1rf3

Structurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling

Method: X-RAY DIFFRACTION Dmax: 83.8 Å Quality: REASONABLE

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

TNF receptor associated factor 3

Homo sapiens

UniProt Q13114

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 377–568 Fragment:Recognition motif (residues 377-568) 24-residue peptide from Lymphotoxin-B Receptor × 3 (P36941) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;15% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.50 Å R-free 0.315

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.

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRAF3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–192; UniProt 377–568

24-residue peptide from Lymphotoxin-B Receptor

OrganismNot specified

UniProt P36941

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 × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 385–408 Fragment:Recognition motif (residues 385-408) TNF receptor associated factor 3 × 3 (Q13114) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;294 K;15% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K Resolution 3.50 Å R-free 0.315

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.

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TNR3_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–24; UniProt 385–408

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 1rf3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1rf3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1rf3
Deposition date deposition_date2003-11-07
Structure title titleStructurally Distinct Recognition Motifs in Lymphotoxin-B Receptor and CD40 for TRAF-mediated Signaling
Keywords keywordsCD40, NF-KB signaling, LTBR, TNF receptor, TRAF3 crystallography, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier21.37
Radius of gyration Rg (electron density) rg_electron20.79
Forward intensity I(0) i010546800.00
Molecular weight molecular_weight24302.0 kDa
Excluded volume excluded_volume30491 ų
Envelope volume envelope_volume38579 ų
Hydration-shell volume shell_volume17073 ų
Envelope diameter envelope_diameter86.1
Shell Rg shell_rg24.93
Envelope Rg envelope_rg21.59
Shape Rg shape_rg20.76
Total Rg total_rg21.53
Total atoms total_atoms1709
Residues n_residues216
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 dmax83.8
Rg (real space) rg_real21.67
Rg uncertainty (real space) rg_real_error1.05
I(0) (real space) i0_real1.0550e+07
I(0) uncertainty (real space) i0_real_error1.7440e+05
Rg (reciprocal space) rg_reciprocal21.61
I(0) (reciprocal space) i0_reciprocal10550000.0000
Solution quality estimate total_estimate0.7492
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.2
Skewness Skewness skewness0.777
Kurtosis Kurtosis kurtosis0.574
Angular range angular_range— – 0.3700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1552000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.407; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.531; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1rf3a1
Class classb — All beta proteins
Fold Fold foldb.8 — TRAF domain-like
Superfamily Superfamily superfamilyb.8.1 — TRAF domain-like
Family Family familyb.8.1.1 — MATH domain
Domain ID domain_idd1rf3a2
Class classh — Coiled coil proteins
Fold Fold foldh.1 — Parallel coiled-coil
Superfamily Superfamily superfamilyh.1.2 — Trimerization domain of TRAF
Family Family familyh.1.2.1 — Trimerization domain of TRAF
Domain ID domain_idd1rf3b_
Class classj — Peptides
Fold Fold foldj.116 — Fragments of TNF receptors
Superfamily Superfamily superfamilyj.116.1 — Fragments of TNF receptors
Family Family familyj.116.1.1 — Fragments of TNF receptors

CATH v4.4 (1 domains)

Domain ID domain_id1rf3A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A

8. Citations (1)

9. Files and Curves (10)