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- PDB-3k64: Crystal structure of FBF-2/fem-3 PME complex -

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Basic information

Entry
Database: PDB / ID: 3k64
TitleCrystal structure of FBF-2/fem-3 PME complex
Components
  • 5'-R(*UP*GP*UP*GP*UP*CP*AP*UP*U)-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 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*GP*UP*CP*AP*UP*U)-3'


Theoretical massNumber of molelcules
Total (without water)49,7732
Polymers49,7732
Non-polymers00
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-11 kcal/mol
Surface area19780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.675, 96.675, 101.542
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*CP*AP*UP*U)-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.: 495 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
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→26.3201 Å / Num. obs: 36362 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 22.919 Å2 / Rsym value: 0.118 / Net I/σ(I): 23.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 1849 / Rsym value: 0.838 / % possible all: 100

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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→26.3201 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1913 1845 -R-free selection was copied from the structure factor file of PDB ENTRY 3K5Q
Rwork0.1525 ---
obs-36362 99.9 %-
Refinement stepCycle: LAST / Resolution: 2→26.3201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 185 0 495 3862
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_deg0.639
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)
10.3875-0.60790.18680.38030.442.80320.23270.70770.542-1.06060.32110.488-0.4049-0.04791.19380.4280.0124-0.12190.33130.22090.325822.0054-2.5161-30.5641
20.2438-0.0442-0.23920.2861-0.30940.34170.10910.20240.0881-0.10710.12280.1007-0.0513-00.00010.1381-0.02720.01980.12530.01690.162728.6507-7.7959-21.0556
30.03410.0324-0.74920.5443-0.72421.7640.09970.00580.18170.10520.02910.0656-0.10250.1284-00.1437-0.01240.03330.1232-0.01630.152330.6284-8.8459-9.1541
40.26970.4716-0.31060.2763-1.00990.2880.11140.06280.10980.13240.05220.0571-0.16060.1194-00.1454-0.04530.03720.1644-0.01390.158326.8079-15.76350.081
50.70770.622-0.61930.4285-0.68780.40820.2017-0.05620.22680.0872-00.1312-0.02060.09760.00350.1118-0.0250.02370.15370.00260.146323.9834-22.51837.2297
61.04060.8903-0.33280.9744-0.76760.27330.1745-0.2767-0.02560.0897-0.07050.1179-0.01980.05530.00010.1123-0.0405-0.01220.18890.02350.094525.0293-32.030112.0864
70.43730.89790.0490.8752-0.5801-0.18980.133-0.03540.13390.1881-0.1-0.0421-0.00050.0485-00.1184-0.0441-0.02810.17490.04130.156216.5577-41.211615.4695
80.61390.65830.43411.4509-0.1336-0.00750.062-0.0812-0.03090.3723-0.043-0.0003-0.07790.0813-00.1921-0.0314-0.03940.14490.04310.1457.5585-52.085118.8387
90.69580.38190.03761.1956-0.50090.8817-0.03420.0836-0.11210.0218-0.0444-0.0470.09230.2135-00.12270.0103-0.00640.14460.02030.11019.9184-61.26212.8197
100.57360.03260.14160.3288-0.24140.3867-0.04140.4973-0.0102-0.17470.07240.17520.3852-0.07710.00780.21610.0034-0.00380.1902-0.0150.0863-0.1385-64.11944.5358
110.05850.4104-0.3064-0.1746-0.1909-0.6751-0.14110.08440.1861-0.34410.15380.25770.14020.1028-00.3169-0.1296-0.05160.260.09360.212110.1506-33.2661-3.3772
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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