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5ijc

The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex

Method: X-RAY DIFFRACTION Dmax: 133.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Toll-like receptor 4,Variable lymphocyte receptor B

Eptatretus burgeri

UniProt Q4G1L2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 126–200 Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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
2 Insufficient information Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 126–200 Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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

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 5IJC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2O6R Structural diversity of the hagfish Variable Lymphocyte Receptors B61 Deposited 2006-12-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–200（177 aa） Fragment：Leucine-rich repeat (LRR), residues 24-200
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；30% PEG 4000, 0.1M Tris-Hcl, 0.2M sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Resolution 2.30 Å R-free 0.259
2Z62 Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 128–199（72 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–199（67 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 128–199（72 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 128–199（72 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–82（59 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–82（59 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–82（59 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–82（59 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
2Z7X Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 133–199（67 aa）
Chain B 133–199（67 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 PLM PALMITIC ACID × 1 Z41 (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.10 Å R-free 0.270
2Z80 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 136–199（64 aa） Fragment：TLR2, UNP residues 1-284(human), VLRB.61, UNP residues 136-199(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.1M Tris-HCl pH8.5, 28% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.80 Å R-free 0.254
2Z80 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 136–199（64 aa） Fragment：TLR2, UNP residues 1-284(human), VLRB.61, UNP residues 136-199(Inshore hagfish)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.1M Tris-HCl pH8.5, 28% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.80 Å R-free 0.254
2Z81 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–199（67 aa） Fragment：TLR2, UNP residues 27-506(Mouse), VLRB.61, UNP residues 136-199(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PCJ (2R)-3-{[(2S)-3-HYDROXY-2-(PALMITOYLAMINO)PROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2M ammonium sulfate, 0.1M Tris-HCl pH8.5, 34% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 1.80 Å R-free 0.232
2Z82 Crystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide Deposited 2007-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–199（67 aa） Fragment：TLR2, UNP residues 27-506(Mouse), VLRB.61, UNP residues 133-199(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PDJ (2R)-3-{[(2R)-2-AMINO-3-HYDROXYPROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2M ammonium sulfate, 0.1M Tris-HCl pH8.5 and 34% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.60 Å R-free 0.277
3A79 Crystal structure of TLR2-TLR6-Pam2CSK4 complex Deposited 2009-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 133–200（68 aa） Fragment：extracellular domain, UNP residues 1-506(mouse), UNP residues 133-200(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 PXS (2S)-propane-1,2-diyl dihexadecanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；2.0M ammonium sulfate, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.90 Å R-free 0.280
3A7B Crystal structure of TLR2-Streptococcus Pneumoniae lipoteichoic acid complex Deposited 2009-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–200（68 aa） Fragment：extracellular domain, UNP residues 1-506(mouse), UNP residues 133-200(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 LTC (2S)-1-({3-O-[2-(acetylamino)-4-amino-2,4,6-trideoxy-beta-D-galactopyranosyl]-alpha-D-glucopyranosyl}oxy)-3-(heptanoyloxy)propan-2-yl (7Z)-pentadec-7-enoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；50mM ammonium citrate pH 7.0, 20% PEG 4000, 30% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.53 Å R-free 0.270
3A7C Crystal structure of TLR2-PE-DTPA complex Deposited 2009-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–200（68 aa） Fragment：extracellular domain, UNP residues 1-506(mouse), UNP residues 133-200(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PDK (10S,13R)-3-{2-[{2-[bis(carboxymethyl)amino]ethyl}(carboxymethyl)amino]ethyl}-10-hydroxy-5,16-dioxo-13-(tetradecanoyloxy)-9,11,15-trioxa-3,6-diaza-10-phosphanonacosan-1-oic acid 10-oxide × 1 LU LUTETIUM (III) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M ammonium sulfate, 0.1M Na-HEPES pH 7.5, 25% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.290
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 conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 126–199（74 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 126–199（74 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 126–199（74 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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–199（74 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 conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 126–199（74 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
3V44 Crystal structure of the N-terminal fragment of zebrafish TLR5 Deposited 2011-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 126–200（75 aa） Fragment：zebrafish Toll-like receptor 5b (UNP residues 22-342) and hagfish variable lymphocyte receptor B.61 (UNP residues 126-200)
Mutation：V24E, L124V, Q159K, R227K, S229T, D334N NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20% MPD, 0.1 M Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.83 Å R-free 0.238
3V47 Crystal structure of the N-terminal fragment of zebrafish TLR5 in complex with Salmonella flagellin Deposited 2011-12-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 126–200（75 aa） Fragment：zebrafish Toll-like receptor 5b (UNP residues 22-390), hagfish variable lymphocyte receptor B.61 (UNP residues 126-200)
Chain B 126–200（75 aa） Fragment：zebrafish Toll-like receptor 5b (UNP residues 22-390), hagfish variable lymphocyte receptor B.61 (UNP residues 126-200)
Mutation：V24E, L124V, Q159K, R227K, S229T, D334N Mutation：V24E, L124V, Q159K, R227K, S229T, D334N NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；296 K；15% PEG8000, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Resolution 2.47 Å R-free 0.259
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 131–201（71 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 131–201（71 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 MLI MALONATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 131–201（71 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARN Crystal structure of the N-terminal domain of Drosophila Toll receptor Deposited 2012-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 131–201（71 aa） Fragment：TOLL RECEPTOR RESIDUES 28-228, VARIABLE LYMPHOCYTE RECEPTOR B.61 RESIDUES 131-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；PH 7
Resolution 2.41 Å R-free 0.216
4ARR Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C Deposited 2012-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–201（69 aa） Fragment：TOLL RECEPTOR (UNP RESIDUES 28-228), VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 133-201)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；SODIUM MALONATE AND 5-AMINO-2,4, 6-TRIIODOISOPHTHALIC ACID, pH 7
Resolution 3.00 Å R-free 0.254
4ARR Crystal structure of the N-terminal domain of Drosophila Toll receptor with the magic triangle I3C Deposited 2012-04-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 133–201（69 aa） Fragment：TOLL RECEPTOR (UNP RESIDUES 28-228), VARIABLE LYMPHOCYTE RECEPTOR B.61 (UNP RESIDUES 133-201)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 I3C 5-amino-2,4,6-triiodobenzene-1,3-dicarboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；SODIUM MALONATE AND 5-AMINO-2,4, 6-TRIIODOISOPHTHALIC ACID, pH 7
Resolution 3.00 Å R-free 0.254
4BV4 Structure and allostery in Toll-Spatzle recognition Deposited 2013-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 133–201（69 aa） Fragment：PROTEIN TOLL, RESIDUES 28-397, VARIABLE LYMPHOCYTE RECEPTOR B, RESIDUES 133-201
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；15% PEG 8000, 0.1M TRIS PH 7.5, 0.1 M MGCL2
Resolution 2.35 Å R-free 0.227
4QDH Crystal Structure of the C-terminal Domain of Mouse TLR9 Deposited 2014-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–81（61 aa） Fragment：SEE REMARK 999
Chain A 126–200（75 aa） Fragment：SEE REMARK 999
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.77；295 K；100 mM sodium citrate, 1.5 M ammonium sulfate, pH 4.77, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.40 Å R-free 0.247
4QDH Crystal Structure of the C-terminal Domain of Mouse TLR9 Deposited 2014-05-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–81（61 aa） Fragment：SEE REMARK 999
Chain B 126–200（75 aa） Fragment：SEE REMARK 999
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.77；295 K；100 mM sodium citrate, 1.5 M ammonium sulfate, pH 4.77, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Resolution 2.40 Å R-free 0.247
4QXE Crystal structure of LGR4 fused with hagfish VLR Deposited 2014-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 133–200（68 aa） Fragment：R-spondin Receptor, UNP residues 27-396, UNP residues 133-200
Mutation：D75G NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1M HEPES pH 7.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.20 Å R-free 0.237
4QXF crystal structure of human LGR4 and Rspo1 Deposited 2014-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 128–200（73 aa） Fragment：UNP residues 27-252, UNP residues 128-200
Mutation：D75G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.25 Å R-free 0.243
4QXF crystal structure of human LGR4 and Rspo1 Deposited 2014-07-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 128–200（73 aa） Fragment：UNP residues 27-252, UNP residues 128-200
Mutation：D75G No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.25 Å R-free 0.243
5GY2 Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5 Deposited 2016-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 aa）
Mutation：V24E/L124V/Q159K/R227K/S229T/D334N NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；291 K；PEG 300, sodium acetate, pH 4.4
Resolution 2.10 Å R-free 0.236
5GY2 Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5 Deposited 2016-09-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 126–200（75 aa）
Mutation：V24E/L124V/Q159K/R227K/S229T/D334N NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；291 K；PEG 300, sodium acetate, pH 4.4
Resolution 2.10 Å R-free 0.236
5IJB The ligand-free structure of the mouse TLR4/MD-2 complex Deposited 2016-03-01 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 126–200（75 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
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 conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 126–200（75 aa） Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)
Chain B 126–200（75 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 126–200（75 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
6BXA Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 2 (VLR2) bound Deposited 2017-12-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；16% PEG 8K, 180 mM ammonium citrate, 90 mM MES pH 6.0, 10 mM urea
Resolution 2.30 Å R-free 0.218
6BXA Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 2 (VLR2) bound Deposited 2017-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 126–200（75 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；16% PEG 8K, 180 mM ammonium citrate, 90 mM MES pH 6.0, 10 mM urea
Resolution 2.30 Å R-free 0.218
6BXC Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound Deposited 2017-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；15% Peg3350, 170 mM MgNO3, 80 mM MES pH 6.0, 15% ethylene glycol
Resolution 2.50 Å R-free 0.270
6BXC Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound Deposited 2017-12-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 126–200（75 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；15% Peg3350, 170 mM MgNO3, 80 mM MES pH 6.0, 15% ethylene glycol
Resolution 2.50 Å R-free 0.270
7MLM Crystal structure of mouse TLR4/MD-2 in complex with sulfatides Deposited 2021-04-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 126–200（75 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 ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 126–200（75 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

30 other PDB entries and 49 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q4G1L2_EPTBU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 561–635； UniProt 126–200 Author chain B； PDBConstruct 561–635； UniProt 126–200

Toll-like receptor 4,Variable lymphocyte receptor B

Eptatretus burgeri

UniProt Q9QUK6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–544 Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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
2 Insufficient information Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 26–544 Fragment：TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200) Lymphocyte antigen 96 × 1 （Q9JHF9） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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

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 5IJC 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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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
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 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 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 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
8WSA Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 Complex Deposited 2023-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 26–629（604 aa）
Chain B 26–629（604 aa）
Not recorded 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

9 other PDB entries and 13 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 42–560； UniProt 26–544 Author chain B； PDBConstruct 42–560； UniProt 26–544

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 Insufficient information Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 19–160 Fragment：UNP residues 19-160 Toll-like receptor 4,Variable lymphocyte receptor B × 1 （Q9QUK6,Q4G1L2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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
2 Insufficient information Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 19–160 Fragment：UNP residues 19-160 Toll-like receptor 4,Variable lymphocyte receptor B × 1 （Q9QUK6,Q4G1L2） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 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

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 5IJC 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 oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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
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 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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 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 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 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 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
8WSA Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 Complex Deposited 2023-10-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 19–160（142 aa）
Chain D 19–160（142 aa）
Not recorded 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

9 other PDB entries and 13 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 42–183； UniProt 19–160 Author chain D； PDBConstruct 42–183； 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

SAXS profile for 5ijc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ijc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ijc
Deposition date deposition_date2016-03-01
Structure title titleThe crystal structure of mouse TLR4/MD-2/neoseptin-3 complex
Keywords keywordsImmune response, protein complex, small molecule agonist, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.46 Å
Radius of gyration Rg (electron density) rg_electron39.92 Å
Forward intensity I(0) i0416073000.00
Molecular weight molecular_weight171180.0 kDa
Excluded volume excluded_volume216020 ų
Envelope volume envelope_volume287810 ų
Hydration-shell volume shell_volume60693 ų
Envelope diameter envelope_diameter142.6 Å
Shell Rg shell_rg45.29 Å
Envelope Rg envelope_rg39.33 Å
Shape Rg shape_rg39.92 Å
Total Rg total_rg40.25 Å
Total atoms total_atoms12051
Residues n_residues1454
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax133.0 Å
Rg (real space) rg_real40.44 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real4.1610e+08
I(0) uncertainty (real space) i0_real_error7.4500e+06
Rg (reciprocal space) rg_reciprocal40.46 Å
I(0) (reciprocal space) i0_reciprocal416100000.0000
Solution quality estimate total_estimate0.8668
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.1 Å
Skewness Skewness skewness0.349
Kurtosis Kurtosis kurtosis-0.170
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha43890000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.753
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5ijcA00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id5ijcB00
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id5ijcC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily770 —
Domain ID domain_id5ijcD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily770 —
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8. Citations (1)

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9. Files and Curves (10)