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- PDB-4z0c: Crystal structure of TLR13-ssRNA13 complex -

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Basic information

Entry
Database: PDB / ID: 4z0c
TitleCrystal structure of TLR13-ssRNA13 complex
Components
  • DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')
  • Toll-like receptor 13
KeywordsIMMUNE SYSTEM / immune receptor / Toll-like receptor / ssRNA
Function / homology
Function and homology information


toll-like receptor 13 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway / regulation of MAPK cascade / response to virus / transmembrane signaling receptor activity / signaling receptor activity / rRNA binding / endosome membrane ...toll-like receptor 13 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway / regulation of MAPK cascade / response to virus / transmembrane signaling receptor activity / signaling receptor activity / rRNA binding / endosome membrane / endosome / inflammatory response / innate immune response / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Toll-like receptor / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / TIR domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / TIR domain profile. / 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
Similarity search - Domain/homology
RNA / RNA (> 10) / Toll-like receptor 13
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSong, W. / Han, Z. / Chai, J.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13.
Authors: Wen Song / Jia Wang / Zhifu Han / Yifan Zhang / Heqiao Zhang / Weiguang Wang / Junbiao Chang / Bingshu Xia / Shilong Fan / Dekai Zhang / Jiawei Wang / Hong-Wei Wang / Jijie Chai /
Abstract: Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an ...Toll-like receptors (TLRs) have crucial roles in innate immunity, functioning as pattern-recognition receptors. TLR13 recognizes a conserved sequence from bacterial 23S rRNA and then triggers an immune response. Here we report the crystal structure of the mouse TLR13 ectodomain bound by a 13-nt single-stranded (ss) RNA derived from 23S rRNA. The ssRNA induces TLR13 dimerization but assumes a stem-loop-like structure that is completely different from that in the bacterial ribosome but nevertheless is crucial for TLR13 recognition. Most of the RNA nucleotides are splayed out to make base-specific contacts with the concave surface of TLR13, and RNA-specific interactions are important to allow TLR13 to distinguish RNA from DNA. Interestingly, a viral-derived 16-nt ssRNA predicted to form a similar stem-loop-like structure also induces TLR13 activation. Together, our results reveal the structural mechanism of TLR13's sequence- and conformation-specific recognition of ssRNA.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Derived calculations
Revision 1.2Oct 28, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _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_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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 13
D: Toll-like receptor 13
B: DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')
C: DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,96630
Polymers170,9964
Non-polymers6,97126
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint123 kcal/mol
Surface area60940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.549, 115.209, 167.611
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Toll-like receptor 13


Mass: 81335.352 Da / Num. of mol.: 2 / Fragment: UNP residues 69-777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr13
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q6R5N8
#2: RNA chain DNA (5'-R(P*AP*CP*GP*GP*AP*AP*AP*GP*AP*CP*CP*CP*C)-3')


Mass: 4162.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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: obtained synthetically
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: 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.: 20 / Source method: obtained synthetically / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1%(w/v) tryptone, 0.05M HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid) sodium pH 7.0 and 12%(v/v) polyethylene glycol (PEG) 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 89687 / % possible obs: 92.9 % / Redundancy: 8.5 % / Net I/σ(I): 27.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.9 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.244 4486 5 %
Rwork0.191 --
obs-89687 92.5 %
Displacement parametersBiso mean: 37.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11454 0 1006 361 12821
Refinement TLS params.Method: refined / Origin x: -28.2271 Å / Origin y: -30.423 Å / Origin z: 41.8152 Å
111213212223313233
T0.0883 Å2-0.0036 Å20.0035 Å2-0.122 Å20.0379 Å2--0.0866 Å2
L0.2496 °20.0003 °2-0.0766 °2-0.0487 °20.0448 °2--0.2902 °2
S0.0227 Å °-0.0845 Å °-0.0052 Å °0.0189 Å °-0.0242 Å °-0.0089 Å °0.028 Å °-0.0223 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA69 - 777
2X-RAY DIFFRACTION1allA901 - 7741
3X-RAY DIFFRACTION1allB1 - 13
4X-RAY DIFFRACTION1allC1 - 13
5X-RAY DIFFRACTION1allD69 - 777
6X-RAY DIFFRACTION1allD901 - 7741
7X-RAY DIFFRACTION1allS1 - 361

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