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Yorodumi- PDB-2z65: Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex -
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Open data
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Basic information
| Entry | Database: PDB / ID: 2z65 | |||||||||
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| Title | Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / TLR4 / toll-like receptor / MD-2 / LPS / E5564 / eritoran / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane / Secreted | |||||||||
| Function / homology | Function and homology informationdetection of fungus / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor 4 binding / detection of lipopolysaccharide / regulation of dendritic cell cytokine production ...detection of fungus / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor 4 binding / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / lipopolysaccharide receptor complex / MyD88-independent TLR4 cascade / negative regulation of interleukin-23 production / cellular response to oxidised low-density lipoprotein particle stimulus / TRIF-mediated programmed cell death / wound healing involved in inflammatory response / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of stress-activated MAPK cascade / Toll Like Receptor 4 (TLR4) Cascade / intestinal epithelial structure maintenance / Caspase activation via Death Receptors in the presence of ligand / positive regulation of interleukin-1 production / macrophage activation / Regulation of TLR by endogenous ligand / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / positive regulation of platelet activation / positive regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interleukin-17 production / MyD88 deficiency (TLR2/4) / positive regulation of cytokine production involved in inflammatory response / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / IRAK4 deficiency (TLR2/4) / negative regulation of cold-induced thermogenesis / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of macrophage cytokine production / T-helper 1 type immune response / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / RSV-host interactions / negative regulation of osteoclast differentiation / positive regulation of reactive oxygen species biosynthetic process / cellular response to lipoteichoic acid / negative regulation of type II interferon production / negative regulation of interleukin-6 production / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytosis / cellular defense response / phagocytic cup / stress-activated MAPK cascade / coreceptor activity / positive regulation of chemokine production / cellular response to platelet-derived growth factor stimulus / ruffle / JNK cascade / positive regulation of B cell proliferation / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / nitric oxide biosynthetic process / positive regulation of smooth muscle cell proliferation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of interferon-beta production / TRAF6-mediated induction of TAK1 complex within TLR4 complex / lipopolysaccharide-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / lipopolysaccharide binding / Heme signaling / cellular response to mechanical stimulus / : / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / cellular response to amyloid-beta / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / cellular response to lipopolysaccharide Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) Eptatretus burgeri (inshore hagfish) | |||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Lee, J.-O. / Kim, H.M. / Park, B.S. | |||||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2007Title: Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran Authors: Kim, H.M. / Park, B.S. / Kim, J.-I. / Kim, S.E. / Lee, J. / Oh, S.C. / Enkhbayar, P. / Matsushima, N. / Lee, H. / Yoo, O.J. / Lee, J.-O. | |||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 2z65.cif.gz | 191.6 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb2z65.ent.gz | 150.9 KB | Display | PDB format |
| PDBx/mmJSON format | 2z65.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 2z65_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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| Full document | 2z65_full_validation.pdf.gz | 1.2 MB | Display | |
| Data in XML | 2z65_validation.xml.gz | 42.9 KB | Display | |
| Data in CIF | 2z65_validation.cif.gz | 54 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z65 ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z65 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 2z62SC ![]() 2z63C ![]() 2z64SC ![]() 2z66C S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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| Details | AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN |
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Components
-Protein , 2 types, 4 molecules ABCD
| #1: Protein | Mass: 31141.719 Da / Num. of mol.: 2 Fragment: TV3, UNP residues 27-228(human), E5564, UNP residues 19-158(Inshore hagfish) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)Gene: TLR4, VLRB.61 / Plasmid: pVL1393 / Production host: ![]() #2: Protein | Mass: 16184.761 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MD-2 / Plasmid: pVL1393 / Production host: ![]() |
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-Sugars , 2 types, 6 molecules 
| #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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| #4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 165 molecules 


| #5: Chemical | | #6: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | Y |
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| Nonpolymer details | POLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAINS M1401, M(1301-1304), M1201, N1401, N1301, AND ...POLYSACCHA |
| Sequence details | THIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 229TH LYS AND 230TH GLU. |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.24 % |
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| Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 4.5 Details: 0.2M Ammonium Sulfate, 0.1M Sodium Acetate, 20% PEG 4000, 5% Ethanol, pH 4.5, VAPOR DIFFUSION, temperature 296K |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2007 / Details: mirrors |
| Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
| Reflection | Resolution: 2.7→50 Å / Num. all: 30860 / Num. obs: 27898 / % possible obs: 90.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.089 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 2Z62, 2Z64 Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.864 / SU B: 33.68 / SU ML: 0.35 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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| Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 50.542 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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| Refine LS restraints |
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| Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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| LS refinement shell | Resolution: 2.7→2.769 Å / Total num. of bins used: 20
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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| Refinement TLS group |
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About Yorodumi



Homo sapiens (human)
Eptatretus burgeri (inshore hagfish)
X-RAY DIFFRACTION
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