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

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Basic information

Entry
Database: PDB / ID: 7cgi
TitleCrystal Structure of PUF-8 in Complex with PBE-RNA
Components
  • PBE-5U (5'-R(P*UP*GP*UP*AP*UP*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: 2.796 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)44,4453
Polymers44,4102
Non-polymers351
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-8 kcal/mol
Surface area16310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.261, 89.261, 117.019
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-5U (5'-R(P*UP*GP*UP*AP*UP*AP*UP*A)-3')


Mass: 2512.529 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.: 15 / 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: 53.13 %
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: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.796→31.559 Å / Num. obs: 12260 / % possible obs: 99.9 % / Redundancy: 11.5 % / Biso Wilson estimate: 37.06 Å2 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.04 / Rrim(I) all: 0.139 / Χ2: 0.442 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.859.80.6235940.8710.2040.6580.425100
2.85-2.910.70.5715880.9130.1760.5990.42399.7
2.9-2.9611.40.5275920.9350.1590.5510.43100
2.96-3.0211.30.4466100.9540.1350.4660.42799.3
3.02-3.0811.30.3986050.9580.120.4160.431100
3.08-3.1511.50.3545740.9670.1060.370.431100
3.15-3.2311.50.3155960.9780.0950.3290.41599.5
3.23-3.3211.50.246160.9870.0720.2510.42799.8
3.32-3.4211.50.1985940.9890.060.2070.435100
3.42-3.5311.30.1736120.9890.0530.1810.457100
3.53-3.6510.60.1365910.9920.0430.1430.45899.8
3.65-3.811.20.1166180.9950.0360.1210.459100
3.8-3.97130.1076040.9970.030.1110.464100
3.97-4.18130.0916180.9980.0260.0950.446100
4.18-4.4412.80.0796140.9980.0230.0820.472100
4.44-4.7912.50.0666150.9990.0190.0690.442100
4.79-5.2711.40.0716400.9980.0210.0740.426100
5.27-6.0311.60.0826240.9970.0250.0860.434100
6.03-7.5812.30.076440.9990.020.0730.416100
7.58-409.80.0467110.9990.0150.0490.52299.7

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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: 2.796→31.559 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2488 600 4.93 %
Rwork0.2033 11581 -
obs0.2056 12181 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 137.36 Å2 / Biso mean: 32.8872 Å2 / Biso min: 7.38 Å2
Refinement stepCycle: final / Resolution: 2.796→31.559 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 169 1 15 2964
Biso mean--28.69 21.7 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023023
X-RAY DIFFRACTIONf_angle_d0.4584122
X-RAY DIFFRACTIONf_chiral_restr0.037464
X-RAY DIFFRACTIONf_plane_restr0.004508
X-RAY DIFFRACTIONf_dihedral_angle_d18.9931818
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.796-3.07730.27811610.23492818100
3.0773-3.52210.30461480.21762841100
3.5221-4.43550.2241410.18212898100
4.4355-31.5590.2211500.2013302499

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