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- PDB-3v6y: crystal structure of FBF-2 in complex with a mutant gld-1 FBEa13 RNA -

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Basic information

Entry
Database: PDB / ID: 3v6y
Titlecrystal structure of FBF-2 in complex with a mutant gld-1 FBEa13 RNA
Components
  • Fem-3 mRNA-binding factor 2
  • RNA (5'-R(*UP*AP*CP*UP*GP*UP*GP*CP*CP*AP*UP*AP*C)-3')
KeywordsRNA binding protein/RNA / PUF repeats / 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 / negative regulation of translation / 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 / RNA (> 10) / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsQiu, C. / Kershner, A. / Wang, Y. / Holley, C.H. / Wilinski, D. / Keles, S. / Kimble, J. / Wickens, M. / Hall, T.M.T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Divergence of PUF protein specificity through variations in an RNA-binding pocket
Authors: Qiu, C. / Kershner, A. / Wang, Y. / Holley, C.H. / Wilinski, D. / Keles, S. / Kimble, J. / Wickens, M. / Hall, T.M.T.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release

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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*AP*CP*UP*GP*UP*GP*CP*CP*AP*UP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)51,0982
Polymers51,0982
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-8 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.797, 99.797, 105.598
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


Mass: 47019.055 Da / Num. of mol.: 1 / Fragment: unp residues 164-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q09312
#2: RNA chain RNA (5'-R(*UP*AP*CP*UP*GP*UP*GP*CP*CP*AP*UP*AP*C)-3')


Mass: 4078.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% (w/v) PEG8000, 8% (v/v) ethylene glycol, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: May 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. all: 20680 / Num. obs: 20644 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 26.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2042 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→31.207 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 1056 5.13 %random
Rwork0.1847 ---
obs0.1877 20601 99.63 %-
all-20677 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.801 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.1845 Å20 Å20 Å2
2---4.1845 Å20 Å2
3---8.369 Å2
Refinement stepCycle: LAST / Resolution: 2.5→31.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 214 0 108 3451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083413
X-RAY DIFFRACTIONf_angle_d1.0064642
X-RAY DIFFRACTIONf_dihedral_angle_d15.971314
X-RAY DIFFRACTIONf_chiral_restr0.068544
X-RAY DIFFRACTIONf_plane_restr0.004556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.61370.33421290.25642413X-RAY DIFFRACTION100
2.6137-2.75140.30981320.22092452X-RAY DIFFRACTION100
2.7514-2.92370.28681400.20322430X-RAY DIFFRACTION100
2.9237-3.14930.25521430.18982441X-RAY DIFFRACTION100
3.1493-3.46580.27511220.18722450X-RAY DIFFRACTION100
3.4658-3.96650.27931420.2042400X-RAY DIFFRACTION98
3.9665-4.9940.17681230.15182467X-RAY DIFFRACTION100
4.994-31.20960.20161250.16862492X-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)
10.49960.1864-0.08210.18420.07320.10720.55010.38450.0833-0.5424-0.05770.40670.016-0.09920.03810.807-0.0377-0.22110.51020.05870.462616.162313.8702-45.9322
20.12280.03340.02360.14420.13530.6638-0.0972-0.12630.0771-0.10750.1424-0.0326-0.0177-0.0094-00.33880.0207-0.00060.31320.0640.288322.107417.694-36.4604
30.7378-0.47240.56090.5904-0.90751.43780.0066-0.06260.0730.1510.11450.2538-0.261-0.113-0.00010.29720.04970.04590.25410.06190.300524.45621.5547-22.6595
40.9485-0.65341.22451.1365-0.7051.6684-0.0084-0.188-0.08820.07420.23760.1993-0.176-0.14260.00330.24080.02740.02970.21180.05260.186435.40039.4302-6.848
50.8903-0.64090.28660.6346-0.2270.7605-0.0852-0.403-0.06440.50750.01690.1764-0.3232-0.1179-0.00310.42130.0084-0.04780.35220.03790.199144.19175.13845.706
60.8448-0.62340.06760.70530.02070.2165-0.0382-0.24660.03180.11750.3360.2143-0.0484-0.00520.1360.28290.0341-0.07370.19720.08080.263650.1152-10.89664.5865
70.4373-0.2945-0.02530.45790.25740.60840.19520.0018-0.216-0.20840.01950.3965-0.00240.1290.0180.37380.036-0.12480.18680.01450.468453.9295-23.96241.7397
80.4822-0.2770.46620.2945-0.26410.4465-0.02080.22980.0917-0.12080.0366-0.14120.05980.3509-0.00010.335-0.0163-0.03940.27970.02670.366466.9054-19.00994.2649
91.06750.4030.11060.61240.13070.71780.4760.0405-0.6302-0.1737-0.3-0.13240.29120.1678-0.03770.65660.1054-0.20710.3323-0.09040.351458.793-31.9279-5.8182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 167:184)
2X-RAY DIFFRACTION2chain 'A' and (resseq 185:216)
3X-RAY DIFFRACTION3chain 'A' and (resseq 217:282)
4X-RAY DIFFRACTION4chain 'A' and (resseq 283:383)
5X-RAY DIFFRACTION5chain 'A' and (resseq 384:410)
6X-RAY DIFFRACTION6chain 'A' and (resseq 411:477)
7X-RAY DIFFRACTION7chain 'A' and (resseq 478:514)
8X-RAY DIFFRACTION8chain 'A' and (resseq 515:544)
9X-RAY DIFFRACTION9chain 'A' and (resseq 545:567)

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