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- PDB-3ul8: Crystal structure of the TV3 mutant V134L -

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Entry
Database: PDB / ID: 3ul8
TitleCrystal structure of the TV3 mutant V134L
ComponentsToll-like receptor 4, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / LRR / protein binding / MD-2 / extracellular matrix
Function / homology
Function and homology information


nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / 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 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production ...nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / detection of fungus / 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 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / negative regulation of interleukin-23 production / I-kappaB phosphorylation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / Toll Like Receptor 4 (TLR4) Cascade / Caspase activation via Death Receptors in the presence of ligand / wound healing involved in inflammatory response / B cell proliferation involved in immune response / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / macrophage activation / Regulation of TLR by endogenous ligand / microglia differentiation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / NADP+ nucleosidase activity / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / MyD88 deficiency (TLR2/4) / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / IRAK4 deficiency (TLR2/4) / positive regulation of reactive oxygen species biosynthetic process / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / phagocytic cup / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / T-helper 1 type immune response / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / negative regulation of osteoclast differentiation / positive regulation of nitric-oxide synthase biosynthetic process / positive regulation of interferon-alpha production / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / ERK1 and ERK2 cascade / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / nitric oxide biosynthetic process / positive regulation of interferon-beta production / positive regulation of interleukin-12 production / 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 / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / Heme signaling / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / signaling receptor activity / gene expression / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium
Similarity search - Function
Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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 / Leucine Rich repeat / TIR domain ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / 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 / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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 / Alpha Beta
Similarity search - Domain/homology
beta-L-fucopyranose / Toll-like receptor 4 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.1Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jan 31, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_unobs_or_zero_occ_atoms / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 3.0Jul 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.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 3.1Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 4, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4695
Polymers31,4011
Non-polymers1,0684
Water57632
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)32.040, 50.500, 192.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 31400.982 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 27-228, UNP RESIDUES 126-199 / Mutation: V134L
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

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Sugars , 3 types, 3 molecules

#2: 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.: 1
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
#3: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 33 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE 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: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 5.5
Details: 0.1M Bis-Tris(pH5.5), 36% PEG 1000, 0.2M Lithium sulfate, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2010
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 11557 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.5→2.59 Å

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z62

2z62


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: maximum likelihood
RfactorNum. reflectionSelection details
Rfree0.2996 568 RANDOM
Rwork0.2401 --
all-10887 -
obs-10887 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2196 0 68 32 2296
LS refinement shellResolution: 2.5→2.59 Å

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