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- PDB-6noh: Crystal structure of FBF-2 repeat 5 mutant (C363S, R364Y, Q367S) ... -

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Basic information

Entry
Database: PDB / ID: 6noh
TitleCrystal structure of FBF-2 repeat 5 mutant (C363S, R364Y, Q367S) in complex with 8-nt RNA
Components
  • Fem-3 mRNA-binding factor 2
  • RNA (5'-R(*UP*GP*UP*AP*AP*AP*UP*A)-3')
Keywordsrna binding protein/rna / PUM repeat protein / RNA BINDING PROTEIN / rna binding protein-rna complex
Function / homology
Function and homology information


sex differentiation / P granule / post-transcriptional regulation of gene expression / mRNA 3'-UTR binding / cell differentiation / negative regulation of translation / RNA binding / 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 / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsMcCann, K.L. / Wang, Y. / Qiu, C. / Hall, T.M.T.
CitationJournal: Elife / Year: 2019
Title: Engineering a conserved RNA regulatory protein repurposes its biological function in vivo .
Authors: Bhat, V.D. / McCann, K.L. / Wang, Y. / Fonseca, D.R. / Shukla, T. / Alexander, J.C. / Qiu, C. / Wickens, M. / Lo, T.W. / Tanaka Hall, T.M. / Campbell, Z.T.
History
DepositionJan 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fem-3 mRNA-binding factor 2
B: RNA (5'-R(*UP*GP*UP*AP*AP*AP*UP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,31015
Polymers49,5032
Non-polymers80713
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint30 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.397, 96.397, 99.853
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Fem-3 mRNA-binding factor 2 / FBF-2


Mass: 46967.922 Da / Num. of mol.: 1 / Mutation: C363S, R364Y, Q367S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q09312
#2: RNA chain RNA (5'-R(*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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris pH 8.6, 15% [w/v] PEG 8000, 8% [v/v] ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 25098 / % possible obs: 99.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 36.64 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.047 / Rrim(I) all: 0.112 / Χ2: 1.227 / Net I/σ(I): 9.3 / Num. measured all: 142174
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.70.70412660.8190.3230.7761100
2.29-2.335.80.6312230.860.2870.6930.965100
2.33-2.385.70.51612470.8860.2360.5680.978100
2.38-2.425.70.44512530.9110.2030.491.089100
2.42-2.485.70.38612670.9310.1760.4251.034100
2.48-2.535.70.36812400.9390.1680.4051.073100
2.53-2.65.80.312360.9540.1370.331.12100
2.6-2.675.70.26312650.9630.120.291.145100
2.67-2.755.70.22912590.9730.1050.2531.226100
2.75-2.835.80.20112590.9770.0920.2221.32100
2.83-2.945.70.17912400.9760.0820.1971.409100
2.94-3.055.70.15512370.9840.0710.1711.459100
3.05-3.195.70.13112610.9860.0590.1441.293100
3.19-3.365.70.12312480.9880.0570.1361.495100
3.36-3.575.60.10112710.990.0470.1111.522100
3.57-3.855.50.08312520.9920.040.0931.539100
3.85-4.235.50.07112560.9940.0340.0791.39399.8
4.23-4.855.50.06412570.9950.030.0711.399.7
4.85-6.15.50.06212700.9950.030.0691.204100
6.1-505.30.0512910.9970.0230.0550.98699.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5Q

3k5q


Resolution: 2.249→34.676 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2056 1994 7.96 %
Rwork0.1588 --
obs0.1625 25061 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.249→34.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3197 150 52 129 3528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073465
X-RAY DIFFRACTIONf_angle_d0.7944680
X-RAY DIFFRACTIONf_dihedral_angle_d3.6682876
X-RAY DIFFRACTIONf_chiral_restr0.044539
X-RAY DIFFRACTIONf_plane_restr0.004569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2491-2.30530.24951430.19761632X-RAY DIFFRACTION100
2.3053-2.36760.23261430.19191643X-RAY DIFFRACTION100
2.3676-2.43730.26111430.17181653X-RAY DIFFRACTION100
2.4373-2.51590.25911420.17891631X-RAY DIFFRACTION100
2.5159-2.60580.23611460.17381653X-RAY DIFFRACTION100
2.6058-2.71010.21851420.17091628X-RAY DIFFRACTION100
2.7101-2.83340.24931450.17171664X-RAY DIFFRACTION100
2.8334-2.98270.24261330.16131624X-RAY DIFFRACTION100
2.9827-3.16950.20881380.16391651X-RAY DIFFRACTION100
3.1695-3.4140.2141400.16471659X-RAY DIFFRACTION100
3.414-3.75720.19481390.14711652X-RAY DIFFRACTION100
3.7572-4.30.17451440.13661645X-RAY DIFFRACTION100
4.3-5.41420.16111500.1441653X-RAY DIFFRACTION100
5.4142-34.68040.20741460.16511679X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4948-0.42940.43721.0366-0.66451.13830.0761-0.0423-0.1456-0.01320.11350.2388-0.0027-0.12730.00130.201-0.0109-0.01250.23050.05010.269274.209897.829-4.7852
20.1314-0.59040.14722.2057-0.41450.0394-0.04110.01530.017-0.20580.0970.03510.0150.0063-0.00010.3165-0.0122-0.01020.2370.00350.231999.766566.887315.5892
30.29290.0103-0.24330.03510.04080.26340.54760.2011-0.2928-0.2941-0.24050.06860.56260.27010.1310.6220.0979-0.3710.12640.07360.334382.969973.3646-0.3374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 168 through 383 )
2X-RAY DIFFRACTION2chain 'A' and (resid 384 through 569 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 8 )

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