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- PDB-3ulv: Structure of quaternary complex of human TLR3ecd with three Fabs ... -

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Basic information

Entry
Database: PDB / ID: 3ulv
TitleStructure of quaternary complex of human TLR3ecd with three Fabs (Form2)
Components
  • Fab1068 heavy chain
  • Fab1068 light chain
  • Fab12 heavy chain
  • Fab12 light chain
  • Fab15 heavy chain
  • Fab15 light chain
  • Toll-like receptor 3
KeywordsIMMUNE SYSTEM / Toll-like receptor-3 / TLR3 / innate immunity / leucine rich repeat / LRR / immunoglobulin
Function / homology
Function and homology information


TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / I-kappaB phosphorylation ...TLR3 deficiency - HSE / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / response to dsRNA / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / Toll Like Receptor 3 (TLR3) Cascade / I-kappaB phosphorylation / TLR3-mediated TICAM1-dependent programmed cell death / inflammatory response to wounding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / detection of virus / activation of NF-kappaB-inducing kinase activity / RIP-mediated NFkB activation via ZBP1 / hyperosmotic response / endolysosome membrane / positive regulation of cytokine production involved in inflammatory response / Trafficking and processing of endosomal TLR / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / RSV-host interactions / cellular response to exogenous dsRNA / response to exogenous dsRNA / negative regulation of osteoclast differentiation / cellular response to interferon-beta / positive regulation of interferon-alpha production / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / JNK cascade / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / extracellular matrix / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / cellular response to virus / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / male gonad development / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / early endosome / endosome membrane / defense response to bacterium / positive regulation of apoptotic process / lysosomal membrane / Golgi membrane / innate immune response / positive regulation of gene expression / endoplasmic reticulum membrane / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.522 Å
AuthorsLuo, J. / Gilliland, G.L. / Obmolova, O. / Malia, T. / Teplyakov, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Lateral Clustering of TLR3:dsRNA Signaling Units Revealed by TLR3ecd:3Fabs Quaternary Structure.
Authors: Luo, J. / Obmolova, G. / Malia, T.J. / Wu, S.J. / Duffy, K.E. / Marion, J.D. / Bell, J.K. / Ge, P. / Zhou, Z.H. / Teplyakov, A. / Zhao, Y. / Lamb, R.J. / Jordan, J.L. / San Mateo, L.R. / ...Authors: Luo, J. / Obmolova, G. / Malia, T.J. / Wu, S.J. / Duffy, K.E. / Marion, J.D. / Bell, J.K. / Ge, P. / Zhou, Z.H. / Teplyakov, A. / Zhao, Y. / Lamb, R.J. / Jordan, J.L. / San Mateo, L.R. / Sweet, R.W. / Gilliland, G.L.
History
DepositionNov 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1May 30, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _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 2.1Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 3
L: Fab15 light chain
H: Fab15 heavy chain
C: Fab12 light chain
D: Fab12 heavy chain
E: Fab1068 light chain
F: Fab1068 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,07624
Polymers221,7277
Non-polymers4,35017
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)363.300, 131.660, 154.200
Angle α, β, γ (deg.)90.00, 91.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 6 types, 6 molecules LHCDEF

#2: Antibody Fab15 light chain


Mass: 23239.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Antibody Fab15 heavy chain


Mass: 24458.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Antibody Fab12 light chain


Mass: 22749.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#5: Antibody Fab12 heavy chain


Mass: 24575.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#6: Antibody Fab1068 light chain


Mass: 23606.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#7: Antibody Fab1068 heavy chain


Mass: 24302.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: synthetic FAB library / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein / Non-polymers , 2 types, 7 molecules A

#11: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#1: Protein Toll-like receptor 3 / TLR3ecd


Mass: 78794.617 Da / Num. of mol.: 1 / Fragment: UNP residues 22-702
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: O15455

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Sugars , 3 types, 11 molecules

#8: 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.: 4
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
#9: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: 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.: 6
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

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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: 8.31 Å3/Da / Density % sol: 85.21 %
Crystal growTemperature: 293 K / pH: 4.5
Details: 0.1 M sodium acetate, pH 4.5, 2.54 M ammonium sulfate, 5% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 19, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 48292 / % possible obs: 52.8 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.208 / Net I/σ(I): 8.9
Reflection shellResolution: 3.5→3.7 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.3 / % possible all: 11.7

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: dev_896)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2A0Z, 1ZIW, 3ULS, 3NA9, 3QPQ

2a0z

1ziw

3uls

3na9

3qpq


Resolution: 3.522→48.448 Å / SU ML: 0.47 / σ(F): 1.99 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 2396 4.97 %
Rwork0.2307 --
obs0.2318 48255 53.55 %
all-48256 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.804 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-28.9111 Å20 Å23.3287 Å2
2--70.6955 Å20 Å2
3---26.4866 Å2
Refinement stepCycle: LAST / Resolution: 3.522→48.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15315 0 276 0 15591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215985
X-RAY DIFFRACTIONf_angle_d0.61321756
X-RAY DIFFRACTIONf_dihedral_angle_d14.15804
X-RAY DIFFRACTIONf_chiral_restr0.0422506
X-RAY DIFFRACTIONf_plane_restr0.0032745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.522-3.5940.4454270.3313375X-RAY DIFFRACTION8
3.594-3.67210.3025330.2837773X-RAY DIFFRACTION15
3.6721-3.75750.3191460.26491051X-RAY DIFFRACTION21
3.7575-3.85150.3313630.25771271X-RAY DIFFRACTION25
3.8515-3.95550.2951660.25571540X-RAY DIFFRACTION30
3.9555-4.07190.3045860.2621698X-RAY DIFFRACTION34
4.0719-4.20320.25291130.2431957X-RAY DIFFRACTION39
4.2032-4.35340.22611070.21722199X-RAY DIFFRACTION44
4.3534-4.52760.26331350.21842445X-RAY DIFFRACTION49
4.5276-4.73350.24731410.21632749X-RAY DIFFRACTION55
4.7335-4.98280.23221590.21413060X-RAY DIFFRACTION61
4.9828-5.29460.26691760.21183440X-RAY DIFFRACTION68
5.2946-5.70280.25752080.23433879X-RAY DIFFRACTION77
5.7028-6.27560.26812430.24784447X-RAY DIFFRACTION88
6.2756-7.18120.2812580.24774979X-RAY DIFFRACTION98
7.1812-9.03790.24762620.23335016X-RAY DIFFRACTION99
9.0379-48.4530.20852730.21194980X-RAY DIFFRACTION96

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