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- PDB-3uvu: Structural basis of nuclear import of Flap endonuclease 1 (FEN1) -

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Basic information

Entry
Database: PDB / ID: 3uvu
TitleStructural basis of nuclear import of Flap endonuclease 1 (FEN1)
Components
  • Flap endonuclease 1 (Fen1) peptide
  • Importin subunit alpha-2
KeywordsPROTEIN BINDING/PEPTIDE / Fen 1 / Flap Endonuclease 1 / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / 5'-flap endonuclease activity / positive regulation of viral life cycle / UV protection / NLS-dependent protein nuclear import complex ...flap endonuclease activity / positive regulation of sister chromatid cohesion / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / 5'-flap endonuclease activity / positive regulation of viral life cycle / UV protection / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / 5'-3' exonuclease activity / nuclear import signal receptor activity / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / protein import into nucleus / cytoplasmic stress granule / RNA-DNA hybrid ribonuclease activity / double-strand break repair / host cell / manganese ion binding / double-stranded DNA binding / endonuclease activity / DNA-binding transcription factor binding / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / postsynaptic density / DNA repair / nucleolus / glutamatergic synapse / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / membrane / cytosol
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / PIN-like domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Flap endonuclease 1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.38 Å
AuthorsBarros, A.C. / Takeda, A.A.S. / Fontes, M.R.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural basis of nuclear import of flap endonuclease 1 (FEN1).
Authors: de Barros, A.C. / Takeda, A.A. / Chang, C.W. / Kobe, B. / Fontes, M.R.
History
DepositionNov 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jan 29, 2020Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3Feb 28, 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

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Assembly

Deposited unit
B: Flap endonuclease 1 (Fen1) peptide
A: Importin subunit alpha-2


Theoretical massNumber of molelcules
Total (without water)57,4382
Polymers57,4382
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint3 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.870, 89.561, 100.343
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Flap endonuclease 1 (Fen1) peptide / FEN-1 / DNase IV / Flap structure-specific endonuclease 1 / Maturation factor 1 / MF1 / hFEN-1


Mass: 2107.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P39748
#2: Protein Importin subunit alpha-2


Mass: 55330.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.08 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Sodium citrate, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2010
RadiationMonochromator: Double Flat Crystal Monochromator with Fixed-exit
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.38→40 Å / Num. all: 28970 / Num. obs: 28376 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 48.675 Å2 / Rmerge(I) obs: 0.105
Reflection shellResolution: 2.38→2.443 Å / Redundancy: 3 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 15.04 / Num. unique all: 28970 / % possible all: 98

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.38→36.71 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.923 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.213 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21508 1443 5.1 %RANDOM
Rwork0.16787 ---
all0.1703 28970 --
obs0.1703 26792 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.675 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.38→36.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3320 0 0 157 3477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0223378
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.9694605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1935442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.67525.772123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24115571
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7511511
X-RAY DIFFRACTIONr_chiral_restr0.130.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022471
X-RAY DIFFRACTIONr_nbd_refined0.2180.21718
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22362
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.26
X-RAY DIFFRACTIONr_mcbond_it1.181.52262
X-RAY DIFFRACTIONr_mcangle_it2.10323569
X-RAY DIFFRACTIONr_scbond_it3.40531245
X-RAY DIFFRACTIONr_scangle_it5.5274.51036
LS refinement shellResolution: 2.38→2.443 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 96 -
Rwork0.26 1728 -
obs--86.36 %

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