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

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Basic information

Entry
Database: PDB / ID: 7cgk
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: 2.4 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-5A (5'-R(P*UP*GP*UP*AP*AP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4763
Polymers44,4412
Non-polymers351
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.796, 89.796, 117.551
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-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.: 57 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
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: 2.4→40 Å / Num. obs: 19494 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 32.41 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.031 / Rrim(I) all: 0.116 / Χ2: 0.717 / Net I/σ(I): 5.5 / Num. measured all: 243899
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4412.30.6019610.9430.1720.6260.462100
2.44-2.4912.60.5389330.9550.1520.560.473100
2.49-2.5312.50.4889590.9430.1380.5080.481100
2.53-2.5912.50.4259630.9650.1210.4420.477100
2.59-2.6412.40.3529550.9730.1010.3670.501100
2.64-2.712.20.339440.9770.0950.3440.51100
2.7-2.7711.30.2719520.9840.0820.2840.535100
2.77-2.8511.70.2579620.9860.0760.2690.547100
2.85-2.9313.10.2299510.9880.0630.2380.544100
2.93-3.0213.50.1939720.990.0520.20.58100
3.02-3.1313.50.1719450.9940.0460.1770.607100
3.13-3.2613.50.1459770.9950.0390.1510.678100
3.26-3.4113.20.1089670.9970.0290.1120.78100
3.41-3.58130.0989760.9970.0270.1020.825100
3.58-3.8112.60.0819810.9980.0220.0840.992100
3.81-4.111.10.0749860.9970.0220.0771.009100
4.1-4.5212.70.0679820.9980.0190.071.17100
4.52-5.1713.10.06210000.9990.0170.0651.062100
5.17-6.5112.40.06610210.9980.0180.0680.921100
6.51-40110.04811070.9990.0140.0511.1199.8

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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: 2.4→38.002 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 982 5.05 %
Rwork0.1869 18454 -
obs0.1894 19436 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.51 Å2 / Biso mean: 37.5417 Å2 / Biso min: 19.45 Å2
Refinement stepCycle: final / Resolution: 2.4→38.002 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2765 171 1 57 2994
Biso mean--33.03 34.44 -
Num. residues----354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083015
X-RAY DIFFRACTIONf_angle_d0.9764116
X-RAY DIFFRACTIONf_chiral_restr0.052466
X-RAY DIFFRACTIONf_plane_restr0.005506
X-RAY DIFFRACTIONf_dihedral_angle_d18.2411813
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.5260.28191320.21622567
2.526-2.68420.24371390.20922591
2.6842-2.89140.25661450.21652596
2.8914-3.18220.26861440.22342595
3.1822-3.64240.24951390.19622617
3.6424-4.58780.20481360.15892675
4.5878-38.0020.21051470.16512813

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