4eo7

Crystal structure of the TIR domain of human myeloid differentiation primary response protein 88.

Method: X-RAY DIFFRACTION Dmax: 54.7 Å Quality: GOOD

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

Myeloid differentiation primary response protein MyD88

Homo sapiens

UniProt Q99836

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 157–296 Fragment:TIR domain, UNP residues 157-296 Non-standard monomer:Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.5;277 K;25% PEG 3350, 0.1M BIS-TRIS pH 6.5,0.2M NaCl, VAPOR DIFFUSION, temperature 277K Resolution 1.45 Å R-free 0.208

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.

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MYD88_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–144; UniProt 157–296

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 4eo7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4eo7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4eo7
Deposition date deposition_date2012-04-13
Structure title titleCrystal structure of the TIR domain of human myeloid differentiation primary response protein 88.
Keywords keywords;Adapter Protein, toll like receptor, BETA-ALPHA-BETA FOLD, PARALLEL BETA SHEET, TIR-Domain, Innate immune signaling, Signaling protein, TIRAP/MAL, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier16.21
Radius of gyration Rg (electron density) rg_electron14.67
Forward intensity I(0) i05335280.00
Molecular weight molecular_weight16745.0 kDa
Excluded volume excluded_volume21117 ų
Envelope volume envelope_volume24573 ų
Hydration-shell volume shell_volume13944 ų
Envelope diameter envelope_diameter56.1
Shell Rg shell_rg20.84
Envelope Rg envelope_rg15.14
Shape Rg shape_rg14.65
Total Rg total_rg15.99
Total atoms total_atoms1171
Residues n_residues143
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 dmax54.7
Rg (real space) rg_real16.09
Rg uncertainty (real space) rg_real_error0.32
I(0) (real space) i0_real5.3350e+06
I(0) uncertainty (real space) i0_real_error7.0910e+04
Rg (reciprocal space) rg_reciprocal16.11
I(0) (reciprocal space) i0_reciprocal5335000.0000
Solution quality estimate total_estimate0.7766
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.7
Skewness Skewness skewness0.134
Kurtosis Kurtosis kurtosis-0.221
Angular range angular_range— – 0.4900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1427000.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4eo7a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.2 — Toll/Interleukin receptor TIR domain
Family Family familyc.23.2.0 — automated matches
Domain ID domain_idd4eo7a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id4eo7A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10140 — Toll/interleukin-1 receptor homology (TIR) domain

8. Citations (1)

9. Files and Curves (10)