← Back to search
5nao

NMR structure of TLR4 transmembrane domain (624-657) in DPC micelles

Method: SOLUTION NMR Dmax: 63.9 Å Quality: REASONABLE
▼

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

Toll-like receptor 4

Homo sapiens

UniProt O00206

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 623–657 Fragment：UNP residues 623-657 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；313 K；Ionic strength (raw mmCIF value) 20；Pressure AMBIENT NMR sample composition：1.0 mM [U-100% 13C; U-100% 15N] TLR4-TM, 100 mM [U-99% 2H] DPC, 20 mM sodium phosphate, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 5NAO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2Z62 Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–228（202 aa） Fragment：TLR4, UNP residues 27-228(human), VLRB.61, UNP residues 128-199(Inshore hagfish)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, VAPOR DIFFUSION, temperature 296K
Resolution 1.70 Å R-free 0.208
2Z63 Crystal structure of the TV8 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–527（501 aa） Fragment：TLR4, UNP residues 27-527(human), VLRB.61, UNP residues 133-199(Inshore hagfish)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；277 K；0.2M Sodium Citrate, 0.1M Bis-Tris Propane, 27% PEG 1000, pH 6.50, VAPOR DIFFUSION, temperature 277K
Resolution 2.00 Å R-free 0.298
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–228（202 aa） Fragment：TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.70 Å R-free 0.289
2Z65 Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 27–228（202 aa） Fragment：TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish)
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K
Resolution 2.70 Å R-free 0.289
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION
Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION
Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain C 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION
Resolution 1.90 Å R-free 0.219
2Z66 Crystal structure of the VT3 hybrid of human TLR4 and hagfish VLRB.61 Deposited 2007-07-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain D 383–627（245 aa） Fragment：VLRB.61, UNP residues 24-82(Inshore hagfish), TLR4, UNP residues 383-228(human)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；0.2M Lithium Sulfate, 0.1M Sodium Acetate, 24% PEG 4000, pH 5.50, temperature 277K, VAPOR DIFFUSION
Resolution 1.90 Å R-free 0.219
3FXI Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex Deposited 2009-01-21 Different construct Different 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 27–631（605 aa） Fragment：extracellular domain, residues 27-631
Chain B 27–631（605 aa） Fragment：extracellular domain, residues 27-631
Not recorded FTT 3-HYDROXY-TETRADECANOIC ACID × 8 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 PO4 PHOSPHATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；50mM MgCl2, 0.1M Na-HEPES pH 7.5, 30% PEG MME 550, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 3.10 Å R-free 0.281
3UL7 Crystal structure of the TV3 mutant F63W Deposited 2011-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–228（201 aa） Fragment：UNP RESIDUES 28-228, UNP RESIDUES 126-199
Mutation：F63W NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris (pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 2.37 Å R-free 0.271
3UL8 Crystal structure of the TV3 mutant V134L Deposited 2011-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199
Mutation：V134L NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 2.50 Å R-free 0.300
3UL9 structure of the TV3 mutant M41E Deposited 2011-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–228（201 aa） Fragment：UNP RESIDUES 28-228, UNP RESIDUES 126-199
Mutation：M41E NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FUL beta-L-fucopyranose × 1 SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；296 K；0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 2.45 Å R-free 0.306
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199
Mutation：F63W NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 3.60 Å R-free 0.341
3ULA Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex Deposited 2011-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 27–228（202 aa） Fragment：UNP RESIDUES 27-228, UNP RESIDUES 126-199
Mutation：F63W NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 E55 3-O-DECYL-2-DEOXY-6-O-{2-DEOXY-3-O-[(3R)-3-METHOXYDECYL]-6-O-METHYL-2-[(11Z)-OCTADEC-11-ENOYLAMINO]-4-O-PHOSPHONO-BETA-D-GLUCOPYRANOSYL}-2-[(3-OXOTETRADECANOYL)AMINO]-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；296 K；0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K
Resolution 3.60 Å R-free 0.341
4G8A Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS Deposited 2012-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 23–629（607 aa） Fragment：UNP RESIDUES 23-629
Chain B 23–629（607 aa） Fragment：UNP RESIDUES 23-629
Mutation：D299G, T399I Mutation：D299G, T399I NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 LP4 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose × 2 LP5 (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE × 2 DAO LAURIC ACID × 2 MYR MYRISTIC ACID × 2 KDO 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；26-30% (w/v) PEG1000, 0.1M Tris-HCl (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.249
5NAM NMR structure of TLR4 transmembrane domain (624-670) in DMPG/DHPC bicelles Deposited 2017-02-28 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 623–670（48 aa） Fragment：UNP residues 623-670
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；313 K；Ionic strength (raw mmCIF value) 10；Pressure AMBIENT
NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPG, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 71 mM DHPC, 29 mM DMPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5 mM [U-13C; U-15N] TLR4-TM, 50 mM [U-2H] DPC, 10 mM imidazole, 0.01 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
8WO1 Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex Deposited 2023-10-06 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 27–631（605 aa）
Chain B 27–631（605 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 2 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 X6N [(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate × 2 A1L01 (3~{S})-3-decanoyloxytetradecanoic acid × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.24 Å
8WTA Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex Deposited 2023-10-18 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 27–631（605 aa）
Chain B 27–631（605 aa）
Not recorded GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 4 0IL (3R)-3-(tetradecanoyloxy)tetradecanoic acid × 2 XIQ 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9J03 Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex Deposited 2024-08-02 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 27–631（605 aa）
Chain B 27–631（605 aa）
Not recorded 2IL (3R)-3-(dodecanoyloxy)tetradecanoic acid × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 GP4 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose × 2 X6Z [(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å

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

View Construct and Data Evidence
UniProt name TLR4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–35； UniProt 623–657

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 5nao

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nao
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id5nao
Deposition date deposition_date2017-02-28
Structure title titleNMR structure of TLR4 transmembrane domain (624-657) in DPC micelles
Keywords keywordsToll-like receptor, PROTEIN RECEPTOR, transmembrane domain, PROTEIN, signaling protein; SIGNALING PROTEIN
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier16.01 Å
Radius of gyration Rg (electron density) rg_electron15.94 Å
Forward intensity I(0) i016351500.00
Molecular weight molecular_weight38858.0 kDa
Excluded volume excluded_volume51109 ų
Envelope volume envelope_volume13380 ų
Hydration-shell volume shell_volume7461 ų
Envelope diameter envelope_diameter65.0 Å
Shell Rg shell_rg21.29 Å
Envelope Rg envelope_rg18.73 Å
Shape Rg shape_rg15.96 Å
Total Rg total_rg16.22 Å
Total atoms total_atoms5690
Residues n_residues350
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
▼

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

Maximum dimension Dmax dmax63.9 Å
Rg (real space) rg_real16.50 Å
Rg uncertainty (real space) rg_real_error0.85 Å
I(0) (real space) i0_real1.6350e+07
I(0) uncertainty (real space) i0_real_error2.3770e+05
Rg (reciprocal space) rg_reciprocal16.45 Å
I(0) (reciprocal space) i0_reciprocal16350000.0000
Solution quality estimate total_estimate0.5391
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks5
Primary peak position r_peak_primary5.7 Å
Skewness Skewness skewness0.482
Kurtosis Kurtosis kurtosis-0.773
Angular range angular_range— – 0.4950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6643.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.001; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.004; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

9. Files and Curves (10)