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- PDB-3w3l: Crystal structure of human TLR8 in complex with Resiquimod (R848)... -

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Basic information

Entry
Database: PDB / ID: 3w3l
TitleCrystal structure of human TLR8 in complex with Resiquimod (R848) crystal form 1
ComponentsToll-like receptor 8
KeywordsIMMUNE SYSTEM / Leucine Rich Repeat / RNA / Glycosylation / RNA Recognition / ssRNA / Receptor / RNA Receptor / Innate Immunity / RNA Binding / Secreted / Resiquimod / Antivirus and Antitumor Drug / Antivirus and Antitumor Drug Binding
Function / homology
Function and homology information


Toll Like Receptor 7/8 (TLR7/8) Cascade / toll-like receptor 8 signaling pathway / negative regulation of interleukin-12 production / endolysosome membrane / positive regulation of innate immune response / Trafficking and processing of endosomal TLR / pattern recognition receptor activity / toll-like receptor signaling pathway / immunoglobulin mediated immune response / canonical NF-kappaB signal transduction ...Toll Like Receptor 7/8 (TLR7/8) Cascade / toll-like receptor 8 signaling pathway / negative regulation of interleukin-12 production / endolysosome membrane / positive regulation of innate immune response / Trafficking and processing of endosomal TLR / pattern recognition receptor activity / toll-like receptor signaling pathway / immunoglobulin mediated immune response / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / regulation of protein phosphorylation / response to virus / cellular response to mechanical stimulus / positive regulation of interleukin-6 production / double-stranded RNA binding / positive regulation of type II interferon production / signaling receptor activity / defense response to virus / single-stranded RNA binding / endosome membrane / inflammatory response / external side of plasma membrane / Golgi membrane / innate immune response / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / DNA binding / RNA binding / identical protein binding / plasma membrane
Similarity search - Function
TIR domain / Leucine Rich Repeat / 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 ...TIR domain / Leucine Rich Repeat / 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
Chem-RX8 / Toll-like receptor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsTanji, H. / Ohto, U. / Shimizu, T.
CitationJournal: Science / Year: 2013
Title: Structural reorganization of the Toll-like receptor 8 dimer induced by agonistic ligands
Authors: Tanji, H. / Ohto, U. / Shibata, T. / Miyake, K. / Shimizu, T.
History
DepositionDec 22, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_biol
Item: _pdbx_struct_assembly_prop.biol_id
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 8
B: Toll-like receptor 8
C: Toll-like receptor 8
D: Toll-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,31843
Polymers371,3414
Non-polymers14,97739
Water16,123895
1
A: Toll-like receptor 8
D: Toll-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,27022
Polymers185,6712
Non-polymers7,59920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14410 Å2
ΔGint72 kcal/mol
Surface area61340 Å2
MethodPISA
2
B: Toll-like receptor 8
C: Toll-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,04921
Polymers185,6712
Non-polymers7,37819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint71 kcal/mol
Surface area61550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.470, 138.870, 169.661
Angle α, β, γ (deg.)90.000, 92.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Toll-like receptor 8


Mass: 92835.367 Da / Num. of mol.: 4 / Fragment: UNP residues 27-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR8, UNQ249/PRO286 / Production host: Drosophila (fruit flies) / Strain (production host): S2 / References: UniProt: Q9NR97

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Sugars , 3 types, 27 molecules

#2: Polysaccharide
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[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: 910.823 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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.: 4
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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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, 907 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-RX8 / 1-[4-amino-2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-1-yl]-2-methylpropan-2-ol / R848, Resiquimod


Mass: 314.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H22N4O2 / Comment: antivirus*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 2.74 Å3/Da / Density % sol: 55.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 14%(w/v) PEG3350, 0.1M MES, 0.15M ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.33→59.26 Å / Num. obs: 159473 / % possible obs: 93.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.27 Å2 / Rsym value: 0.079 / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→45.075 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8167 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 7995 5.01 %RANDOM
Rwork0.196 ---
obs0.1982 159443 93.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.03 Å2 / Biso mean: 43.7859 Å2 / Biso min: 5.83 Å2
Refinement stepCycle: LAST / Resolution: 2.33→45.075 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24143 0 986 895 26024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625720
X-RAY DIFFRACTIONf_angle_d1.27734959
X-RAY DIFFRACTIONf_chiral_restr0.1054153
X-RAY DIFFRACTIONf_plane_restr0.0064363
X-RAY DIFFRACTIONf_dihedral_angle_d21.5629830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.33-2.35340.35641890.30743931412072
2.3534-2.38110.3752210.29934054427575
2.3811-2.41020.33812090.28684214442377
2.4102-2.44070.32362170.27034270448780
2.4407-2.47280.31192280.26514480470882
2.4728-2.50670.30372460.25744561480785
2.5067-2.54250.32022260.25874698492486
2.5425-2.58040.31052620.25644734499688
2.5804-2.62070.33232840.24884877516190
2.6207-2.66370.27942480.24064891513991
2.6637-2.70960.29882720.23395042531493
2.7096-2.75890.27772520.23175048530094
2.7589-2.81190.27432780.21275212549096
2.8119-2.86930.27532620.22055237549997
2.8693-2.93170.26862630.22745282554598
2.9317-2.99990.28142520.2285367561998
2.9999-3.07490.28122590.22135369562898
3.0749-3.1580.24872820.22135367564999
3.158-3.25090.2793230.219553205643100
3.2509-3.35580.25413100.20954185728100
3.3558-3.47570.2473050.200154135718100
3.4757-3.61480.2573150.189353715686100
3.6148-3.77930.21292650.169754415706100
3.7793-3.97840.19722820.16154315713100
3.9784-4.22750.19923170.158653845701100
4.2275-4.55360.19952920.152954495741100
4.5536-5.01130.19282870.158954155702100
5.0113-5.73520.20923040.166254305734100
5.7352-7.2210.20852960.182554745770100
7.221-45.08310.20842490.19385268551794
Refinement TLS params.Method: refined / Origin x: 8.6321 Å / Origin y: -23.6671 Å / Origin z: 41.2484 Å
111213212223313233
T0.1696 Å20.0258 Å20.0025 Å2-0.1805 Å2-0.0774 Å2--0.0472 Å2
L0.377 °20.4121 °2-0.2407 °2-1.2094 °2-0.7035 °2--0.5347 °2
S-0.0895 Å °0.1438 Å °-0.0753 Å °-0.3815 Å °0.1092 Å °-0.0921 Å °0.192 Å °-0.0892 Å °-0.0099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA31 - 818
2X-RAY DIFFRACTION1allD - A900 - 1032
3X-RAY DIFFRACTION1allB31 - 818
4X-RAY DIFFRACTION1allC - B900 - 1032
5X-RAY DIFFRACTION1allC31 - 818
6X-RAY DIFFRACTION1allB - C900 - 1032
7X-RAY DIFFRACTION1allD31 - 818
8X-RAY DIFFRACTION1allD900 - 1032
9X-RAY DIFFRACTION1allC - A1 - 1019
10X-RAY DIFFRACTION1allD - A1 - 1369

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