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- PDB-6noc: Crystal structure of FBF-2 repeat 5 mutant (C363A, R364Y) in comp... -

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Basic information

Entry
Database: PDB / ID: 6noc
TitleCrystal structure of FBF-2 repeat 5 mutant (C363A, R364Y) 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 2.849 Å
AuthorsMcCann, K. / 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 ...Data collection / Database references / Experimental preparation / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / exptl_crystal / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal.density_Matthews / _exptl_crystal.density_percent_sol

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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')


Theoretical massNumber of molelcules
Total (without water)49,5292
Polymers49,5292
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-2 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.999, 95.999, 100.428
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: 46992.973 Da / Num. of mol.: 1 / Mutation: C363A, R364Y
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 12% [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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.849→50 Å / Num. obs: 12319 / % possible obs: 99.6 % / Redundancy: 10.7 % / Rpim(I) all: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 2.849→2.9 Å / Redundancy: 8.8 % / CC1/2: 0.872 / Rpim(I) all: 0.336 / % possible all: 99.2

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Processing

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

3k5q


Resolution: 2.849→27.458 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 1217 9.99 %
Rwork0.2192 10968 -
obs0.225 12185 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.23 Å2 / Biso mean: 51.2686 Å2 / Biso min: 15.96 Å2
Refinement stepCycle: final / Resolution: 2.849→27.458 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 168 0 23 3387
Biso mean---23.71 -
Num. residues----410
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8489-2.96290.3761310.2991208133998
2.9629-3.09760.39211340.299212301364100
3.0976-3.26060.33161350.268612191354100
3.2606-3.46450.33371380.26861215135399
3.4645-3.73140.28151350.221612301365100
3.7314-4.10580.27371350.2151181131697
4.1058-4.69740.27151330.20321186131996
4.6974-5.90850.25791310.19731247137899
5.9085-27.45910.18841450.163512521397100
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)
12.08640.6199-1.17752.5955-1.41072.74090.0991-0.01690.17110.15130.12920.5023-0.088-0.2527-0.19340.3385-0.0783-0.00680.29570.01360.433721.456-18.83713.9543
22.03680.4055-0.80233.1744-0.75251.15340.23420.26770.403-0.3230.07110.378-0.1048-0.0587-0.3120.4385-0.0075-0.00730.33320.11360.35136.3219-4.1475-10.9742
31.56430.4956-0.1044.7945-0.64380.3414-0.04230.0138-0.09680.3397-0.0079-0.13870.0660.16380.01760.3978-0.00320.04110.2918-0.00060.28253.63120.9824-14.3661
42.87210.97321.29524.94250.66250.62520.5496-0.34960.42560.2193-0.03520.563-0.71350.1723-0.43040.7584-0.08740.27780.32430.06370.474333.30688.46993.1353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 167 through 308 )A167 - 308
2X-RAY DIFFRACTION2chain 'A' and (resid 309 through 424 )A309 - 424
3X-RAY DIFFRACTION3chain 'A' and (resid 425 through 567 )A425 - 567
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 8 )B1 - 8

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