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- EMDB-30294: Cryo-EM structure of mouse TLR3 in complex with UNC93B1 -

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Basic information

Entry
Database: EMDB / ID: EMD-30294
TitleCryo-EM structure of mouse TLR3 in complex with UNC93B1
Map data
Sample
  • Complex: Complex of TLR3 and UNC93B1
    • Protein or peptide: Toll-like receptor 3
    • Protein or peptide: Protein unc-93 homolog B1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


Trafficking and processing of endosomal TLR / type III interferon production / positive regulation of type III interferon production / response to dsRNA / toll-like receptor 7 signaling pathway / regulation of dendritic cell cytokine production / inflammatory response to wounding / Toll-like receptor binding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway ...Trafficking and processing of endosomal TLR / type III interferon production / positive regulation of type III interferon production / response to dsRNA / toll-like receptor 7 signaling pathway / regulation of dendritic cell cytokine production / inflammatory response to wounding / Toll-like receptor binding / toll-like receptor 3 signaling pathway / necroptotic signaling pathway / toll-like receptor 9 signaling pathway / early phagosome / positive regulation of cytokine production involved in inflammatory response / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / cellular response to exogenous dsRNA / response to exogenous dsRNA / antigen processing and presentation / positive regulation of type I interferon production / cellular response to interferon-beta / positive regulation of interferon-alpha production / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / JNK cascade / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / intracellular protein transport / microglial cell activation / response to virus / cell morphogenesis / cellular response to virus / defense response / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / transmembrane signaling receptor activity / positive regulation of angiogenesis / antigen processing and presentation of exogenous peptide antigen via MHC class II / male gonad development / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of type II interferon production / double-stranded RNA binding / cellular response to xenobiotic stimulus / signaling receptor activity / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / adaptive immune response / membrane => GO:0016020 / lysosome / early endosome / endosome membrane / endosome / inflammatory response / positive regulation of apoptotic process / innate immune response / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane
Similarity search - Function
Ion channel regulatory protein, UNC-93 / Ion channel regulatory protein UNC-93 / Protein unc-93 homolog B1 / Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain ...Ion channel regulatory protein, UNC-93 / Ion channel regulatory protein UNC-93 / Protein unc-93 homolog B1 / Toll-like receptor 3 trans-membrane domain / Toll-like receptor 3 trans-membrane domain / 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
Protein unc-93 homolog B1 / Toll-like receptor 3
Similarity search - Component
Biological speciesMus musculoides (Temminck's mouse) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsOhto U / Ishida H / Shimizu T
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Cryo-EM structures of Toll-like receptors in complex with UNC93B1.
Authors: Hanako Ishida / Jinta Asami / Zhikuan Zhang / Tomohiro Nishizawa / Hideki Shigematsu / Umeharu Ohto / Toshiyuki Shimizu /
Abstract: Nucleic acid-sensing Toll-like receptors (TLRs) play a pivotal role in innate immunity by recognizing foreign DNA and RNA. Compartmentalization of these TLRs in the endosome limits their activation ...Nucleic acid-sensing Toll-like receptors (TLRs) play a pivotal role in innate immunity by recognizing foreign DNA and RNA. Compartmentalization of these TLRs in the endosome limits their activation by self-derived nucleic acids and reduces the possibility of autoimmune reactions. Although chaperone Unc-93 homolog B1, TLR signaling regulator (UNC93B1) is indispensable for the trafficking of TLRs from the endoplasmic reticulum to the endosome, mechanisms of UNC93B1-mediated TLR regulation remain largely unknown. Here, we report two cryo-EM structures of human and mouse TLR3-UNC93B1 complexes and a human TLR7-UNC93B1 complex. UNC93B1 exhibits structural similarity to the major facilitator superfamily transporters. Both TLRs interact with the UNC93B1 amino-terminal six-helix bundle through their transmembrane and luminal juxtamembrane regions, but the complexes of TLR3 and TLR7 with UNC93B1 differ in their oligomerization state. The structural information provided here should aid in designing compounds to combat autoimmune diseases.
History
DepositionMay 23, 2020-
Header (metadata) releaseJan 6, 2021-
Map releaseJan 6, 2021-
UpdateFeb 24, 2021-
Current statusFeb 24, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: PDB-7c77
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30294.png

Downloads & links

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Map

FileDownload / File: emd_30294.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.245 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.057950724 - 0.095593706
Average (Standard dev.)-2.2201239e-06 (±0.002691853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2451.2451.245
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z249.000249.000249.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0580.096-0.000

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Supplemental data

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Sample components

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Entire : Complex of TLR3 and UNC93B1

EntireName: Complex of TLR3 and UNC93B1
Components
  • Complex: Complex of TLR3 and UNC93B1
    • Protein or peptide: Toll-like receptor 3
    • Protein or peptide: Protein unc-93 homolog B1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of TLR3 and UNC93B1

SupramoleculeName: Complex of TLR3 and UNC93B1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculoides (Temminck's mouse)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: Expi293F

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 103.785797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKGCSSYLMY SFGGLLSLWI LLVSSTNQCT VRYNVADCSH LKLTHIPDDL PSNITVLNLT HNQLRRLPPT NFTRYSQLAI LDAGFNSIS KLEPELCQIL PLLKVLNLQH NELSQISDQT FVFCTNLTEL DLMSNSIHKI KSNPFKNQKN LIKLDLSHNG L SSTKLGTG ...String:
MKGCSSYLMY SFGGLLSLWI LLVSSTNQCT VRYNVADCSH LKLTHIPDDL PSNITVLNLT HNQLRRLPPT NFTRYSQLAI LDAGFNSIS KLEPELCQIL PLLKVLNLQH NELSQISDQT FVFCTNLTEL DLMSNSIHKI KSNPFKNQKN LIKLDLSHNG L SSTKLGTG VQLENLQELL LAKNKILALR SEELEFLGNS SLRKLDLSSN PLKEFSPGCF QTIGKLFALL LNNAQLNPHL TE KLCWELS NTSIQNLSLA NNQLLATSES TFSGLKWTNL TQLDLSYNNL HDVGNGSFSY LPSLRYLSLE YNNIQRLSPR SFY GLSNLR YLSLKRAFTK QSVSLASHPN IDDFSFQWLK YLEYLNMDDN NIPSTKSNTF TGLVSLKYLS LSKTFTSLQT LTNE TFVSL AHSPLLTLNL TKNHISKIAN GTFSWLGQLR ILDLGLNEIE QKLSGQEWRG LRNIFEIYLS YNKYLQLSTS SFALV PSLQ RLMLRRVALK NVDISPSPFR PLRNLTILDL SNNNIANINE DLLEGLENLE ILDFQHNNLA RLWKRANPGG PVNFLK GLS HLHILNLESN GLDEIPVGVF KNLFELKSIN LGLNNLNKLE PFIFDDQTSL RSLNLQKNLI TSVEKDVFGP PFQNLNS LD MRFNPFDCTC ESISWFVNWI NQTHTNISEL STHYLCNTPH HYYGFPLKLF DTSSCKDSAP FELLFIISTS MLLVFILV V LLIHIEGWRI SFYWNVSVHR ILGFKEIDTQ AEQFEYTAYI IHAHKDRDWV WEHFSPMEEQ DQSLKFCLEE RDFEAGVLG LEAIVNSIKR SRKIIFVITH HLLKDPLCRR FKVHHAVQQA IEQNLDSIIL IFLQNIPDYK LNHALCLRRG MFKSHCILNW PVQKERINA FHHKLQVALG SRNSAH

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Macromolecule #2: Protein unc-93 homolog B1

MacromoleculeName: Protein unc-93 homolog B1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 67.03925 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEVEPPLYPV AGAAGPQGDE DRHGVPDGPE APLDELVGAY PNYNEEEEER RYYRRKRLGV VKNVLAASTG VTLTYGVYLG LLQMQLILH YDETYREVKY GNMGLPDIDS KMLMGINVTP IAALLYTPVL IRFFGTKWMM FLAVGIYALF VSTNYWERYY T LVPSAVAL ...String:
MEVEPPLYPV AGAAGPQGDE DRHGVPDGPE APLDELVGAY PNYNEEEEER RYYRRKRLGV VKNVLAASTG VTLTYGVYLG LLQMQLILH YDETYREVKY GNMGLPDIDS KMLMGINVTP IAALLYTPVL IRFFGTKWMM FLAVGIYALF VSTNYWERYY T LVPSAVAL GMAIVPLWAS MGNYITRMSQ KYYEYSHYKE QDEQGPQQRP PRGSHAPYLL VFQAIFYSFF HLSFACAQLP MI YFLNNYL YDLNHTLINV QSCGTKSQGI LNGFNKTVLR TLPRSKNLIV VESVLMAVAF LAMLMVLGLC GAAYRPTEEI DLR SVGWGN IFQLPFKHVR DFRLRHLVPF FIYSGFEVLF ACTGFALGYG VCSMGLERLA YLLIAYSLGA SASSVLGLLG LWLP RSVPL VAGAGLHLLL TLSLFFWAPA PRVLQHSWIF YFVAALWGVG SALNKTGLST LLGILYEDKE RQDFIFTIYH WWQAV AIFV VYLGSSLPMK AKLAVLLVTL VAAAASYLWM EQKLQQGLVP RQPRIPKPQH KVRGYRYLEE DNSDESDMEG EQGQGD CAE DEAPQAGPLG AEPAGPCRKP CPYEQALGGD GPEEQ

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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: 7.5
Details: 25 mM Hepes-NaOH, pH 7.5, 0.2 M NaCl, and 0.01% GDN
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3cig

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 72000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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