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- PDB-3k5q: Crystal structure of FBF-2/FBE complex -

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Basic information

Entry
Database: PDB / ID: 3k5q
TitleCrystal structure of FBF-2/FBE complex
Components
  • 5'-R(P*UP*GP*UP*AP*CP*UP*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 / SAD / Resolution: 2.2 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 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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(P*UP*GP*UP*AP*CP*UP*AP*UP*A)-3'


Theoretical massNumber of molelcules
Total (without water)49,7802
Polymers49,7802
Non-polymers00
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-8 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.803, 98.803, 103.039
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 included between GST and FBF-2.
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: F21H12.5, fbf-2, FBF-2 (AMINO ACIDS 164-575) / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q09312
#2: RNA chain 5'-R(P*UP*GP*UP*AP*CP*UP*AP*UP*A)-3'


Mass: 2817.711 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Bicine pH 9.0, 2% 1,4-Dioxane, 10% polyethylene glycol 20,000, and 10 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID10.97937
SYNCHROTRONAPS 22-ID21
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 26, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
211
ReflectionResolution: 2.2→30.8567 Å / Num. obs: 28976 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Biso Wilson estimate: 31.067 Å2 / Rsym value: 0.097 / Net I/σ(I): 24.1
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.789 / % possible all: 100

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Processing

Software
NameVersionClassification
SERGUIfrom SER-CATdata collection
APSdata collection
SOLVEphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30.8567 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 1481 -RANDOM
Rwork0.1582 ---
obs-28976 99.9 %-
Solvent computationBsol: 35.409 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso mean: 40.81 Å2
Baniso -1Baniso -2Baniso -3
1--4.068 Å20 Å20 Å2
2---4.068 Å20 Å2
3---8.137 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.8567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 189 0 247 3618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.678
X-RAY DIFFRACTIONf_dihedral_angle_d10.077
X-RAY DIFFRACTIONf_chiral_restr0.046
X-RAY DIFFRACTIONf_plane_restr0.003
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)
10.0380.03810.651.0029-1.05451.23530.0168-0.58640.13480.59060.27530.0384-0.73710.17180.15540.3441-0.0371-0.06270.4844-0.23890.2829-22.0619-3.85430.858
20.58260.4292-0.26790.49160.45480.64320.0526-0.0779-0.0730.03340.17-0.2589-0.1540.028-00.23610.00810.03980.2323-0.08980.2537-29.0531-8.97621.5578
30.2965-0.5973-0.48690.9191.3161.5450.139-0.18920.304-0.16550.2926-0.2022-0.2278-0.04570.01630.2806-0.03440.10170.2309-0.06320.3113-31.5245-9.67639.5468
40.2928-0.4105-0.43160.81751.20191.42730.2025-0.18190.3621-0.2880.2062-0.2243-0.3266-0.06910.14870.2519-0.01450.11380.2308-0.10910.3064-28.1234-16.47830.1872
50.5616-0.2026-0.37490.67781.08160.42130.1939-0.03140.3268-0.14930.0733-0.0024-0.2019-0.01730.01990.23470.00080.06940.2184-0.08720.2545-25.7939-23.5409-6.8478
61.2132-1.04240.01391.2991.05890.07130.2718-0.0616-0.0291-0.16110.0367-0.0817-0.12380.03310.0290.2128-0.00320.02620.2481-0.08140.1836-26.8709-33.0511-11.7043
70.7832-1.84410.38741.10480.5351-0.35240.2042-0.08150.2879-0.1767-0.02390.043-0.0661-0.01510.00060.18380.0361-0.01440.2025-0.06750.1865-18.344-42.4351-14.9851
80.6454-0.4236-0.26071.08580.4948-0.1762-0.066-0.01480.0495-0.4260.081-0.141-0.1829-0.08420.00030.21220.01270.02710.1889-0.07860.174-9.1355-52.5346-18.5249
90.6619-0.50750.23662.55880.51980.4284-0.1348-0.2194-0.06570.09950.18380.05490.21950.0105-00.2128-0.00660.00690.24130.00040.205-11.231-62.2369-12.7452
100.19130.1006-0.00130.37990.2781-0.12270.2191-0.5011-0.58440.3520.0499-0.57820.16460.1476-0.00030.31040.0442-0.02010.37730.02170.284-1.0076-65.1521-4.8384
11-0.3599-0.324-0.8805-0.0728-0.6104-0.3929-0.0075-0.37370.28780.27980.2387-0.28390.0110.0686-00.34710.1041-0.06530.485-0.26620.42-11.2487-34.6393.8423
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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