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- PDB-6nof: Crystal structure of FBF-2 repeat 5 mutant (C363A, R364Y, Q367S) ... -

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Basic information

Entry
Database: PDB / ID: 6nof
TitleCrystal structure of FBF-2 repeat 5 mutant (C363A, 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: 2.251 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

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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)49,98410
Polymers49,4872
Non-polymers4978
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint20 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.544, 96.544, 101.066
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 46951.922 Da / Num. of mol.: 1 / Mutation: C363A, R364Y, Q367
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.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 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: 25386 / % possible obs: 99.9 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.048 / Rrim(I) all: 0.115 / Χ2: 1.102 / Net I/σ(I): 8.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.70.77212660.8020.350.8481100
2.29-2.335.70.71112420.810.3240.7821.016100
2.33-2.385.70.57912590.8480.2630.6371.025100
2.38-2.425.70.48812790.9070.2210.5361.067100
2.42-2.485.70.40612710.9210.1840.4471.075100
2.48-2.535.70.38412740.9330.1740.4221.099100
2.53-2.65.70.34112470.9450.1550.3751.172100
2.6-2.675.70.29612740.9560.1340.3251.151100
2.67-2.755.70.25212660.9640.1140.2771.203100
2.75-2.835.70.22612820.970.1020.2481.198100
2.83-2.945.70.19612470.9750.0890.2161.205100
2.94-3.055.70.16512730.9770.0750.1821.252100
3.05-3.195.70.14112770.9840.0650.1561.195100
3.19-3.365.70.12112690.9870.0550.1331.208100
3.36-3.575.70.09812760.9910.0450.1081.138100
3.57-3.855.60.08112500.9920.0370.091.09899.8
3.85-4.235.60.06812880.9950.0310.0751.01799.8
4.23-4.855.50.05812730.9960.0270.0640.96899.5
4.85-6.15.60.05312820.9970.0240.0580.95599.7
6.1-505.50.04312910.9980.020.0470.98698.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K5Q

3k5q


Resolution: 2.251→32.211 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.08
RfactorNum. reflection% reflection
Rfree0.2222 2007 7.91 %
Rwork0.164 --
obs0.1685 25366 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 140.03 Å2 / Biso mean: 46.5307 Å2 / Biso min: 20.91 Å2
Refinement stepCycle: final / Resolution: 2.251→32.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 168 32 109 3505
Biso mean--54.46 45.06 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2507-2.3070.28331400.211616701810
2.307-2.36940.25641440.200716561800
2.3694-2.43910.25321410.192316271768
2.4391-2.51780.29071490.188716841833
2.5178-2.60770.26531380.190916821820
2.6077-2.71210.27921390.189416371776
2.7121-2.83540.25881420.180917011843
2.8354-2.98480.27331480.19316591807
2.9848-3.17170.2331350.18516551790
3.1717-3.41630.25791520.176616671819
3.4163-3.75960.20681460.15816771823
3.7596-4.30260.19721450.13716601805
4.3026-5.41660.17071430.135616841827
5.4166-32.21430.1851450.147217001845
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)
12.8971-0.94850.96672.7855-1.93173.97540.16670.0942-0.2709-0.05430.26120.605-0.0343-0.3472-0.35760.23610.03110.00490.2560.02940.381970.2277101.651-10.7135
20.6336-1.72780.17135.3913-1.36620.3169-0.0176-0.0365-0.03570.07680.07810.0705-0.09050.0493-0.05510.3071-0.0323-0.05260.2425-0.01270.216795.950372.849414.2159
32.2960.6888-1.37220.2129-0.41331.12310.62550.2774-0.3697-1.2445-0.33321.00830.1805-0.0463-0.37460.790.0878-0.33740.3169-0.04490.441281.727975.4795-1.9359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 168 through 323 )A168 - 323
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 569 )A324 - 569
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 8 )B1 - 8

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