1w0t

hTRF1 DNA-binding domain in complex with telomeric DNA.

Method: X-RAY DIFFRACTION Dmax: 68.4 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

TELOMERIC REPEAT BINDING FACTOR 1

HOMO SAPIENS

UniProt P54274

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric(4) Consistent with all polymer counts Chain A; UniProt 379–431 Chain B; UniProt 379–431 Fragment:DNA-BINDING DOMAIN, RESIDUES 379-431 ;5'-D(*CP*TP*GP*TP*TP*AP*GP*GP*GP*TP *TP*AP*GP*GP*GP*TP*TP*AP*G)-3' ; × 1 ;5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP *AP*CP*CP*CP*TP*AP*AP*CP*A)-3' ; × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;PROTEIN WAS CRYSTALLISED IN 50 MM MES, PH 6.0, 0.1 M KCL, 2 MM MGCL2 AND 10 % PEG 400 AND CRYOPROTECTED IN 20 % GLYCEROL Resolution 2.00 Å R-free 0.273

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

57 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–53; UniProt 379–431 Author chain B; PDBConstruct 1–53; UniProt 379–431

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1w0t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w0t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w0t
Deposition date deposition_date2004-06-11
Structure title titlehTRF1 DNA-binding domain in complex with telomeric DNA.
Keywords keywords;TELOMERE, DNA-BINDING PROTEIN, HOMEODOMAIN, MITOSIS, CELL CYCLE, NUCLEAR PROTEIN, CHROMOSOMAL PROTEIN, PHOSPHORYLATION, ADP-RIBOSYLATION, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.04
Radius of gyration Rg (electron density) rg_electron19.87
Forward intensity I(0) i017506900.00
Molecular weight molecular_weight24602.0 kDa
Excluded volume excluded_volume27666 ų
Envelope volume envelope_volume35679 ų
Hydration-shell volume shell_volume15828 ų
Envelope diameter envelope_diameter68.4
Shell Rg shell_rg24.91
Envelope Rg envelope_rg20.05
Shape Rg shape_rg19.85
Total Rg total_rg20.48
Total atoms total_atoms1687
Residues n_residues142
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax68.4
Rg (real space) rg_real20.11
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real1.7510e+07
I(0) uncertainty (real space) i0_real_error2.3540e+05
Rg (reciprocal space) rg_reciprocal20.10
I(0) (reciprocal space) i0_reciprocal17510000.0000
Solution quality estimate total_estimate0.8743
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.5
Skewness Skewness skewness0.410
Kurtosis Kurtosis kurtosis-0.391
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2326000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 0.993

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1w0ta_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.4 — DNA-binding domain of telomeric protein
Domain ID domain_idd1w0tb_
Class classa — All alpha proteins
Fold Fold folda.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamilya.4.1 — Homeodomain-like
Family Family familya.4.1.4 — DNA-binding domain of telomeric protein

CATH v4.4 (2 domains)

Domain ID domain_id1w0tA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id1w0tB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like

8. Citations (1)

9. Files and Curves (10)