← Back to search
6j07

Crystal structure of human TERB2 and TERB1

Method: X-RAY DIFFRACTION Dmax: 47.2 Å Quality: REASONABLE
▼

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

Telomere repeats-binding bouquet formation protein 2

Homo sapiens

UniProt Q8NHR7

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 4–110 Fragment：NTD domain Telomere repeats-binding bouquet formation protein 1 × 1 （Q8NA31） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 9；291 K；0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 4% (w/v) Polyethylene glycol 20000 Resolution 3.30 Å R-free 0.337

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.

Other PDB Difference from Current Entry 6J07 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6GNX Crystal structure of the MAJIN-TERB2 heterotetrameric complex - selenomethionine derivative Deposited 2018-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 169–220（52 aa）
Chain D 169–220（52 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol, 55.5 mM MES pH 3.11, 44.5 mM imidazole pH 10.23; 12.5% w/v PEG 1000; 12.5% w/v PEG 3350; 12.5% v/v MPD
Resolution 2.90 Å R-free 0.304
6GNY Crystal structure of the MAJIN-TERB2 heterotetrameric complex Deposited 2018-06-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 168–207（40 aa）
Chain D 168–207（40 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12M 1,6-Hexanediol; 0.12M 1-Butanol; 0.12M 1,2-Propanediol (racemic); 0.12M 2-Propanol; 0.12M 1,4-Butanediol; 0.12M 1,3-Propanediol; 39.1 mM bicine pH 5.03; 60.9 mM Trizma pH 10.83; 18.3% w/v PEG 1000; 18.3% w/v PEG 3350; 18.3% v/v MPD
Resolution 1.85 Å R-free 0.207
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 174–209（36 aa） Fragment：TERB2 binding motif
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol
Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 174–209（36 aa） Fragment：TERB2 binding motif
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol
Resolution 2.90 Å R-free 0.262
6J08 Crystal structure of human MAJIN and TERB2 Deposited 2018-12-21 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 174–209（36 aa） Fragment：TERB2 binding motif
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 6.8；291 K；100 mM HEPES pH 6.8, 0.2 M Potassium thiocyanate, 22% (w/v) Polyethylene glycol 3350, 25% (v/v) Glycerol
Resolution 2.90 Å R-free 0.262

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TERB2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–107； UniProt 4–110

Telomere repeats-binding bouquet formation protein 1

Homo sapiens

UniProt Q8NA31

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 590–649 Fragment：TERB2 binding motif Telomere repeats-binding bouquet formation protein 2 × 1 （Q8NHR7） ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：EVAPORATION；pH 9；291 K；0.1 M Bicine pH 9.0, 2% (v/v) 1,4-Dioxane, 4% (w/v) Polyethylene glycol 20000 Resolution 3.30 Å R-free 0.337

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.

Other PDB Difference from Current Entry 6J07 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5XUP Crystal structure of TRF1 and TERB1 Deposited 2017-06-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 644–655（12 aa） Fragment：TRF1 binding motif (UNP RESIDUES 644-655)
Chain D 644–655（12 aa） Fragment：TRF1 binding motif (UNP RESIDUES 644-655)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；10% 2-propanol, 0.1M Tris-HCl
Resolution 2.10 Å R-free 0.221

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TERB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–60； UniProt 590–649

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 6j07

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6j07
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6j07
Deposition date deposition_date2018-12-21
Structure title titleCrystal structure of human TERB2 and TERB1
Keywords keywordstelomere, meiosis, protein-protein complex, nuclear envelope attachment, 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_guinier18.15 Å
Radius of gyration Rg (electron density) rg_electron17.42 Å
Forward intensity I(0) i07168600.00
Molecular weight molecular_weight19108.0 kDa
Excluded volume excluded_volume23817 ų
Envelope volume envelope_volume30016 ų
Hydration-shell volume shell_volume14999 ų
Envelope diameter envelope_diameter69.3 Å
Shell Rg shell_rg23.09 Å
Envelope Rg envelope_rg18.49 Å
Shape Rg shape_rg17.38 Å
Total Rg total_rg18.55 Å
Total atoms total_atoms2663
Residues n_residues167
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax47.2 Å
Rg (real space) rg_real17.22 Å
Rg uncertainty (real space) rg_real_error0.05 Å
I(0) (real space) i0_real6.8320e+06
I(0) uncertainty (real space) i0_real_error5.3370e+04
Rg (reciprocal space) rg_reciprocal18.17 Å
I(0) (reciprocal space) i0_reciprocal7169000.0000
Solution quality estimate total_estimate0.6843
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary21.1 Å
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.419
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha2.7830
Highest regularization parameter α highest_alpha945600.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.991; Stabil: 0.976; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)