SAXSdb — 8w8m

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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 homooligomer Homooligomer Protein × 102 PDB declaration: 102-meric（102） Consistent with protein copy count	Chain 1A； UniProt 153–296 Chain 1B； UniProt 153–296 Chain 1C； UniProt 153–296 Chain 1D； UniProt 153–296 Chain 1E； UniProt 153–296 Chain 1F； UniProt 153–296 Chain 2A； UniProt 153–296 Chain 2B； UniProt 153–296 Chain 2C； UniProt 153–296 Chain 2D； UniProt 153–296 Chain 2E； UniProt 153–296 Chain 2F； UniProt 153–296 Chain 3A； UniProt 153–296 Chain 3B； UniProt 153–296 Chain 3C； UniProt 153–296 Chain 3D； UniProt 153–296 Chain 3E； UniProt 153–296 Chain 3F； UniProt 153–296 Chain A1； UniProt 153–296 Chain A2； UniProt 153–296 Chain A3； UniProt 153–296 Chain B1； UniProt 153–296 Chain B2； UniProt 153–296 Chain B3； UniProt 153–296 Chain C1； UniProt 153–296 Chain C2； UniProt 153–296 Chain C3； UniProt 153–296 Chain D1； UniProt 153–296 Chain D2； UniProt 153–296 Chain D3； UniProt 153–296 Chain E1； UniProt 153–296 Chain E2； UniProt 153–296 Chain E3； UniProt 153–296 Chain F1； UniProt 153–296 Chain F2； UniProt 153–296 Chain F3； UniProt 153–296 Chain G1； UniProt 153–296 Chain G2； UniProt 153–296 Chain G3； UniProt 153–296 Chain H1； UniProt 153–296 Chain H2； UniProt 153–296 Chain H3； UniProt 153–296 Chain I1； UniProt 153–296 Chain I2； UniProt 153–296 Chain I3； UniProt 153–296 Chain J1； UniProt 153–296 Chain J2； UniProt 153–296 Chain J3； UniProt 153–296 Chain K1； UniProt 153–296 Chain K2； UniProt 153–296 Chain K3； UniProt 153–296 Chain L1； UniProt 153–296 Chain L2； UniProt 153–296 Chain L3； UniProt 153–296 Chain M1； UniProt 153–296 Chain M2； UniProt 153–296 Chain M3； UniProt 153–296 Chain N1； UniProt 153–296 Chain N2； UniProt 153–296 Chain N3； UniProt 153–296 Chain O1； UniProt 153–296 Chain O2； UniProt 153–296 Chain O3； UniProt 153–296 Chain P1； UniProt 153–296 Chain P2； UniProt 153–296 Chain P3； UniProt 153–296 Chain Q1； UniProt 153–296 Chain Q2； UniProt 153–296 Chain Q3； UniProt 153–296 Chain R1； UniProt 153–296 Chain R2； UniProt 153–296 Chain R3； UniProt 153–296 Chain S1； UniProt 153–296 Chain S2； UniProt 153–296 Chain S3； UniProt 153–296 Chain T1； UniProt 153–296 Chain T2； UniProt 153–296 Chain T3； UniProt 153–296 Chain U1； UniProt 153–296 Chain U2； UniProt 153–296 Chain U3； UniProt 153–296 Chain V1； UniProt 153–296 Chain V2； UniProt 153–296 Chain V3； UniProt 153–296 Chain W1； UniProt 153–296 Chain W2； UniProt 153–296 Chain W3； UniProt 153–296 Chain X1； UniProt 153–296 Chain X2； UniProt 153–296 Chain X3； UniProt 153–296 Chain Y1； UniProt 153–296 Chain Y2； UniProt 153–296 Chain Y3； UniProt 153–296 Chain YD； UniProt 153–296 Chain YE； UniProt 153–296 Chain YF； UniProt 153–296 Chain Z1； UniProt 153–296 Chain Z2； UniProt 153–296 Chain Z3； UniProt 153–296 Chain ZD； UniProt 153–296 Chain ZE； UniProt 153–296 Chain ZF； UniProt 153–296	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.28 Å

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 8W8M	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 mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	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
2Z5V Solution structure of the TIR domain of human MyD88 Deposited 2007-07-19	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 148–296（149 aa） Fragment：MyD88 TIR domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Pressure 1	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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
8YYM Cryo-EM structure of cylindrical fiber of MyD88 TIR Deposited 2024-04-04	Different construct Different mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 1A； PDBConstruct 1–144； UniProt 153–296 Author chain 1B； PDBConstruct 1–144； UniProt 153–296 Author chain 1C； PDBConstruct 1–144； UniProt 153–296 Author chain 1D； PDBConstruct 1–144； UniProt 153–296 Author chain 1E； PDBConstruct 1–144； UniProt 153–296 Author chain 1F； PDBConstruct 1–144； UniProt 153–296 Author chain 2A； PDBConstruct 1–144； UniProt 153–296 Author chain 2B； PDBConstruct 1–144； UniProt 153–296 Author chain 2C； PDBConstruct 1–144； UniProt 153–296 Author chain 2D； PDBConstruct 1–144； UniProt 153–296 Author chain 2E； PDBConstruct 1–144； UniProt 153–296 Author chain 2F； PDBConstruct 1–144； UniProt 153–296 Author chain 3A； PDBConstruct 1–144； UniProt 153–296 Author chain 3B； PDBConstruct 1–144； UniProt 153–296 Author chain 3C； PDBConstruct 1–144； UniProt 153–296 Author chain 3D； PDBConstruct 1–144； UniProt 153–296 Author chain 3E； PDBConstruct 1–144； UniProt 153–296 Author chain 3F； PDBConstruct 1–144； UniProt 153–296 Author chain A1； PDBConstruct 1–144； UniProt 153–296 Author chain A2； PDBConstruct 1–144； UniProt 153–296 Author chain A3； PDBConstruct 1–144； UniProt 153–296 Author chain B1； PDBConstruct 1–144； UniProt 153–296 Author chain B2； PDBConstruct 1–144； UniProt 153–296 Author chain B3； PDBConstruct 1–144； UniProt 153–296 Author chain C1； PDBConstruct 1–144； UniProt 153–296 Author chain C2； PDBConstruct 1–144； UniProt 153–296 Author chain C3； PDBConstruct 1–144； UniProt 153–296 Author chain D1； PDBConstruct 1–144； UniProt 153–296 Author chain D2； PDBConstruct 1–144； UniProt 153–296 Author chain D3； PDBConstruct 1–144； UniProt 153–296 Author chain E1； PDBConstruct 1–144； UniProt 153–296 Author chain E2； PDBConstruct 1–144； UniProt 153–296 Author chain E3； PDBConstruct 1–144； UniProt 153–296 Author chain F1； PDBConstruct 1–144； UniProt 153–296 Author chain F2； PDBConstruct 1–144； UniProt 153–296 Author chain F3； PDBConstruct 1–144； UniProt 153–296 Author chain G1； PDBConstruct 1–144； UniProt 153–296 Author chain G2； PDBConstruct 1–144； UniProt 153–296 Author chain G3； PDBConstruct 1–144； UniProt 153–296 Author chain H1； PDBConstruct 1–144； UniProt 153–296 Author chain H2； PDBConstruct 1–144； UniProt 153–296 Author chain H3； PDBConstruct 1–144； UniProt 153–296 Author chain I1； PDBConstruct 1–144； UniProt 153–296 Author chain I2； PDBConstruct 1–144； UniProt 153–296 Author chain I3； PDBConstruct 1–144； UniProt 153–296 Author chain J1； PDBConstruct 1–144； UniProt 153–296 Author chain J2； PDBConstruct 1–144； UniProt 153–296 Author chain J3； PDBConstruct 1–144； UniProt 153–296 Author chain K1； PDBConstruct 1–144； UniProt 153–296 Author chain K2； PDBConstruct 1–144； UniProt 153–296 Author chain K3； PDBConstruct 1–144； UniProt 153–296 Author chain L1； PDBConstruct 1–144； UniProt 153–296 Author chain L2； PDBConstruct 1–144； UniProt 153–296 Author chain L3； PDBConstruct 1–144； UniProt 153–296 Author chain M1； PDBConstruct 1–144； UniProt 153–296 Author chain M2； PDBConstruct 1–144； UniProt 153–296 Author chain M3； PDBConstruct 1–144； UniProt 153–296 Author chain N1； PDBConstruct 1–144； UniProt 153–296 Author chain N2； PDBConstruct 1–144； UniProt 153–296 Author chain N3； PDBConstruct 1–144； UniProt 153–296 Author chain O1； PDBConstruct 1–144； UniProt 153–296 Author chain O2； PDBConstruct 1–144； UniProt 153–296 Author chain O3； PDBConstruct 1–144； UniProt 153–296 Author chain P1； PDBConstruct 1–144； UniProt 153–296 Author chain P2； PDBConstruct 1–144； UniProt 153–296 Author chain P3； PDBConstruct 1–144； UniProt 153–296 Author chain Q1； PDBConstruct 1–144； UniProt 153–296 Author chain Q2； PDBConstruct 1–144； UniProt 153–296 Author chain Q3； PDBConstruct 1–144； UniProt 153–296 Author chain R1； PDBConstruct 1–144； UniProt 153–296 Author chain R2； PDBConstruct 1–144； UniProt 153–296 Author chain R3； PDBConstruct 1–144； UniProt 153–296 Author chain S1； PDBConstruct 1–144； UniProt 153–296 Author chain S2； PDBConstruct 1–144； UniProt 153–296 Author chain S3； PDBConstruct 1–144； UniProt 153–296 Author chain T1； PDBConstruct 1–144； UniProt 153–296 Author chain T2； PDBConstruct 1–144； UniProt 153–296 Author chain T3； PDBConstruct 1–144； UniProt 153–296 Author chain U1； PDBConstruct 1–144； UniProt 153–296 Author chain U2； PDBConstruct 1–144； UniProt 153–296 Author chain U3； PDBConstruct 1–144； UniProt 153–296 Author chain V1； PDBConstruct 1–144； UniProt 153–296 Author chain V2； PDBConstruct 1–144； UniProt 153–296 Author chain V3； PDBConstruct 1–144； UniProt 153–296 Author chain W1； PDBConstruct 1–144； UniProt 153–296 Author chain W2； PDBConstruct 1–144； UniProt 153–296 Author chain W3； PDBConstruct 1–144； UniProt 153–296 Author chain X1； PDBConstruct 1–144； UniProt 153–296 Author chain X2； PDBConstruct 1–144； UniProt 153–296 Author chain X3； PDBConstruct 1–144； UniProt 153–296 Author chain Y1； PDBConstruct 1–144； UniProt 153–296 Author chain Y2； PDBConstruct 1–144； UniProt 153–296 Author chain Y3； PDBConstruct 1–144； UniProt 153–296 Author chain YD； PDBConstruct 1–144； UniProt 153–296 Author chain YE； PDBConstruct 1–144； UniProt 153–296 Author chain YF； PDBConstruct 1–144； UniProt 153–296 Author chain Z1； PDBConstruct 1–144； UniProt 153–296 Author chain Z2； PDBConstruct 1–144； UniProt 153–296 Author chain Z3； PDBConstruct 1–144； UniProt 153–296 Author chain ZD； PDBConstruct 1–144； UniProt 153–296 Author chain ZE； PDBConstruct 1–144； UniProt 153–296 Author chain ZF； PDBConstruct 1–144； UniProt 153–296

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	8w8m
Deposition date deposition_date	2023-09-04
Structure title title	Cryo-EM structure of helical filament of MyD88 TIR
Keywords keywords	signaling protein, innate immunity, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	168.50 Å
Forward intensity I(0) i0	33548100000.00
Molecular weight molecular_weight	1626900.0 kDa
Excluded volume excluded_volume	2059000 Å³
Envelope volume envelope_volume	7691600 Å³
Hydration-shell volume shell_volume	391640 Å³
Envelope diameter envelope_diameter	384.4 Å
Shell Rg shell_rg	181.40 Å
Envelope Rg envelope_rg	139.80 Å
Shape Rg shape_rg	168.50 Å
Total Rg total_rg	168.50 Å
Total atoms total_atoms	113934
Residues n_residues	13770
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	394.6 Å
Rg (real space) rg_real	170.10 Å
Rg uncertainty (real space) rg_real_error	0.94 Å
I(0) (real space) i0_real	3.3610e+10
I(0) uncertainty (real space) i0_real_error	7.4930e+08
Rg (reciprocal space) rg_reciprocal	134.20 Å
I(0) (reciprocal space) i0_reciprocal	26750000000.0000
Solution quality estimate total_estimate	0.7220
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	306.9 Å
Skewness Skewness skewness	-0.371
Kurtosis Kurtosis kurtosis	-1.131
Angular range angular_range	— – 0.0450 Å⁻¹
Current regularization parameter α current_alpha	0.5066
Highest regularization parameter α highest_alpha	805500000.0000
Real-space data points n_real_points	10
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.517; Stabil: 0.945; Sysdev: 1.000; Positv: 1.000; Valcen: 0.000; Smooth: 0.000

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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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8. Citations (2)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	3.28 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	14934

Description description	Myeloid differentiation primary response protein MyD88
Molecular weight formula_weight	16841.8 kDa
Source method src_method	man
Copy count entity_count	102

Polymer type type	polypeptide(L)
Chain IDs strand_id	;D2,D3,E1,E2,E3,F1,F2,F3,D1,A2,A3,B1,B2,B3,C1,C2,C3,A1,J2,J3,K1,K2,K3,L1,L2,L3,J1,G2,G3,H1,H2,H3,I1,I2,I3,G1,M2,M3,N1,N2,N3,O1,O2,O3,M1,P2,P3,Q1,Q2,Q3,R1,R2,R3,P1,S2,S3,T1,T2,T3,U1,U2,U3,S1,V2,V3,W1,W2,W3,X1,X2,X3,V1,Y2,Y3,Z1,Z2,Z3,1A,2A,3A,Y1,2B,3B,1C,2C,3C,1D,2D,3D,1B,ZD,YE,ZE,1E,YF,ZF,1F,YD,2E,3E,2F,3F ;
Atom count atom_count	113934

Cryo-EM structure of helical filament of MyD88 TIR

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

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

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/w8/8w8m/8w8m.fit
pddf	/app/data/pr_computation/w8/8w8m/8w8m.pr.out
profile	/app/data/saxs_computation/w8/8w8m/8w8m.dat