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- EMDB-39301: hTLR3/minibinder 8.6 -

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Basic information

Entry
Database: EMDB / ID: EMD-39301
TitlehTLR3/minibinder 8.6
Map data
Sample
  • Complex: hTLR3/minibinder 8.6 complex
    • Protein or peptide: Toll-like receptor 3
    • Protein or peptide: minibinder 8.6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsProtein design / binder / Innate immune / TLR / DE NOVO PROTEIN
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 / pattern recognition receptor activity / cellular response to exogenous dsRNA / 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 / positive regulation of interleukin-12 production / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / extracellular matrix / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / 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 virus / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of inflammatory response / cellular response to mechanical stimulus / 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 / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.88 Å
AuthorsKim H
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: De novo design of TLR3 binders
Authors: Kim H / Adams C / Burtner A / Lee DS / Dobbins C / Criswell C / Coventry B / Kim HM / King N
History
DepositionFeb 28, 2024-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39301.png

Downloads & links

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Map

FileDownload / File: emd_39301.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 360 pix.
= 239.04 Å		0.66 Å/pix.
x 360 pix.
= 239.04 Å		0.66 Å/pix.
x 360 pix.
= 239.04 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21
Minimum - Maximum-0.0017666062 - 2.358071
Average (Standard dev.)0.00091680896 (±0.02201462)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 239.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39301_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_39301_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_39301_half_map_2.map
Projections & Slices
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Sample components

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Entire : hTLR3/minibinder 8.6 complex

EntireName: hTLR3/minibinder 8.6 complex
Components
  • Complex: hTLR3/minibinder 8.6 complex
    • Protein or peptide: Toll-like receptor 3
    • Protein or peptide: minibinder 8.6
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: hTLR3/minibinder 8.6 complex

SupramoleculeName: hTLR3/minibinder 8.6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Toll-like receptor 3

MacromoleculeName: Toll-like receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.672383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KCTVSHEVAD CSHLKLTQVP DDLPTNITVL NLTHNQLRRL PAANFTRYSQ LTSLDVGFNT ISKLEPELCQ KLPMLKVLNL QHNELSQLS DKTFAFCTNL TELHLMSNSI QKIKNNPFVK QKNLITLDLS HNGLSSTKLG TQVQLENLQE LLLSNNKIQA L KSEELDIF ...String:
KCTVSHEVAD CSHLKLTQVP DDLPTNITVL NLTHNQLRRL PAANFTRYSQ LTSLDVGFNT ISKLEPELCQ KLPMLKVLNL QHNELSQLS DKTFAFCTNL TELHLMSNSI QKIKNNPFVK QKNLITLDLS HNGLSSTKLG TQVQLENLQE LLLSNNKIQA L KSEELDIF ANSSLKKLEL SSNQIKEFSP GCFHAIGRLF GLFLNNVQLG PSLTEKLCLE LANTSIRNLS LSNSQLSTTS NT TFLGLKW TNLTMLDLSY NNLNVVGNDS FAWLPQLEYF FLEYNNIQHL FSHSLHGLFN VRYLNLKRSF TKQSISLASL PKI DDFSFQ WLKCLEHLNM EDNDIPGIKS NMFTGLINLK YLSLSNSFTS LRTLTNETFV SLAHSPLHIL NLTKNKISKI ESDA FSWLG HLEVLDLGLN EIGQELTGQE WRGLENIFEI YLSYNKYLQL TRNSFALVPS LQRLMLRRVA LKNVDSSPSP FQPLR NLTI LDLSNNNIAN INDDMLEGLE KLEILDLQHN NLARLWKHAN PGGPIYFLKG LSHLHILNLE SNGFDEIPVE VFKDLF ELK IIDLGLNNLN TLPASVFNNQ VSLKSLNLQK NLITSVEKKV FGPAFRNLTE LDMRFNPFDC TCESIAWFVN WINETHT NI PELSSHYLCN TPPHYHGFPV RLFDTSSCKD SA

UniProtKB: Toll-like receptor 3

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Macromolecule #2: minibinder 8.6

MacromoleculeName: minibinder 8.6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.519198 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SLEEEAERVV EELVKEFNLS RTQEIALRRY AEYAARATAS EEVIEELLRD VAERLS

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 69.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 510475
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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