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- PDB-3l82: X-ray Crystal structure of TRF1 and Fbx4 complex -

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Basic information

Entry
Database: PDB / ID: 3l82
TitleX-ray Crystal structure of TRF1 and Fbx4 complex
Components
  • F-box only protein 4
  • Telomeric repeat-binding factor 1
KeywordsCELL CYCLE / TRFH domain / helix / GTPase domain / ADP-ribosylation / Cell division / Chromosomal protein / Cytoskeleton / DNA-binding / Mitosis / Nucleus / Phosphoprotein / Telomere / Ubl conjugation pathway
Function / homology
Function and homology information


positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / positive regulation of protein polyubiquitination / meiotic telomere clustering / t-circle formation ...positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / positive regulation of protein polyubiquitination / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / common myeloid progenitor cell proliferation / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / telomere capping / Telomere C-strand (Lagging Strand) Synthesis / : / positive regulation of telomere maintenance / nuclear telomere cap complex / regulation of DNA damage checkpoint / ankyrin repeat binding / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / cellular homeostasis / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / negative regulation of protein localization to nucleus / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / SCF ubiquitin ligase complex / post-transcriptional regulation of gene expression / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / telomeric DNA binding / negative regulation of DNA replication / Association of TriC/CCT with target proteins during biosynthesis / negative regulation of telomere maintenance via telomerase / telomere maintenance via telomerase / Telomere Extension By Telomerase / ubiquitin-like ligase-substrate adaptor activity / Packaging Of Telomere Ends / ubiquitin ligase complex / negative regulation of fibroblast proliferation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / positive regulation of telomere maintenance via telomerase / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere maintenance / Meiotic synapsis / positive regulation of protein ubiquitination / cellular response to ionizing radiation / protein destabilization / regulation of protein stability / DNA Damage/Telomere Stress Induced Senescence / fibrillar center / spindle / protein polyubiquitination / ubiquitin-protein transferase activity / cellular senescence / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / microtubule binding / chromosome, telomeric region / nuclear body / protein ubiquitination / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
F-box only protein 4 / Telomere repeat-binding factor, dimerisation domain / : / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily ...F-box only protein 4 / Telomere repeat-binding factor, dimerisation domain / : / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / F-box domain / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Homeobox-like domain superfamily / Alpha Horseshoe / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Telomeric repeat-binding factor 1 / F-box only protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsZeng, Z.X. / Wang, W. / Yang, Y.T. / Chen, Y. / Yang, X.M. / Diehl, J.A. / Liu, X.D. / Lei, M.
CitationJournal: Dev.Cell / Year: 2010
Title: Structural Basis of Selective Ubiquitination of TRF1 by SCF(Fbx4)
Authors: Zeng, Z. / Wang, W. / Yang, Y. / Chen, Y. / Yang, X. / Diehl, J.A. / Liu, X. / Lei, M.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 25, 2013Group: Derived calculations
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 1
B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)50,9252
Polymers50,9252
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Telomeric repeat-binding factor 1

A: Telomeric repeat-binding factor 1

B: F-box only protein 4

B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)101,8494
Polymers101,8494
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
crystal symmetry operation6_545x+1/2,-y-1/2,-z+1/41
Buried area5720 Å2
ΔGint-47 kcal/mol
Surface area38580 Å2
MethodPISA
3
A: Telomeric repeat-binding factor 1

B: F-box only protein 4


Theoretical massNumber of molelcules
Total (without water)50,9252
Polymers50,9252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_544-y+1/2,x-1/2,z-1/41
Buried area1680 Å2
ΔGint-11 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.097, 68.097, 234.421
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Telomeric repeat-binding factor 1 / TTAGGG repeat-binding factor 1 / NIMA-interacting protein 2 / Telomeric protein Pin2/TRF1


Mass: 24946.230 Da / Num. of mol.: 1 / Fragment: Dimerization domain residues 58-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Plasmid: pGEX6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P54274
#2: Protein F-box only protein 4


Mass: 25978.363 Da / Num. of mol.: 1 / Fragment: F-box domain residues 162-387
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO4, FBX4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9UKT5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.2
Details: 300 mM NH4H2PO4, 100 mM sodium citrate pH 6.2, 10% n-propanol and 10 mM DTT, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9792, 0.9794
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 23, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97941
ReflectionResolution: 2.4→50 Å / Num. all: 21712 / Num. obs: 21197 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 54.3

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2634 3742 -
Rwork0.2374 --
all-41195 -
obs-19553 93.7 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.603 Å20 Å20 Å2
2---7.603 Å20 Å2
3---15.206 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 0 60 3137
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008023
X-RAY DIFFRACTIONc_angle_deg1.28514
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water.param

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