SAXSdb — 8wsa

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

Toll-like receptor 4

Mus musculus

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 26–629 Chain B； UniProt 26–629	Not recorded	Lymphocyte antigen 96 × 2 （Q9JHF9） GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 A1L01 (3~{S})-3-decanoyloxytetradecanoic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 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	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 8WSA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Z64 Crystal structure of mouse TLR4 and mouse MD-2 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 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–625（599 aa） Fragment：TLR4, UNP residues 27-625	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；0.1M Na-Cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.84 Å R-free 0.290
3VQ1 Crystal structure of mouse TLR4/MD-2/lipid IVa complex Deposited 2012-03-17	Different construct 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 22–627（606 aa） Fragment：UNP residues 22-627 Chain B 22–627（606 aa） Fragment：UNP residues 22-627	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG4000, 0.2M Na acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.277
3VQ2 Crystal structure of mouse TLR4/MD-2/LPS complex Deposited 2012-03-17	Different construct 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 22–627（606 aa） Fragment：UNP residues 22-627 Chain B 22–627（606 aa） Fragment：UNP residues 22-627	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；18% PEG3350, 0.2M sodium tartrate, 0.1M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.48 Å R-free 0.267
5IJB The ligand-free structure of the mouse TLR4/MD-2 complex Deposited 2016-03-01	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 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 12% PEG10000	Resolution 2.91 Å R-free 0.308
5IJB The ligand-free structure of the mouse TLR4/MD-2 complex Deposited 2016-03-01	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 B 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 12% PEG10000	Resolution 2.91 Å R-free 0.308
5IJC The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex Deposited 2016-03-01	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 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 V2A neoseptin 3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000	Resolution 2.57 Å R-free 0.234
5IJC The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex Deposited 2016-03-01	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 B 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 V2A neoseptin 3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000	Resolution 2.57 Å R-free 0.234
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) Chain B 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	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 A 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 DAO LAURIC ACID × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	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 Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 26–544（519 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 DAO LAURIC ACID × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
7MLM Crystal structure of mouse TLR4/MD-2 in complex with sulfatides Deposited 2021-04-28	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 × 4 PDB declaration: tetrameric	Chain A 26–544（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZKM N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Tris pH8.0, 0.8 M sodium formate, 8% PEG 8000, 8% PEG 1000	Resolution 2.10 Å R-free 0.244
7MLM Crystal structure of mouse TLR4/MD-2 in complex with sulfatides Deposited 2021-04-28	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 A 26–544（519 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZKM N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Tris pH8.0, 0.8 M sodium formate, 8% PEG 8000, 8% PEG 1000	Resolution 2.10 Å R-free 0.244
8WQT Cryo-EM Structure of Mouse TLR4/MD-2/DLAM1 complex Deposited 2023-10-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–629（604 aa） Chain B 26–629（604 aa）	Not recorded	2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 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 2.60 Å
8WRY Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex Deposited 2023-10-16	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 26–629（604 aa） Chain B 26–629（604 aa）	Not recorded	2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 4 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 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 2.60 Å

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

View Construct and Data Evidence

UniProt name	TLR4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–604； UniProt 26–629 Author chain B； PDBConstruct 1–604； UniProt 26–629

Lymphocyte antigen 96

Mus musculus

UniProt Q9JHF9

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 × 4 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 （Q9QUK6） GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 A1L01 (3~{S})-3-decanoyloxytetradecanoic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 14 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	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 8WSA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2Z64 Crystal structure of mouse TLR4 and mouse MD-2 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 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 21–155（135 aa） Fragment：MD-2, UNP residues 21-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；296 K；0.1M Na-Cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 296K	Resolution 2.84 Å R-free 0.290
3VQ1 Crystal structure of mouse TLR4/MD-2/lipid IVa complex Deposited 2012-03-17	Different construct 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 C 17–160（144 aa） Chain D 17–160（144 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；15% PEG4000, 0.2M Na acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.70 Å R-free 0.277
3VQ2 Crystal structure of mouse TLR4/MD-2/LPS complex Deposited 2012-03-17	Different construct 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 C 17–160（144 aa） Chain D 17–160（144 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；18% PEG3350, 0.2M sodium tartrate, 0.1M Bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.48 Å R-free 0.267
5IJB The ligand-free structure of the mouse TLR4/MD-2 complex Deposited 2016-03-01	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 C 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 12% PEG10000	Resolution 2.91 Å R-free 0.308
5IJB The ligand-free structure of the mouse TLR4/MD-2 complex Deposited 2016-03-01	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 D 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Bicine, pH 7.5, 12% PEG10000	Resolution 2.91 Å R-free 0.308
5IJC The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex Deposited 2016-03-01	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 D 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 V2A neoseptin 3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000	Resolution 2.57 Å R-free 0.234
5IJC The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex Deposited 2016-03-01	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 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 V2A neoseptin 3 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 12% PEG8000	Resolution 2.57 Å R-free 0.234
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 19–160（142 aa） Fragment：UNP residues 19-160 Chain D 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 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	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	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 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 DAO LAURIC ACID × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
5IJD The crystal structure of mouse TLR4/MD-2/lipid A complex Deposited 2016-03-01	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 Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 19–160（142 aa） Fragment：UNP residues 19-160	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 1 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 1 DAO LAURIC ACID × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400	Resolution 2.70 Å R-free 0.285
7MLM Crystal structure of mouse TLR4/MD-2 in complex with sulfatides Deposited 2021-04-28	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 × 4 PDB declaration: tetrameric	Chain C 19–160（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 ZKM N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Tris pH8.0, 0.8 M sodium formate, 8% PEG 8000, 8% PEG 1000	Resolution 2.10 Å R-free 0.244
7MLM Crystal structure of mouse TLR4/MD-2 in complex with sulfatides Deposited 2021-04-28	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 19–160（142 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 ZKM N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Tris pH8.0, 0.8 M sodium formate, 8% PEG 8000, 8% PEG 1000	Resolution 2.10 Å R-free 0.244
8WQT Cryo-EM Structure of Mouse TLR4/MD-2/DLAM1 complex Deposited 2023-10-12	Different oligomeric state 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 × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 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 2.60 Å
8WRY Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 Complex Deposited 2023-10-16	Different oligomeric state 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 × 4 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 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 2.60 Å

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

View Construct and Data Evidence

UniProt name	LY96_MOUSE
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8wsa
Deposition date deposition_date	2023-10-17
Structure title title	Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 Complex
Keywords keywords	Innate immune system, Toll-like receptors, TLR4 agonist, Vaccine adjuvants, Disaccharide-based lipid A mimetics, 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	42.99 Å
Radius of gyration Rg (electron density) rg_electron	42.71 Å
Forward intensity I(0) i0	837126000.00
Molecular weight molecular_weight	160270.0 kDa
Excluded volume excluded_volume	156360 Å³
Envelope volume envelope_volume	329350 Å³
Hydration-shell volume shell_volume	65336 Å³
Envelope diameter envelope_diameter	150.5 Å
Shell Rg shell_rg	47.15 Å
Envelope Rg envelope_rg	41.76 Å
Shape Rg shape_rg	42.72 Å
Total Rg total_rg	42.89 Å
Total atoms total_atoms	12132
Residues n_residues	1462
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	144.1 Å
Rg (real space) rg_real	42.99 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	8.3710e+08
I(0) uncertainty (real space) i0_real_error	1.6060e+07
Rg (reciprocal space) rg_reciprocal	42.99 Å
I(0) (reciprocal space) i0_reciprocal	837100000.0000
Solution quality estimate total_estimate	0.8581
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.5 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.157
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	41880000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.727

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Toll-like receptor 4
Molecular weight formula_weight	68651.3 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	12132

NPCIEVVPNITYQCMDQKLSKVPDDIPSSTKNIDLSFNPLKILKSYSFSNFSELQWLDLSRCEIETIEDKAWHGLHHLSNLILTGNPIQSFSPGSFSGLTSLENLVAVETKLASLESFPIGQLITLKKLNVAHNFIHSCKLPAYFSNLTNLVHVDLSYNYIQTITVNDLQFLRENPQVNLSLDMSLNPIDFIQDQAFQGIKLHELTLRGNFNSSNIMKTCLQNLAGLHVHRLILGEFKDERNLEIFEPSIMEGLCDVTIDEFRLTYTNDFSDDIVKFHCLANVSAMSLAGVSIKYLEDVPKHFKWQSLSIIRCQLKQFPTLDLPFLKSLTLTMNKGSISFKKVALPSLSYLDLSRNALSFSGCCSYSDLGTNSLRHLDLSFNGAIIMSANFMGLEELQHLDFQHSTLKRVTEFSAFLSLEKLLYLDISYTNTKIDFDGIFLGLTSLNTLKMAGNSFKDNTLSNVFANTTNLTFLDLSKCQLEQISWGVFDTLHRLQLLNMSHNNLLFLDSSHYNQLYSLSTLDCSFNRIETSKGILQHFPKSLAFFNLTNNSVACICEHQKFLQWVKEQKQFLVNVEQMTCATPVEMNTSLVLDFNNSTCYMYK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Lymphocyte antigen 96
Molecular weight formula_weight	16411.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

EKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHRRDVN

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Trichoplusia ni

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	(3~{S})-3-decanoyloxytetradecanoic acid
Molecular weight formula_weight	398.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 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	14

Entity 6 Entity 6 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	2

Entity 7 Entity 7 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 8 Entity 8 non-polymer

Description description	[(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate
Molecular weight formula_weight	274.2 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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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	—

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	714161

fit	/app/data/saxs_computation/ws/8wsa/8wsa.fit
pddf	/app/data/pr_computation/ws/8wsa/8wsa.pr.out
profile	/app/data/saxs_computation/ws/8wsa/8wsa.dat

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)