8wta

Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex

Method: ELECTRON MICROSCOPY D_max: 140.2 Å Quality: GOOD

▼

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

Toll-like receptor 4

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	Other combination Heteromer Protein × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 27–631 Chain B； UniProt 27–631	Not recorded	Lymphocyte antigen 96 × 2 （B3Y6A6） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 4 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 XIQ 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.90 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 8WTA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Z62 Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–228（202 aa） Fragment：TLR4, UNP residues 27-228(human), VLRB.61, UNP residues 128-199(Inshore hagfish)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, VAPOR DIFFUSION, temperature 296K	Resolution 1.70 Å R-free 0.208
2Z63 Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–527（501 aa） Fragment：TLR4, UNP residues 27-527(human), VLRB.61, UNP residues 133-199(Inshore hagfish)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；0.2M Sodium Citrate, 0.1M Bis-Tris Propane, 27% PEG 1000, pH 6.50, VAPOR DIFFUSION, temperature 277K	Resolution 2.00 Å R-free 0.298
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–228（202 aa） Fragment：TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.70 Å R-free 0.289
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–228（202 aa） Fragment：TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.70 Å R-free 0.289
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION	Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION	Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION	Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION	Resolution 1.90 Å R-free 0.219
3FXI Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex Deposited 2009-01-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–631（605 aa） Fragment：extracellular domain, residues 27-631 Chain B 27–631（605 aa） Fragment：extracellular domain, residues 27-631	Not recorded	FTT 3-HYDROXY-TETRADECANOIC ACID × 8 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 PO4 PHOSPHATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；50mM MgCl2, 0.1M Na-HEPES pH 7.5, 30% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 3.10 Å R-free 0.281
3UL7 Crystal structure of the TV3 mutant F63W Deposited 2011-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–228（201 aa） Fragment：UNP RESIDUES 28-228, UNP RESIDUES 126-199	Mutation：F63W	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris (pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 2.37 Å R-free 0.271
3UL8 Crystal structure of the TV3 mutant V134L Deposited 2011-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199	Mutation：V134L	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 2.50 Å R-free 0.300
3UL9 structure of the TV3 mutant M41E Deposited 2011-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–228（201 aa） Fragment：UNP RESIDUES 28-228, UNP RESIDUES 126-199	Mutation：M41E	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 2.45 Å R-free 0.306
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199	Mutation：F63W	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 3.60 Å R-free 0.341
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199	Mutation：F63W	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K	Resolution 3.60 Å R-free 0.341
4G8A Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS Deposited 2012-07-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 23–629（607 aa） Fragment：UNP RESIDUES 23-629 Chain B 23–629（607 aa） Fragment：UNP RESIDUES 23-629	Mutation：D299G, T399I Mutation：D299G, T399I	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 2 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 KDO 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；26-30% (w/v) PEG1000, 0.1M Tris-HCl (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.249
5NAM NMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC bicelles Deposited 2017-02-28	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 623–670（48 aa） Fragment：UNP residues 623-670	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 10；Pressure AMBIENT NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPG, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 50 mM [U-2H] DPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5NAO NMR structure of TLR4 transmembrane domain (624-657) in DPC micelles Deposited 2017-02-28	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 623–657（35 aa） Fragment：UNP residues 623-657	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] TLR4-TM, 100 mM [U-99% 2H] DPC, 20 mM sodium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8WO1 Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex Deposited 2023-10-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–631（605 aa） Chain B 27–631（605 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 2 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 X6N [(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate × 2 A1L01 (3~{S})-3-decanoyloxytetradecanoic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.24 Å
9J03 Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex Deposited 2024-08-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 27–631（605 aa） Chain B 27–631（605 aa）	Not recorded	2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 X6Z [(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TLR4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–605； UniProt 27–631 Author chain B； PDBConstruct 1–605； UniProt 27–631

Lymphocyte antigen 96

Homo sapiens

UniProt B3Y6A6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 6 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 19–160 Chain D； UniProt 19–160	Not recorded	Toll-like receptor 4 × 2 （O00206） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 4 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 XIQ 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.90 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8WTA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8WO1 Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex Deposited 2023-10-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 19–160（142 aa） Chain D 19–160（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 2 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 X6N [(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate × 2 A1L01 (3~{S})-3-decanoyloxytetradecanoic acid × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.24 Å
9J03 Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex Deposited 2024-08-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 19–160（142 aa） Chain D 19–160（142 aa）	Not recorded	2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 X6Z [(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

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

View Construct and Data Evidence

UniProt name	B3Y6A6_PANTR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–142； UniProt 19–160 Author chain D； PDBConstruct 1–142； UniProt 19–160

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8wta
Deposition date deposition_date	2023-10-18
Structure title title	Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex
Keywords keywords	Innate immune system, Toll-like receptors, TLR4 agonist, Vaccine adjuvants, Disaccharide-based lipid A mimetices, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	42.22 Å
Radius of gyration Rg (electron density) rg_electron	42.01 Å
Forward intensity I(0) i0	877347000.00
Molecular weight molecular_weight	163950.0 kDa
Excluded volume excluded_volume	159950 Å³
Envelope volume envelope_volume	324750 Å³
Hydration-shell volume shell_volume	65619 Å³
Envelope diameter envelope_diameter	148.0 Å
Shell Rg shell_rg	46.24 Å
Envelope Rg envelope_rg	41.32 Å
Shape Rg shape_rg	42.01 Å
Total Rg total_rg	42.19 Å
Total atoms total_atoms	12402
Residues n_residues	1482
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

▼

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

Maximum dimension Dmax dmax	140.2 Å
Rg (real space) rg_real	42.25 Å
Rg uncertainty (real space) rg_real_error	1.27 Å
I(0) (real space) i0_real	8.7730e+08
I(0) uncertainty (real space) i0_real_error	1.6660e+07
Rg (reciprocal space) rg_reciprocal	42.22 Å
I(0) (reciprocal space) i0_reciprocal	877300000.0000
Solution quality estimate total_estimate	0.8574
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.1 Å
Skewness Skewness skewness	0.407
Kurtosis Kurtosis kurtosis	-0.096
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	57000000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.599

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Toll-like receptor 4
Molecular weight formula_weight	68838.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	12402

EPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLDLSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALGAFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHLDLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSLNVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDIIDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTSNKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLGLEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAGNSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPYKCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQLLVEVERMECATPSDKQGMPVLSLNITCQMNK

来源 Source

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Lymphocyte antigen 96
Molecular weight formula_weight	16385.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYFNLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVEAISGSPEEMLFCLEFVILHQPNSN

来源 Source

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	Trichoplusia ni

Entity 3 Entity 3 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose
Molecular weight formula_weight	259.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	(3R)-3-(dodecanoyloxy)tetradecanoic acid
Molecular weight formula_weight	426.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	(3R)-3-(tetradecanoyloxy)tetradecanoic acid
Molecular weight formula_weight	454.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one
Molecular weight formula_weight	188.1 kDa
Source method src_method	syn
Copy count entity_count	2

▶

8. Citations (1)

▶

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	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	302687

fit	/app/data/saxs_computation/wt/8wta/8wta.fit
pddf	/app/data/pr_computation/wt/8wta/8wta.pr.out
profile	/app/data/saxs_computation/wt/8wta/8wta.dat

Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex

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

Toll-like receptor 4

State in the Current Structure

Other States of the Same Protein in the Database

Lymphocyte antigen 96

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

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)