SASDB79: Basic domain of human telomeric repeat-binding factor 2 (TRF2) in...

Basic information

• Entry: Database: SASBDB / ID: SASDB79

Sample

Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex

• Basic domain of telomeric repeat-binding factor 2 (protein), TRF2, Homo sapiens
• telomere DNA duplex (DNA)

Function / homology

Function:

axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / telomere capping / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / 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 nitric-oxide synthase activity / male germ cell nucleus / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / negative regulation of gene expression / protein-containing complex binding / positive regulation of gene expression / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus

Domain/homology:

Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / 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 / Homeobox-like domain superfamily

Component:

Telomeric repeat-binding factor 2

• Biological species: Homo sapiens (human)
• Citation: Date: 2017 Sep 13; Title: Basic domain of telomere guardian TRF2 reduces D-loop unwinding whereas Rap1 restores it; Authors: Nečasová I / Janoušková E / Klumpler T

Contact author

• Tomas Klumpler (CEITEC - Central European Institute of Technology, Masaryk University)

Models

• Model #1155: ; Type: dummy / Radius of dummy atoms: 2.25 A / Chi-square value: 1.061 / P-value: 0.955000; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Basic domain of human telomeric repeat-binding factor 2 (TRF2) in complex with telomeric DNA duplex; Specimen concentration: 2.9 mg/ml / Entity id: 569 / 570
• Buffer: Name: 20 mM Tris-HCl, 50 mM LiCl / pH: 7.5

Entity #569

Name: TRF2 / Type: protein
Description: Basic domain of telomeric repeat-binding factor 2
Formula weight: 4.587 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: Q15554
Sequence:

GPPGSMAGGG GSSDGSGRAA GRRASRSSGR ARRGRHEPGL GGPAERGAG

Entity #570

Type: DNA / Description: telomere DNA duplex / Formula weight: 10.522 / Num. of mol.: 1
Sequence:

GTTAGGGTTA GGGTTAGCAA TCCCAATCCC AATC

Experimental information

• Beam: Instrument name: CEITEC Rigaku BioSAXS-1000 / City: Brno / 国: Czech Republic / Type of source: X-ray in house / Wavelength: 0.154 Å / Dist. spec. to detc.: 0.4791 mm
• Detector: Name: Pilatus 100K / Pixsize x: 172 mm

Scan

Title: Basic domain of human telomeric repeat-binding fac / Measurement date: May 3, 2016 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 3600 sec. / Number of frames: 6 / Unit: 1/A /

	Min	Max
Q	0.0311	0.3004

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 184 /

	Min	Max
Q	0.0368444	0.300399
P(R) point	1	184
R	0	59.46

Result

Type of curve: single_conc
Comments: The two-phase bead model of the protein-DNA complex was generated using MONSA refinement from SAXS data measured from the complex (top data-model fit) in parallel with data measured from the isolated telomeric DNA duplex (bottom data-model fit; refer to SASBDB entry SASDB89).

	Experimental	Porod
MW	15.1 kDa	-
Volume	-	20.3 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.2278	0.001668	0.22	0.0018
Radius of gyration, Rg	1.776 nm	0.017	1.711 nm	0.058

	Min	Max
D	-	5.95
Guinier point	5	32