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- PDB-2z62: Crystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61 -

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Entry
Database: PDB / ID: 2z62
TitleCrystal structure of the TV3 hybrid of human TLR4 and hagfish VLRB.61
ComponentsToll-like receptor 4, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / TLR / Toll-like receptor / VLR hybrid / MD-2 / LPS / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane
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 / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / lipopolysaccharide receptor complex ...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 / 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 / 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 macrophage cytokine production / positive regulation of smooth muscle cell migration / MyD88-dependent toll-like receptor signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / T-helper 1 type immune response / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / RSV-host interactions / positive regulation of NLRP3 inflammasome complex assembly / 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 / phagocytic cup / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / cellular response to platelet-derived growth factor stimulus / ruffle / positive regulation of B cell proliferation / ERK1 and ERK2 cascade / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / 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 smooth muscle cell proliferation / 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) / 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 / positive regulation of NF-kappaB transcription factor activity / 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 / ER-Phagosome pathway / response to lipopolysaccharide / defense response to Gram-negative bacterium / gene expression
Similarity search - Function
Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine rich repeat N-terminal domain / 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. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / 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 / Alpha Beta
Similarity search - Domain/homology
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: 1.7 Å
AuthorsLee, J.-O. / Kim, H.M. / Park, B.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: 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
DepositionJul 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_symm_contact / struct_asym / struct_conn / 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_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _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
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 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8694
Polymers31,1421
Non-polymers1,7283
Water4,360242
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.945, 54.214, 116.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Toll-like receptor 4, Variable lymphocyte receptor B / hToll / CD284 antigen / TV3


Mass: 31141.719 Da / Num. of mol.: 1
Fragment: TLR4, UNP residues 27-228(human), VLRB.61, UNP residues 128-199(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: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: O00206, UniProt: Q4G1L2
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsPOLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAINS M(701-703), N(801-804), AND L(901-902), RESPECTIVELY.
Sequence detailsTHIS CONSTRUCT INCLUDES A LINKER THAT CONSIST OF 229TH LYS AND 230TH GLU.

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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: 2.23 Å3/Da / Density % sol: 44.89 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 5.5
Details: 0.2M NaCl, 0.1M Bis-Tris Propane, 33% PEG 1000, pH 5.50, 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 210 / Detector: CCD / Date: Oct 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 29573 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.06

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZIW

1ziw


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.122 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.106 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1588 5.1 %RANDOM
Rwork0.19 ---
obs0.19 29573 99.1 %-
all-29841 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2---0.5 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 115 242 2546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222365
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1882.0393228
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84325.30698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48515397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.356158
X-RAY DIFFRACTIONr_chiral_restr0.0780.2392
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021695
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21036
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21586
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2165
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3040.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 119 -
Rwork0.25 2115 -
obs--98.03 %
Refinement TLS params.Method: refined / Origin x: 14.1091 Å / Origin y: 0.014 Å / Origin z: 8.4018 Å
111213212223313233
T-0.1279 Å2-0.0089 Å20.0125 Å2--0.1238 Å2-0.0137 Å2---0.1232 Å2
L0.7018 °2-0.5953 °20.6968 °2-0.9486 °2-0.8044 °2--1.4983 °2
S0.0109 Å °-0.0051 Å °-0.0144 Å °-0.0411 Å °0.0111 Å °0.03 Å °0.0289 Å °-0.0639 Å °-0.022 Å °

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