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- PDB-4r09: Crystal structure of human TLR8 in complex with ORN06S -

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Basic information

Entry
Database: PDB / ID: 4r09
TitleCrystal structure of human TLR8 in complex with ORN06S
ComponentsToll-like receptor 8
KeywordsIMMUNE SYSTEM / Leucine rich repeat / RNA / Glycosylation / innate immunity / RNA recognition / ssRNA / RNA receptor / RNA binding / antiviral binding / 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 / positive regulation of type II interferon production / double-stranded RNA binding / 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-06S / Chem-UPT / URIDINE / Toll-like receptor 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsTanji, H. / Ohto, U. / Shimizu, T.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Toll-like receptor 8 senses degradation products of single-stranded RNA.
Authors: Tanji, H. / Ohto, U. / Shibata, T. / Taoka, M. / Yamauchi, Y. / Isobe, T. / Miyake, K. / Shimizu, T.
History
DepositionJul 30, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 2.0Jul 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_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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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)383,58930
Polymers371,3414
Non-polymers12,24726
Water00
1
A: Toll-like receptor 8
B: Toll-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,03616
Polymers185,6712
Non-polymers6,36514
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint60 kcal/mol
Surface area58800 Å2
MethodPISA
2
C: Toll-like receptor 8
D: Toll-like receptor 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,55314
Polymers185,6712
Non-polymers5,88212
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10160 Å2
ΔGint53 kcal/mol
Surface area58610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.683, 141.342, 170.042
Angle α, β, γ (deg.)90.00, 89.46, 90.00
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: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR8, UNQ249/PRO286 / Cell line (production host): SCHNEIDER 2(S2) CELLS / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9NR97

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Sugars , 4 types, 14 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.: 2
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
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.: 6
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
#4: 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.: 3
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
#8: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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, 12 molecules

#5: Chemical
ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O6
#6: Chemical
ChemComp-06S / O-[(2R,3S,4R,5R)-5-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)-2-({[(S)-({(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-[(thiophosphonooxy)methyl]tetrahydrofuran-3-yl}oxy)(sulfanyl)phosphoryl]oxy}methyl)-4-hydroxytetrahydrofuran-3-yl] dihydrogen (S)-phosphorothioate


Mass: 797.563 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H26N7O16P3S3
#7: Chemical
ChemComp-UPT / 1-[(2R,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-sulfidotetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-4-yl]pyrimidine-2,4(1H,3H)-dione


Mass: 322.232 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11N2O7PS

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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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 12-14% (w/v) PEG 3350, 0.2-0.3M potassium formate, 0.1M sodium citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 114230 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rsym value: 0.148 / Net I/σ(I): 22.2

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→31.56 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.884 / SU B: 14.554 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.718 / ESU R Free: 0.354 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28508 6113 5 %RANDOM
Rwork0.21614 ---
obs0.21967 115689 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.343 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.01 Å2
2---0 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.62→31.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24106 0 789 0 24895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01925478
X-RAY DIFFRACTIONr_bond_other_d0.0010.0224145
X-RAY DIFFRACTIONr_angle_refined_deg1.3232.00134663
X-RAY DIFFRACTIONr_angle_other_deg0.714355438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64852977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43524.9081202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.283154359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.51215124
X-RAY DIFFRACTIONr_chiral_restr0.0890.24059
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0228120
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1026.26711968
X-RAY DIFFRACTIONr_mcbond_other4.1026.26711968
X-RAY DIFFRACTIONr_mcangle_it6.2839.3914921
X-RAY DIFFRACTIONr_mcangle_other6.2839.3914922
X-RAY DIFFRACTIONr_scbond_it3.8316.44513510
X-RAY DIFFRACTIONr_scbond_other3.8316.44513510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9989.5419743
X-RAY DIFFRACTIONr_long_range_B_refined8.748.91527664
X-RAY DIFFRACTIONr_long_range_B_other8.748.91527664
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.619→2.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 382 -
Rwork0.308 7543 -
obs--88.02 %

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