SAXSdb — 2z5v

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

Myeloid differentiation primary response protein MyD88

Homo sapiens

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 148–296	Fragment：MyD88 TIR domain	No other associated polymer	SOLUTION NMR NMR measurement conditions：298 K；Pressure 1	Resolution not provided

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 2Z5V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JS7 Solution NMR structure of human myeloid differentiation primary response (MyD88). Northeast Structural Genomics target HR2869A Deposited 2007-06-29	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 146–296（151 aa） Fragment：C-Terminal TIR domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；303 K；Pressure ambient NMR sample composition 0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 100% D2O \| 100% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
3MOP The ternary Death Domain complex of MyD88, IRAK4, and IRAK2 Deposited 2010-04-23	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain A 20–117（98 aa） Fragment：death domain residues 20-117 Chain B 20–117（98 aa） Fragment：death domain residues 20-117 Chain C 20–117（98 aa） Fragment：death domain residues 20-117 Chain D 20–117（98 aa） Fragment：death domain residues 20-117 Chain E 20–117（98 aa） Fragment：death domain residues 20-117 Chain F 20–117（98 aa） Fragment：death domain residues 20-117	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100-250 mM MgCl2, 8-15 % ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.40 Å R-free 0.261
4DOM Crystal Structure of the TIR-domain of Human Myeloid Differentiation Primary Response protein (MyD88) Deposited 2012-02-09	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 157–296（140 aa） Fragment：TIR domain, UNP residues 157-296	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；pH 8；277 K；30% PEG 8000, 0.1M Immidazole pH 8.0, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.80 Å R-free 0.216
4EO7 Crystal structure of the TIR domain of human myeloid differentiation primary response protein 88. Deposited 2012-04-13	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 157–296（140 aa） 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
7BEQ MicroED structure of the MyD88 TIR domain higher-order assembly Deposited 2020-12-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 155–296（142 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å R-free 0.280
7BER SFX structure of the MyD88 TIR domain higher-order assembly (solved, rebuilt and refined using an identical protocol to the MicroED structure of the MyD88 TIR domain higher-order assembly) Deposited 2020-12-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 155–296（142 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；310 K；MAL TIR (0.5-3 mM) incubated with MyD88 TIR (60-100 mM) in 10 mM HEPES pH 7.5-8, 150 mM NaCl at 310K	Resolution 2.30 Å R-free 0.281
7L6W SFX structure of the MyD88 TIR domain higher-order assembly Deposited 2020-12-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 159–296（138 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；310 K；MAL TIR (0.5-3 micromolar) was incubated with MyD88 TIR domain (60-100 micromolar) in 10 millimolar HEPES at pH 7.5-8, 150 millimolar NaCl at 298-310K.	Resolution 2.30 Å R-free 0.288
8S78 MicroED Structure of TLR2 TIR domain-induced MyD88 TIR domain higher-order assembly Deposited 2024-02-29	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 154–296（143 aa）	Not recorded	No recorded non-water small molecule	ELECTRON CRYSTALLOGRAPHY cryo-EM buffer pH 7.5；TLR2 TIR protein, 10 mM HEPES pH 7.5, 150 mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å R-free 0.267
8W8M Cryo-EM structure of helical filament of MyD88 TIR Deposited 2023-09-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 102 PDB declaration: 102-meric	Chain 1A 153–296（144 aa） Chain 1B 153–296（144 aa） Chain 1C 153–296（144 aa） Chain 1D 153–296（144 aa） Chain 1E 153–296（144 aa） Chain 1F 153–296（144 aa） Chain 2A 153–296（144 aa） Chain 2B 153–296（144 aa） Chain 2C 153–296（144 aa） Chain 2D 153–296（144 aa） Chain 2E 153–296（144 aa） Chain 2F 153–296（144 aa） Chain 3A 153–296（144 aa） Chain 3B 153–296（144 aa） Chain 3C 153–296（144 aa） Chain 3D 153–296（144 aa） Chain 3E 153–296（144 aa） Chain 3F 153–296（144 aa） Chain A1 153–296（144 aa） Chain A2 153–296（144 aa） Chain A3 153–296（144 aa） Chain B1 153–296（144 aa） Chain B2 153–296（144 aa） Chain B3 153–296（144 aa） Chain C1 153–296（144 aa） Chain C2 153–296（144 aa） Chain C3 153–296（144 aa） Chain D1 153–296（144 aa） Chain D2 153–296（144 aa） Chain D3 153–296（144 aa） Chain E1 153–296（144 aa） Chain E2 153–296（144 aa） Chain E3 153–296（144 aa） Chain F1 153–296（144 aa） Chain F2 153–296（144 aa） Chain F3 153–296（144 aa） Chain G1 153–296（144 aa） Chain G2 153–296（144 aa） Chain G3 153–296（144 aa） Chain H1 153–296（144 aa） Chain H2 153–296（144 aa） Chain H3 153–296（144 aa） Chain I1 153–296（144 aa） Chain I2 153–296（144 aa） Chain I3 153–296（144 aa） Chain J1 153–296（144 aa） Chain J2 153–296（144 aa） Chain J3 153–296（144 aa） Chain K1 153–296（144 aa） Chain K2 153–296（144 aa） Chain K3 153–296（144 aa） Chain L1 153–296（144 aa） Chain L2 153–296（144 aa） Chain L3 153–296（144 aa） Chain M1 153–296（144 aa） Chain M2 153–296（144 aa） Chain M3 153–296（144 aa） Chain N1 153–296（144 aa） Chain N2 153–296（144 aa） Chain N3 153–296（144 aa） Chain O1 153–296（144 aa） Chain O2 153–296（144 aa） Chain O3 153–296（144 aa） Chain P1 153–296（144 aa） Chain P2 153–296（144 aa） Chain P3 153–296（144 aa） Chain Q1 153–296（144 aa） Chain Q2 153–296（144 aa） Chain Q3 153–296（144 aa） Chain R1 153–296（144 aa） Chain R2 153–296（144 aa） Chain R3 153–296（144 aa） Chain S1 153–296（144 aa） Chain S2 153–296（144 aa） Chain S3 153–296（144 aa） Chain T1 153–296（144 aa） Chain T2 153–296（144 aa） Chain T3 153–296（144 aa） Chain U1 153–296（144 aa） Chain U2 153–296（144 aa） Chain U3 153–296（144 aa） Chain V1 153–296（144 aa） Chain V2 153–296（144 aa） Chain V3 153–296（144 aa） Chain W1 153–296（144 aa） Chain W2 153–296（144 aa） Chain W3 153–296（144 aa） Chain X1 153–296（144 aa） Chain X2 153–296（144 aa） Chain X3 153–296（144 aa） Chain Y1 153–296（144 aa） Chain Y2 153–296（144 aa） Chain Y3 153–296（144 aa） Chain YD 153–296（144 aa） Chain YE 153–296（144 aa） Chain YF 153–296（144 aa） Chain Z1 153–296（144 aa） Chain Z2 153–296（144 aa） Chain Z3 153–296（144 aa） Chain ZD 153–296（144 aa） Chain ZE 153–296（144 aa） Chain ZF 153–296（144 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.28 Å
8YYM Cryo-EM structure of cylindrical fiber of MyD88 TIR Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 104 PDB declaration: 104-meric	Chain A 153–296（144 aa） Chain AA 153–296（144 aa） Chain AB 153–296（144 aa） Chain AC 153–296（144 aa） Chain B 153–296（144 aa） Chain BA 153–296（144 aa） Chain BB 153–296（144 aa） Chain BC 153–296（144 aa） Chain C 153–296（144 aa） Chain CA 153–296（144 aa） Chain CB 153–296（144 aa） Chain CC 153–296（144 aa） Chain D 153–296（144 aa） Chain DA 153–296（144 aa） Chain DB 153–296（144 aa） Chain DC 153–296（144 aa） Chain E 153–296（144 aa） Chain EA 153–296（144 aa） Chain EB 153–296（144 aa） Chain EC 153–296（144 aa） Chain F 153–296（144 aa） Chain FA 153–296（144 aa） Chain FB 153–296（144 aa） Chain FC 153–296（144 aa） Chain G 153–296（144 aa） Chain GA 153–296（144 aa） Chain GB 153–296（144 aa） Chain GC 153–296（144 aa） Chain H 153–296（144 aa） Chain HA 153–296（144 aa） Chain HB 153–296（144 aa） Chain HC 153–296（144 aa） Chain I 153–296（144 aa） Chain IA 153–296（144 aa） Chain IB 153–296（144 aa） Chain IC 153–296（144 aa） Chain J 153–296（144 aa） Chain JA 153–296（144 aa） Chain JB 153–296（144 aa） Chain JC 153–296（144 aa） Chain K 153–296（144 aa） Chain KA 153–296（144 aa） Chain KB 153–296（144 aa） Chain KC 153–296（144 aa） Chain L 153–296（144 aa） Chain LA 153–296（144 aa） Chain LB 153–296（144 aa） Chain LC 153–296（144 aa） Chain M 153–296（144 aa） Chain MA 153–296（144 aa） Chain MB 153–296（144 aa） Chain MC 153–296（144 aa） Chain N 153–296（144 aa） Chain NA 153–296（144 aa） Chain NB 153–296（144 aa） Chain NC 153–296（144 aa） Chain O 153–296（144 aa） Chain OA 153–296（144 aa） Chain OB 153–296（144 aa） Chain OC 153–296（144 aa） Chain P 153–296（144 aa） Chain PA 153–296（144 aa） Chain PB 153–296（144 aa） Chain PC 153–296（144 aa） Chain Q 153–296（144 aa） Chain QA 153–296（144 aa） Chain QB 153–296（144 aa） Chain QC 153–296（144 aa） Chain R 153–296（144 aa） Chain RA 153–296（144 aa） Chain RB 153–296（144 aa） Chain RC 153–296（144 aa） Chain S 153–296（144 aa） Chain SA 153–296（144 aa） Chain SB 153–296（144 aa） Chain SC 153–296（144 aa） Chain T 153–296（144 aa） Chain TA 153–296（144 aa） Chain TB 153–296（144 aa） Chain TC 153–296（144 aa） Chain U 153–296（144 aa） Chain UA 153–296（144 aa） Chain UB 153–296（144 aa） Chain UC 153–296（144 aa） Chain V 153–296（144 aa） Chain VA 153–296（144 aa） Chain VB 153–296（144 aa） Chain VC 153–296（144 aa） Chain W 153–296（144 aa） Chain WA 153–296（144 aa） Chain WB 153–296（144 aa） Chain WC 153–296（144 aa） Chain X 153–296（144 aa） Chain XA 153–296（144 aa） Chain XB 153–296（144 aa） Chain XC 153–296（144 aa） Chain Y 153–296（144 aa） Chain YA 153–296（144 aa） Chain YB 153–296（144 aa） Chain YC 153–296（144 aa） Chain Z 153–296（144 aa） Chain ZA 153–296（144 aa） Chain ZB 153–296（144 aa） Chain ZC 153–296（144 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9HFV MyD88 peptide_2 bound to SPOP MATH domain Deposited 2024-11-18	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 127–146（20 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20,000, 20% v/v PEG MME 550, 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M MOPS/HEPES-Na pH 7.5	Resolution 1.45 Å R-free 0.214
9HGH MyD88 peptide_1 bound to SPOP MATH domain Deposited 2024-11-19	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 125–141（17 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M diethyleneglycol, 0.03 M triethyleneglycol, 0.03 M tetraethyleneglycol, 0.03 M pentaethyleneglycol, 0.1 M bicine/Trizma base pH 8.5	Resolution 1.90 Å R-free 0.232

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 1–149； UniProt 148–296

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2z5v
Deposition date deposition_date	2007-07-19
Structure title title	Solution structure of the TIR domain of human MyD88
Keywords keywords	signal transduction innate immunity, Cytoplasm, Immune response, Inflammatory response, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	15.03 Å
Radius of gyration Rg (electron density) rg_electron	14.62 Å
Forward intensity I(0) i0	1431500000.00
Molecular weight molecular_weight	331150.0 kDa
Excluded volume excluded_volume	418350 Å³
Envelope volume envelope_volume	35485 Å³
Hydration-shell volume shell_volume	17738 Å³
Envelope diameter envelope_diameter	49.6 Å
Shell Rg shell_rg	22.91 Å
Envelope Rg envelope_rg	16.51 Å
Shape Rg shape_rg	14.62 Å
Total Rg total_rg	14.74 Å
Total atoms total_atoms	46720
Residues n_residues	2820
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	44.3 Å
Rg (real space) rg_real	14.89 Å
Rg uncertainty (real space) rg_real_error	0.18 Å
I(0) (real space) i0_real	1.4320e+09
I(0) uncertainty (real space) i0_real_error	1.2560e+07
Rg (reciprocal space) rg_reciprocal	14.90 Å
I(0) (reciprocal space) i0_reciprocal	1432000000.0000
Solution quality estimate total_estimate	0.9010
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.3 Å
Skewness Skewness skewness	-0.009
Kurtosis Kurtosis kurtosis	-0.455
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	647400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2z5va_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.2 — Toll/Interleukin receptor TIR domain
Family Family family	c.23.2.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2z5vA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10140 — Toll/interleukin-1 receptor homology (TIR) domain

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8. Citations (1)

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Description description	Myeloid differentiation primary response protein MyD88
Molecular weight formula_weight	17387.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	46720

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/z5/2z5v/2z5v.fit
pddf	/app/data/pr_computation/z5/2z5v/2z5v.pr.out
profile	/app/data/saxs_computation/z5/2z5v/2z5v.dat

Solution structure of the TIR domain of human MyD88

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

Myeloid differentiation primary response protein MyD88

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)