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- PDB-8yht: hTLR3/minibinder 7.7 -

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Basic information

Entry
Database: PDB / ID: 8yht
TitlehTLR3/minibinder 7.7
Components
  • Toll-like receptor 3
  • minibinder 7.7
KeywordsDE NOVO PROTEIN / Protein design / binder / Innate immune / TLR
Function / homology
Function and homology information


TLR3 deficiency - HSE / response to dsRNA / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / I-kappaB phosphorylation / Toll Like Receptor 3 (TLR3) Cascade ...TLR3 deficiency - HSE / response to dsRNA / UNC93B1 deficiency - HSE / TICAM1 deficiency - HSE / type III interferon production / positive regulation of type III interferon production / TRAF3 deficiency - HSE / regulation of dendritic cell cytokine production / I-kappaB phosphorylation / Toll Like Receptor 3 (TLR3) Cascade / TLR3-mediated TICAM1-dependent programmed cell death / inflammatory response to wounding / activation of NF-kappaB-inducing kinase activity / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / detection of virus / 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 / toll-like receptor signaling pathway / cellular response to exogenous dsRNA / pattern recognition receptor activity / RSV-host interactions / response to exogenous dsRNA / negative regulation of osteoclast differentiation / ubiquitin-like protein ligase binding / positive regulation of interferon-alpha production / cellular response to interferon-beta / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / JNK cascade / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / positive regulation of interleukin-12 production / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / extracellular matrix / positive regulation of interferon-beta production / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to type II interferon / positive regulation of interleukin-6 production / cellular response to virus / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of type II interferon production / male gonad development / positive regulation of angiogenesis / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / double-stranded RNA binding / 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 / Golgi membrane / lysosomal 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 / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain ...Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / TIR domain / Leucine Rich repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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
Toll-like receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKim, H. / Kim, H.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: De novo design of TLR3 binders
Authors: Kim, H. / Adams, C. / Burtner, A. / Lee, D.S. / Dobbins, C. / Criswell, C. / Coventry, B. / Kim, H.M. / King, N.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 3
B: minibinder 7.7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,36112
Polymers83,3362
Non-polymers3,02510
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Toll-like receptor 3


Mass: 76672.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: O15455
#2: Protein minibinder 7.7


Mass: 6663.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#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.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-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.: 6
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
Has ligand of interestN
Has protein modificationY

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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: hTLR3/minibinder 8.6 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 8000 nm
Image recordingElectron dose: 69.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 739755 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035961
ELECTRON MICROSCOPYf_angle_d0.6168085
ELECTRON MICROSCOPYf_dihedral_angle_d7.871822
ELECTRON MICROSCOPYf_chiral_restr0.046976
ELECTRON MICROSCOPYf_plane_restr0.0041014

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