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

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Basic information

Entry
Database: PDB / ID: 7cgh
TitleCrystal Structure of PUF-8 in Complex with PBE-RNA
Components
  • PBE-5C (5'-R(P*UP*GP*UP*AP*CP*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 / Armadillo-like helical / Armadillo-type fold
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-5C (5'-R(P*UP*GP*UP*AP*CP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4443
Polymers44,4092
Non-polymers351
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-9 kcal/mol
Surface area16360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.237, 88.237, 115.304
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-5C (5'-R(P*UP*GP*UP*AP*CP*AP*UP*A)-3')


Mass: 2511.545 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: 2.53 Å3/Da / Density % sol: 51.32 %
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: 2.398→50 Å / Num. obs: 18498 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 34.49 Å2 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.032 / Rrim(I) all: 0.11 / Χ2: 0.598 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4410.30.6738770.9060.2190.7090.41599.8
2.44-2.499.90.679040.9020.220.7060.428100
2.49-2.5310.90.5759140.9240.1810.6040.431100
2.53-2.5912.10.539030.9430.1590.5540.445100
2.59-2.64120.4669090.9450.1390.4860.445100
2.64-2.712.10.3719090.9720.1120.3880.476100
2.7-2.7712.10.338940.9780.0980.3450.45100
2.77-2.8512.10.299290.9820.0870.3030.46100
2.85-2.9312.20.2578980.9870.0760.2680.472100
2.93-3.0211.90.2179100.9870.0650.2270.5100
3.02-3.1311.50.1749210.990.0530.1820.51599.9
3.13-3.2610.30.1389030.9930.0450.1450.529100
3.26-3.4112.20.1139350.9970.0330.1180.542100
3.41-3.5812.60.0919170.9970.0270.0950.595100
3.58-3.8112.30.0769300.9980.0220.080.639100
3.81-4.1120.0629270.9990.0180.0640.619100
4.1-4.5211.30.0519440.9990.0160.0540.62599.9
4.52-5.1710.70.0419550.9990.0130.0430.567100
5.17-6.5111.90.0479630.9960.0140.0490.63199.7
6.51-50100.03310560.9940.0120.0352.16599.8

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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→39.461 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 930 5.05 %
Rwork0.2024 17487 -
obs0.2045 18417 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.13 Å2 / Biso mean: 37.8153 Å2 / Biso min: 15.9 Å2
Refinement stepCycle: final / Resolution: 2.4→39.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2755 169 1 31 2956
Biso mean--32.23 28.63 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082999
X-RAY DIFFRACTIONf_angle_d1.0194092
X-RAY DIFFRACTIONf_chiral_restr0.054464
X-RAY DIFFRACTIONf_plane_restr0.006502
X-RAY DIFFRACTIONf_dihedral_angle_d19.681800
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4-2.52460.31881340.21912430100
2.5246-2.68270.34131290.23382461100
2.6827-2.88980.29161350.24482444100
2.8898-3.18050.27391280.23842470100
3.1805-3.64040.26851450.20252491100
3.6404-4.58540.17871310.17072538100
4.5854-39.4610.2211280.1872265399

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