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- PDB-3j0a: Homology model of human Toll-like receptor 5 fitted into an elect... -

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Basic information

Entry
Database: PDB / ID: 3j0a
TitleHomology model of human Toll-like receptor 5 fitted into an electron microscopy single particle reconstruction
ComponentsToll-like receptor 5
KeywordsIMMUNE SYSTEM / Toll-like receptor 5 / membrane protein / leucine-rich repeat / asymmetric homodimer / glycoprotein
Function / homology
Function and homology information


Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus ...Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / plasma membrane
Similarity search - Function
Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / 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
Toll-like receptor 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 26 Å
AuthorsModis, Y. / Zhou, K. / Kanai, R. / Lee, P. / Wang, H.W.
CitationJournal: J Struct Biol / Year: 2012
Title: Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin.
Authors: Kaifeng Zhou / Ryuta Kanai / Phong Lee / Hong-Wei Wang / Yorgo Modis /
Abstract: The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain ...The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain interactions. The structure shows that like TLR9, TLR5 dimerizes in the absence of ligand. The asymmetry of the dimer suggests that TLR5 may recognize two flagellin molecules cooperatively to establish an optimal flagellin response threshold. A TLR5 homology model was generated and fitted into the electron microscopy structure. All seven predicted N-linked glycosylation sites are exposed on the molecular surface, away from the dimer interface. Glycosylation at the first five sites was confirmed by tandem mass spectrometry. Two aspartate residues proposed to interact with flagellin (Asp294 and Asp366) are sterically occluded by a glycan at position 342. In contrast, the central region of the ectodomains near the dimer interface is unobstructed by glycans. Ligand binding in this region would be consistent with the ligand binding sites of other TLRs.
History
DepositionJun 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
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.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.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

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Assembly

Deposited unit
A: Toll-like receptor 5
B: Toll-like receptor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,45616
Polymers193,3132
Non-polymers5,14314
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Toll-like receptor 5 / / Toll/interleukin-1 receptor-like protein 3


Mass: 96656.367 Da / Num. of mol.: 2 / Fragment: mature glycoprotein (UNP residues 23-858)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TIL3, TLR5 / Plasmid: pAcGP67-A / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: O60602
#2: Polysaccharide
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Mass: 367.349 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full-length Toll-like receptor 5 / Type: COMPLEX / Details: Asymmetric homodimer. The sample was monodisperse.
Molecular weightValue: 0.2 MDa / Experimental value: YES
Buffer solutionName: 10 mM TEA pH 7.5, 0.1 M NaCl, followed by 1% uranyl-formate stain
pH: 7.5
Details: 10 mM TEA pH 7.5, 0.1 M NaCl, followed by 1% uranyl-formate stain
SpecimenConc.: 0.005 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES / Details: 10 mM TEA, pH 7.5, 0.15 M NaCl,
EM stainingType: NEGATIVE / Material: Uranyl Formate
Specimen supportDetails: Thin-carbon-covered holey carbon copper grid

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Electron microscopy imaging

MicroscopyModel: FEI TECNAI 12 / Date: Aug 1, 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 52000 X / Calibrated magnification: 52000 X / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.2 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: SIDE ENTRY, EUCENTRIC / Specimen holder type: Eucentric / Temperature: 298 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1MODELLERmodel fitting
2REFMACmodel fitting
3IMAGIC3D reconstruction
4SPIDER3D reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: Random conical tilt followed by projection matching refinement
Resolution: 26 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 4241
Details: Final maps were calculated from all the particles by back-projection reconstruction.
Num. of class averages: 100 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Energy minimization
Details: REFINEMENT PROTOCOL--Rigid body and positional refinement DETAILS--Initial local fitting was done using Chimera and then the energy of the model was minimized with MODELLER and REFMAC.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms11492 0 336 0 11828

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