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- PDB-3k5y: Crystal structure of FBF-2/gld-1 FBEa complex -

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Basic information

Entry
Database: PDB / ID: 3k5y
TitleCrystal structure of FBF-2/gld-1 FBEa complex
Components
  • 5'-R(*UP*GP*UP*GP*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 / 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: 2.3 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*CP*CP*AP*UP*A)-3'


Theoretical massNumber of molelcules
Total (without water)49,7952
Polymers49,7952
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.226, 97.226, 101.275
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 / 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*CP*CP*AP*UP*A)-3'


Mass: 2832.727 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.77 Å3/Da / Density % sol: 55.68 %
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: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.613 Å / Num. obs: 24164 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Biso Wilson estimate: 42.613 Å2 / Rsym value: 0.112 / Net I/σ(I): 22
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1210 / Rsym value: 0.75 / % 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: 2.3→48.613 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2151 1237 -Rfree selection was copied from the structure factor file of PDB ENTRY 3K5Q
Rwork0.1712 ---
obs-24164 99.95 %-
Refinement stepCycle: LAST / Resolution: 2.3→48.613 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 187 0 97 3466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.668
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)
10.65811.1987-0.66070.7949-0.34820.67380.0388-0.89991.24391.14970.6071-0.1816-0.72210.0130.05980.66190.0498-0.09160.6134-0.4670.5409-22.2981-2.928726.8911
20.89630.097-0.28420.66790.53571.34890.2083-0.11190.3294-0.14730.1353-0.1548-0.10270.10710.00040.33350.02770.1030.3304-0.08930.4318-28.8836-8.102717.2102
30.0198-0.5394-1.02961.20942.04613.00330.20050.00630.3378-0.22260.0554-0.2322-0.4698-0.2034-0.00030.32040.06360.10050.27410.05480.3663-30.7185-9.01615.3015
40.3217-0.56160.00511.29842.12250.83510.4516-0.25230.3136-0.3811-0.0521-0.0502-0.5886-0.32340.00010.3160.08060.08710.28940.02220.3039-26.9325-15.9064-3.8609
50.5561-1.0565-0.4241.14580.74321.1170.31090.00050.3442-0.06640.0445-0.2531-0.2917-0.12690.00020.23330.04110.06750.31240.00980.2929-24.2228-22.7083-10.9806
61.3852-0.4135-0.77971.83981.35250.81720.36480.2811-0.0424-0.0495-0.1363-0.2218-0.0174-0.0684-0.00010.25010.0680.02440.3585-0.01260.2397-25.3277-32.2672-15.7701
70.5342-2.0844-0.00351.98131.1748-0.05330.30930.04220.2408-0.2492-0.17430.0342-0.089-0.1323-0.00040.27020.0565-0.02530.3207-0.0680.3272-16.8384-41.4922-19.134
81.831-0.36470.83542.3919-0.3030.4290.13540.2897-0.1154-0.4479-0.0083-0.11640.01650.0953-00.33120.0525-0.04580.3061-0.09880.294-7.8874-52.3292-22.5438
91.24-0.85790.0382.12840.64091.539-0.1261-0.3179-0.15080.04340.07010.03140.108-0.1644-0.00060.22120.0112-0.00480.3129-0.01810.2536-10.252-61.458-16.6727
100.37770.49510.25750.37910.22430.5312-0.0532-0.5091-0.91670.12330.0077-0.73080.5592-0.3474-0.00010.49120.0269-0.01910.51740.00530.4011-0.0353-64.6408-8.4652
110.1169-0.8419-0.12940.2027-1.13760.1202-0.4088-0.2980.06970.87110.6798-0.41060.27640.1660.00060.56630.1807-0.07850.6028-0.21710.4856-10.2051-33.288-0.2221
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 - 4

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