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- PDB-1ziw: Human Toll-like Receptor 3 extracellular domain structure -

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Basic information

Entry
Database: PDB / ID: 1ziw
TitleHuman Toll-like Receptor 3 extracellular domain structure
ComponentsToll-like receptor 3
KeywordsIMMUNE SYSTEM / innate immunity
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 / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsWilson, I.A. / Choe, J.
CitationJournal: Science / Year: 2005
Title: Crystal structure of human toll-like receptor 3 (TLR3) ectodomain.
Authors: Choe, J. / Kelker, M.S. / Wilson, I.A.
History
DepositionApr 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_chiral / pdbx_validate_close_contact / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,82817
Polymers77,5011
Non-polymers3,32716
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.497, 155.121, 119.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Toll-like receptor 3


Mass: 77501.273 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Cell line (production host): Hi 5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15455

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Sugars , 2 types, 8 molecules

#2: 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 / Fragment: cryo solvent
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
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Fragment: cryo solvent
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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Non-polymers , 3 types, 370 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Fragment: solvent / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O

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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: 3.2 Å3/Da / Density % sol: 65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG2000, Ammonium Sulfate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111.07812
SYNCHROTRONSSRL BL11-121.1401,1.1412,1.1271
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDMar 15, 2005
ADSC QUANTUM 42CCDMar 13, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.078121
21.14011
31.14121
41.12711
ReflectionResolution: 2.1→50 Å / Num. all: 76650 / Num. obs: 76420 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0013refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.356 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2479 3795 5.1 %RANDOM
Rwork0.20825 ---
all0.2103 71071 --
obs0.2103 71071 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.444 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20 Å2
2--0.06 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 214 362 5628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225370
X-RAY DIFFRACTIONr_angle_refined_deg1.6412.0087284
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82225.673245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60615938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8951517
X-RAY DIFFRACTIONr_chiral_restr0.1060.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023873
X-RAY DIFFRACTIONr_nbd_refined0.2320.22547
X-RAY DIFFRACTIONr_nbtor_refined0.3220.23579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2452
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4430.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5080.216
X-RAY DIFFRACTIONr_mcbond_it2.17533248
X-RAY DIFFRACTIONr_mcangle_it3.38155094
X-RAY DIFFRACTIONr_scbond_it6.49582365
X-RAY DIFFRACTIONr_scangle_it9.043112190
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 289 -
Rwork0.234 5154 -
obs--99.98 %
Refinement TLS params.Method: refined / Origin x: 36.101 Å / Origin y: -19.293 Å / Origin z: 19.007 Å
111213212223313233
T-0.092 Å20.032 Å20.0008 Å2--0.0636 Å20.0122 Å2---0.237 Å2
L1.2329 °20.6114 °2-0.4339 °2-0.5486 °2-0.2068 °2--0.5063 °2
S-0.0297 Å °0.058 Å °0.0244 Å °0.0093 Å °0.0369 Å °0.1273 Å °0.066 Å °0.137 Å °-0.0072 Å °

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