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

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Basic information

Entry
Database: PDB / ID: 7cgj
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: 2.546 Å
AuthorsZheng, X. / Yunyu, S. / Shouhong, G.
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

Downloads & links

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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)44,4843
Polymers44,4492
Non-polymers351
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-6 kcal/mol
Surface area16440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.355, 89.355, 117.898
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-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.: 31 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
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 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.546→40 Å / Num. obs: 16283 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 27.86 Å2 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.051 / Rrim(I) all: 0.17 / Χ2: 0.52 / Net I/σ(I): 4.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.5910.50.7667840.9360.2430.8040.422100
2.59-2.6410.50.6468080.9510.2060.6780.449100
2.64-2.6910.40.5917930.9480.1910.6220.444100
2.69-2.759.60.4777930.970.160.5040.457100
2.75-2.819.40.4397930.9610.150.4650.461100
2.81-2.8710.30.4657870.9660.150.4890.447100
2.87-2.9411.40.4258100.9810.130.4450.459100
2.94-3.0211.40.347990.9840.1040.3560.461100
3.02-3.1111.60.3137870.9880.0950.3270.477100
3.11-3.2111.50.2618100.9890.080.2740.491100
3.21-3.3311.50.2118120.9940.0640.220.517100
3.33-3.4611.40.178010.9950.0520.1780.536100
3.46-3.6211.40.1588150.9950.0490.1660.551100
3.62-3.81110.1238010.9970.0380.1290.602100
3.81-4.059.80.1128170.9970.0370.1180.594100
4.05-4.3610.50.0948270.9970.030.0990.62899.9
4.36-4.811.60.0828180.9990.0250.0860.61799.9
4.8-5.4911.40.0898400.9980.0270.0930.567100
5.49-6.9110.50.0958570.9980.030.10.562100
6.91-409.60.0429310.9990.0140.0440.61899.8

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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: 2.546→37.846 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2416 837 5.16 %
Rwork0.1906 15384 -
obs0.1933 16221 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.89 Å2 / Biso mean: 31.8206 Å2 / Biso min: 7.7 Å2
Refinement stepCycle: final / Resolution: 2.546→37.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 172 1 31 2995
Biso mean--22.24 20.16 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093047
X-RAY DIFFRACTIONf_angle_d1.1024155
X-RAY DIFFRACTIONf_chiral_restr0.054465
X-RAY DIFFRACTIONf_plane_restr0.007511
X-RAY DIFFRACTIONf_dihedral_angle_d18.9621832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.546-2.70520.25321380.20622507
2.7052-2.9140.29251340.242497
2.914-3.20710.36321440.24642529
3.2071-3.67080.25451340.20712543
3.6708-4.62350.19841370.15632595
4.6235-37.8460.18531500.15532713

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