs0.1996 53023 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.1 Å2 / Biso mean: 27.4953 Å2 / Biso min: 11.51 Å2
Refinement stepCycle: final / Resolution: 1.7→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2758 172 1 204 3135
Biso mean--25.42 30.39 -
Num. residues----351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073020
X-RAY DIFFRACTIONf_angle_d0.8954121
X-RAY DIFFRACTIONf_chiral_restr0.048465
X-RAY DIFFRACTIONf_plane_restr0.005505
X-RAY DIFFRACTIONf_dihedral_angle_d17.5551818
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72920.2681470.23432478100
1.7292-1.76070.26521430.22232465100
1.7607-1.79450.28561110.22392483100
1.7945-1.83120.2581380.22682473100
1.8312-1.8710.22931280.22062491100
1.871-1.91450.2451310.21472490100
1.9145-1.96240.27511220.20642490100
1.9624-2.01540.22331350.21032478100
2.0154-2.07470.24961500.20552482100
2.0747-2.14170.22781310.21072494100
2.1417-2.21820.26061360.20972479100
2.2182-2.3070.22921470.20742521100
2.307-2.4120.25051400.20842482100
2.412-2.53910.23861410.21472508100
2.5391-2.69820.21151490.20372512100
2.6982-2.90640.24131430.21262509100
2.9064-3.19870.25261260.21782556100
3.1987-3.66120.19621290.18912572100
3.6612-4.61120.17941400.16232596100
4.6112-35.810.18171430.1774273499

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