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- PDB-3k5z: Crystal structure of FBF-2/gld-1 FBEa G4A mutant complex -

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Basic information

Entry
Database: PDB / ID: 3k5z
TitleCrystal structure of FBF-2/gld-1 FBEa G4A mutant complex
Components
  • 5'-R(*UP*GP*UP*AP*CP*CP*AP*UP*A)-3'
  • Fem-3 mRNA-binding factor 2
KeywordsRNA/RNA BINDING PROTEIN / FBF / fem-3 binding factor / PUF / RNA-binding specificity / base flipping / base stacking / RNA-RNA BINDING PROTEIN 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 / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWang, Y. / Opperman, L. / Wickens, M. / Hall, T.M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein.
Authors: Wang, Y. / Opperman, L. / Wickens, M. / Hall, T.M.
History
DepositionOct 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7792
Polymers49,7792
Non-polymers00
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-6 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.048, 97.048, 101.703
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: 46962.004 Da / Num. of mol.: 1 / Fragment: UNP residues 164-575, RNA-binding domain
Source method: isolated from a genetically manipulated source
Details: A TEV cleavage site is inserted between GST and FBF-2.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F21H12.5, fbf-2 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q09312
#2: RNA chain 5'-R(*UP*GP*UP*AP*CP*CP*AP*UP*A)-3'


Mass: 2816.727 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Tris pH 7.5, 10% polyethylene glycol 8000, and 8% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 4, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→28.0153 Å / Num. obs: 21281 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 33.878 Å2 / Rsym value: 0.128 / Net I/σ(I): 18.2
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1049 / Rsym value: 0.895 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SERGUIfrom SER-CATdata collection
APSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K5Q

3k5q


Resolution: 2.4→28.0153 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1097 -R-free selection was copied from the structure factor file of PDB ENTRY 3K5Q
Rwork0.1602 ---
obs-21281 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→28.0153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 186 0 193 3518
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.731
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)
13.48350.3756-2.3248-0.34520.6223.27940.75231.1816-0.2443-1.2252-0.04031.0988-0.1195-0.80220.6870.62430.0193-0.37420.52590.14130.567814.145319.8799-28.665
20.9448-0.21390.08140.4268-0.89310.76920.1183-0.0566-0.0104-0.47040.24230.5223-0.0241-0.3473-0.00010.29090.0323-0.04190.27130.08730.395521.380920.7845-20.2711
3-0.4071-0.91541.05770.2845-1.66792.2830.0252-0.2478-0.09340.08290.29540.3824-0.3078-0.13950.00320.24590.0360.05650.23610.0680.269723.171621.917-8.354
4-0.0904-0.63011.70810.9122-0.39230.3679-0.06720.10630.08410.10390.57980.3631-0.3202-0.14560.04830.30380.03290.06110.18860.07140.222727.170915.25120.8798
50.1504-0.51080.67390.69920.13511.26160.03150.0340.08750.19470.31310.2742-0.12760.15740.05070.19360.0120.00290.08570.02950.124831.67919.49377.9492
60.5868-0.41490.56661.4416-1.44410.28820.1340.1046-0.10390.44070.14260.0274-0.03030.04610.00390.3136-0.0226-0.02410.1413-0.0210.188740.3215.699312.8858
70.2062-1.77851.16551.1686-0.0491-0.7435-0.1635-0.06350.23580.24470.32540.2025-0.0230.04310.00280.31730.0213-0.06760.1533-0.01770.261544.4317-6.315616.1574
81.2991-0.93760.2942.24510.8471-0.8813-0.0408-0.3153-0.00830.33320.17110.09120.0265-0.0153-00.27880.0293-0.08960.1955-0.01250.17549.1835-19.517719.6426
91.7405-1.02891.141.02450.16940.2624-0.0761-0.13460.0477-0.3295-0.0648-0.0524-0.00580.1809-0.00340.2373-0.01820.00780.196-0.00010.178258.3575-22.017313.6518
100.5340.27650.39210.07410.3531-0.0817-0.16170.563-0.5487-0.91310.102-0.22560.26130.3924-0.00030.37370.01510.09190.30090.00740.147955.8974-32.31745.5032
11-0.4699-0.5833-0.21750.24970.1468-0.41870.12190.1719-0.1298-0.3705-0.08120.00610.15020.180600.51450.0154-0.20140.26820.0180.345134.0757-7.8867-2.8656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resid 168:193A168 - 193
2X-RAY DIFFRACTION2chain A and resid 194:229A194 - 229
3X-RAY DIFFRACTION3chain A and resid 230:276A230 - 276
4X-RAY DIFFRACTION4chain A and resid 277:313A277 - 313
5X-RAY DIFFRACTION5chain A and resid 314:349A314 - 349
6X-RAY DIFFRACTION6chain A and resid 350:404A350 - 404
7X-RAY DIFFRACTION7chain A and resid 405:441A405 - 441
8X-RAY DIFFRACTION8chain A and resid 442:487A442 - 487
9X-RAY DIFFRACTION9chain A and resid 488:545A488 - 545
10X-RAY DIFFRACTION10chain A and resid 546:567A546 - 567
11X-RAY DIFFRACTION11chain BB1

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