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- PDB-3k62: Crystal structure of FBF-2/gld-1 FBEb complex -

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Basic information

Entry
Database: PDB / ID: 3k62
TitleCrystal structure of FBF-2/gld-1 FBEb complex
Components
  • 5'-R(*UP*GP*UP*GP*UP*UP*AP*UP*C)-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 / 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: 1.9 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)49,7732
Polymers49,7732
Non-polymers00
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-10 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.620, 96.620, 101.678
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*GP*UP*UP*AP*UP*C)-3'


Mass: 2810.671 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.75 Å3/Da / Density % sol: 55.32 %
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: 1.9→27.8918 Å / Num. obs: 42208 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 24.688 Å2 / Rsym value: 0.083 / Net I/σ(I): 28.4
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1970 / Rsym value: 0.807 / % possible all: 93.5

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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: 1.9→27.8918 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 2120 -R-free selection was copied from the structure factor file of PDB ENTRY 3K5Q
Rwork0.1584 ---
obs-42208 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→27.8918 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 185 0 417 3784
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.722
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)
1-0.21820.96760.02031.03031.37483.80410.2303-0.7429-0.61491.16490.2310.08130.80150.35221.09450.4619-0.05550.11810.25720.24320.263621.95582.514329.5966
20.32390.2240.02420.5864-0.50630.75440.176-0.1885-0.11230.2070.14080.10290.0354-0.07190.00020.20370.0322-0.01770.18350.02740.250728.58197.796720.1323
30.2632-0.11151.27480.8501-0.73481.95780.10070.0427-0.2946-0.11260.05050.05210.0820.1845-00.18840.0159-0.03350.1699-0.02270.212830.5458.87138.1718
40.3801-0.61440.25670.5784-1.15450.41290.1445-0.1141-0.196-0.08980.01160.11020.16710.125700.17080.0436-0.03730.186-0.0210.182726.746615.7336-1.0278
50.9535-0.72230.84030.7077-0.62450.54810.23870.0803-0.2671-0.09920.00890.17290.08590.11610.00290.12190.0277-0.02870.17960.00890.158923.942722.4756-8.2138
61.325-0.76860.3291.5273-0.9444-0.12480.18350.30860.1101-0.0947-0.03460.1957-0.02080.04470.00590.12350.03840.00250.24020.02980.130425.012632.0339-13.0817
70.5984-1.4044-0.37671.4039-0.5725-0.5590.20610.0862-0.1394-0.2732-0.1279-0.0206-0.02430.09060.00110.16140.05060.02920.22640.06190.20616.545441.2171-16.4495
80.8818-0.7753-0.5431.8106-0.40120.13270.07170.08350.0355-0.4559-0.08660.00310.15950.0537-00.2260.03760.03330.18310.04720.15917.549452.1106-19.8223
91.145-0.6035-0.12782.0867-0.78751.2419-0.0283-0.12080.193-0.0347-0.0837-0.0716-0.07670.2049-00.15250.00120.00980.17260.02450.10999.914261.2483-13.8073
100.25830.2044-0.41780.2567-0.25970.37330.0026-0.53040.17070.1839-0.04360.1851-0.45340.06-00.2756-0.0033-0.01530.2961-0.00390.143-0.01964.0343-5.4857
11-0.3139-0.62810.4489-0.3049-0.4539-0.8152-0.2126-0.163-0.09410.27660.12820.1066-0.06410.0817-0.00350.37340.15520.0720.32680.14220.282310.123433.31982.3739
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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