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- PDB-3ula: Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex -

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Entry
Database: PDB / ID: 3ula
TitleCrystal structure of the TV3 mutant F63W-MD-2-Eritoran complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / LRR / LPS binding / MD-2 / extracellular matrix
Function / homology
Function and homology information


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 / lipopolysaccharide receptor complex / detection of lipopolysaccharide ...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 / lipopolysaccharide receptor complex / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / MyD88-independent TLR4 cascade / I-kappaB phosphorylation / negative regulation of interleukin-23 production / TRIF-mediated programmed cell death / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / positive regulation of stress-activated MAPK cascade / intestinal epithelial structure maintenance / 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 / NAD+ nucleosidase activity, cyclic ADP-ribose generating / nucleotide-binding oligomerization domain containing 2 signaling pathway / 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 / positive regulation of cytokine production involved in inflammatory response / MyD88 deficiency (TLR2/4) / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / IRAK4 deficiency (TLR2/4) / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / T-helper 1 type immune response / toll-like receptor signaling pathway / positive regulation of smooth muscle cell migration / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / RSV-host interactions / negative regulation of osteoclast differentiation / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / negative regulation of type II interferon production / positive regulation of interferon-alpha production / Respiratory syncytial virus (RSV) attachment and entry / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / phagocytic cup / phagocytosis / cellular defense response / stress-activated MAPK cascade / coreceptor activity / positive regulation of chemokine production / ruffle / JNK cascade / cellular response to platelet-derived growth factor stimulus / positive regulation of B cell proliferation / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / ERK1 and ERK2 cascade / positive regulation of MAP kinase activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of interleukin-1 beta production / IKK complex recruitment mediated by RIP1 / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / positive regulation of JNK cascade / lipopolysaccharide binding / Heme signaling / positive regulation of non-canonical NF-kappaB signal transduction / 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 mechanical stimulus / positive regulation of inflammatory response / cellular response to amyloid-beta / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Alpha-Beta Horseshoe / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-E55 / Toll-like receptor 4 / Variable lymphocyte receptor B / Lymphocyte antigen 96
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsKim, H.J. / Cheong, H.K. / Jeon, Y.H.
CitationJournal: Plos One / Year: 2012
Title: Structure-Based Rational Design of a Toll-like Receptor 4 (TLR4) Decoy Receptor with High Binding Affinity for a Target Protein.
Authors: Han, J. / Kim, H.J. / Lee, S.C. / Hong, S. / Park, K. / Jeon, Y.H. / Kim, D. / Cheong, H.K. / Kim, H.S.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Derived calculations
Revision 1.2Aug 23, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 4, Variable lymphocyte receptor B
B: Lymphocyte antigen 96
C: Toll-like receptor 4, Variable lymphocyte receptor B
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,19512
Polymers95,5104
Non-polymers4,6858
Water00
1
A: Toll-like receptor 4, Variable lymphocyte receptor B
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0976
Polymers47,7552
Non-polymers2,3434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lymphocyte antigen 96
C: Toll-like receptor 4, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0976
Polymers47,7552
Non-polymers2,3434
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.210, 126.935, 129.506
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Toll-like receptor 4, Variable lymphocyte receptor B / hToll


Mass: 31425.990 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-228, UNP RESIDUES 126-199 / Mutation: F63W
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND VLRB (UNP RESIDUES 126-199)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: TLR4, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00206, UniProt: Q4G1L2
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 16328.892 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 19-158
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LY96, ESOP1, MD2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y6Y9
#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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Chemical ChemComp-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 / E5564 / ERITORAN


Mass: 1313.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C66H126N2O19P2
Has protein modificationY
Sequence detailsFOR THE CHAIN B/D, THE PROTEIN OF MD2 (UNP RESIDUES 19-158), GLY56 IS NATURAL VARIANT. FOR THE ...FOR THE CHAIN B/D, THE PROTEIN OF MD2 (UNP RESIDUES 19-158), GLY56 IS NATURAL VARIANT. FOR THE CHAIN A/C, THE FUSION PROTEIN OF TLR4 (UNP RESIDUES 27-228) AND VLRB.61 (UNP RESIDUES 126-199).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 4.5
Details: 0.1M sodium acetate (pH4.5), 22% w/v PEG 8000, 0.2M lithium sulfate, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 22, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 15854 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.6→3.79 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z65

2z65


Resolution: 3.6→50 Å / Stereochemistry target values: maximum likelihood
RfactorNum. reflectionSelection details
Rfree0.3406 769 RANDOM
Rwork0.3056 --
all-15790 -
obs-15790 -
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 312 0 6962
LS refinement shellResolution: 3.6→3.79 Å

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