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- EMDB-68398: Cryo-EM structure of the BTNL3-BTNL8-TCR complex -

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Basic information

Entry
Database: EMDB / ID: EMD-68398
TitleCryo-EM structure of the BTNL3-BTNL8-TCR complex
Map data
Sample
  • Complex: BTNL3-BTNL8-TCR
    • Protein or peptide: Butyrophilin-like protein 3
    • Protein or peptide: Butyrophilin-like protein 8
    • Protein or peptide: TCR
    • Protein or peptide: TCR
KeywordsCryo-EM / immune / IMMUNE SYSTEM
Function / homology
Function and homology information


extrathymic T cell selection / Butyrophilin (BTN) family interactions / regulation of cytokine production / T cell receptor signaling pathway / adaptive immune response / external side of plasma membrane / signaling receptor binding / plasma membrane
Similarity search - Function
: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. ...: / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / SPRY-associated domain / SPRY-associated / PRY / Butyrophylin-like, SPRY domain / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Butyrophilin-like protein 8 / Butyrophilin-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDong D / Zhu Y / Huang Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunity / Year: 2026
Title: Butyrophilin-like 3 and 8 tetramers clamp Vγ4Vδ1 T cell receptors for antigen-independent activation.
Authors: De Dong / Huiling Li / Yuwei Zhu / Zebin Lu / Junliang Zhu / Xinyu Tian / Zhiwei Huang /
Abstract: BTNL3 and BTNL8, butyrophilin-like (BTNL) family receptors, are predominantly expressed on intestinal epithelial cells. The BTNL3-BTNL8 complex selectively activates human Vγ4⁺ T cells, which play ...BTNL3 and BTNL8, butyrophilin-like (BTNL) family receptors, are predominantly expressed on intestinal epithelial cells. The BTNL3-BTNL8 complex selectively activates human Vγ4⁺ T cells, which play critical roles in intestinal immune homeostasis and tissue damage repair. Here, we report the structure of the BTNL3-BTNL8-Vγ4Vδ1 T cell receptor (TCR) complex. The structure reveals that BTNL3-BTNL8 forms an antigen-independent tetramer, in contrast to the phosphoantigen-driven association of BTN2A1-BTN3A1. Two BTNL3-BTNL8 heterodimers clamp a head-to-head TCR homodimer to form a 2:2:2 BTNL3:BTNL8:Vγ4Vδ1 TCR complex, with the Vγ4 HV4 and CDR2 loops jointly engaging BTNL3. Structural alignment indicates that the CD1d binding site on TCR overlaps spatially with one monomer within a TCR dimer, suggesting that TCR dimerization sterically precludes simultaneous engagement of CD1d molecules. Together, our results elucidate the structural mechanism of BTNL3-BTNL8-mediated engagement and activation of Vγ4Vδ1 TCR, offering insights into γδ TCR signaling initiation.
History
DepositionJan 14, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68398.png

Downloads & links

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Map

FileDownload / File: emd_68398.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å		1.08 Å/pix.
x 400 pix.
= 430.92 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0773 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.283
Minimum - Maximum-0.472426 - 1.8158789
Average (Standard dev.)0.00013765259 (±0.034950987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 430.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68398_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68398_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : BTNL3-BTNL8-TCR

EntireName: BTNL3-BTNL8-TCR
Components
  • Complex: BTNL3-BTNL8-TCR
    • Protein or peptide: Butyrophilin-like protein 3
    • Protein or peptide: Butyrophilin-like protein 8
    • Protein or peptide: TCR
    • Protein or peptide: TCR

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Supramolecule #1: BTNL3-BTNL8-TCR

SupramoleculeName: BTNL3-BTNL8-TCR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Butyrophilin-like protein 3

MacromoleculeName: Butyrophilin-like protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.305293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAFVLILVLS FYELVSGQWQ VTGPGKFVQA LVGEDAVFSC SLFPETSAEA MEVRFFRNQF HAVVHLYRDG EDWESKQMPQ YRGRTEFVK DSIAGGRVSL RLKNITPSDI GLYGCWFSSQ IYDEEATWEL RVAALGSLPL ISIVGYVDGG IQLLCLSSGW F PQPTAKWK ...String:
MAFVLILVLS FYELVSGQWQ VTGPGKFVQA LVGEDAVFSC SLFPETSAEA MEVRFFRNQF HAVVHLYRDG EDWESKQMPQ YRGRTEFVK DSIAGGRVSL RLKNITPSDI GLYGCWFSSQ IYDEEATWEL RVAALGSLPL ISIVGYVDGG IQLLCLSSGW F PQPTAKWK GPQGQDLSSD SRANADGYSL YDVEISIIVQ ENAGSILCSI HLAEQSHEVE SKVLIGETFF QPSPWRLASI LL GLLCGAL CGVVMGMIIV FFKSKGKIQA ELDWRRKHGQ AELRDARKHA VEVTLDPETA HPKLCVSDLK TVTHRKAPQE VPH SEKRFT RKSVVASQGF QAGKHYWEVD VGQNVGWYVG VCRDDVDRGK NNVTLSPNNG YWVLRLTTEH LYFTFNPHFI SLPP STPPT RVGVFLDYEG GTISFFNTND QSLIYTLLTC QFEGLLRPYI QHAMYDEEKG TPIFICPVSW G

UniProtKB: Butyrophilin-like protein 3

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Macromolecule #2: Butyrophilin-like protein 8

MacromoleculeName: Butyrophilin-like protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.819516 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MALMLSLVLS LLKLGSGQWQ VFGPDKPVQA LVGEDAAFSC FLSPKTNAEA MEVRFFRGQF SSVVHLYRDG KDQPFMQMPQ YQGRTKLVK DSIAEGRISL RLENITVLDA GLYGCRISSQ SYYQKAIWEL QVSALGSVPL ISITGYVDRD IQLLCQSSGW F PRPTAKWK ...String:
MALMLSLVLS LLKLGSGQWQ VFGPDKPVQA LVGEDAAFSC FLSPKTNAEA MEVRFFRGQF SSVVHLYRDG KDQPFMQMPQ YQGRTKLVK DSIAEGRISL RLENITVLDA GLYGCRISSQ SYYQKAIWEL QVSALGSVPL ISITGYVDRD IQLLCQSSGW F PRPTAKWK GPQGQDLSTD SRTNRDMHGL FDVEISLTVQ ENAGSISCSM RHAHLSREVE SRVQIGDTFF EPISWHLATK VL GILCCGL FFGIVGLKIF FSKFQWKIQA ELDWRRKHGQ AELRDARKHA VEVTLDPETA HPKLCVSDLK TVTHRKAPQE VPH SEKRFT RKSVVASQSF QAGKHYWEVD GGHNKRWRVG VCRDDVDRRK EYVTLSPDHG YWVLRLNGEH LYFTLNPRFI SVFP RTPPT KIGVFLDYEC GTISFFNIND QSLIYTLTCR FEGLLRPYIE YPSYNEQNGT PIVICPVTQE SEKEASWQRA SAIPE TSNS ESSSQATTPF LPRGEM

UniProtKB: Butyrophilin-like protein 8

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Macromolecule #3: TCR

MacromoleculeName: TCR / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.590609 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLFSSLLCVF VAFSYSGSSV AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKK AAKSVALTIS ALQLEDSAKY FCALGDPGGL NTDKLIFGKG TRVTVEPRSQ PHTKPSVFVM KNGTNVACLV K EFYPKDIR ...String:
MLFSSLLCVF VAFSYSGSSV AQKVTQAQSS VSMPVRKAVT LNCLYETSWW SYYIFWYKQL PSKEMIFLIR QGSDEQNAKS GRYSVNFKK AAKSVALTIS ALQLEDSAKY FCALGDPGGL NTDKLIFGKG TRVTVEPRSQ PHTKPSVFVM KNGTNVACLV K EFYPKDIR INLVSSKKIT EFDPAIVISP SGKYNAVKLG KYEDSNSVTC SVQHDNKTVH STDFEVKTDS TDHVKPKETE NT KQPSKSC HKPKAIVHTE KVNMMSLTVL GLRMLFAKTV AVNFLLTAKL FFLGSG

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Macromolecule #4: TCR

MacromoleculeName: TCR / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.531496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQWALAVLLA FLSPASQKSS NLEGRTKSVI RQTGSSAEIT CDLAEGSTGY IHWYLHQEGK APQRLLYYDS YTSSVVLESG ISPGKYDTY GSTRKNLRMI LRNLIENDSG VYYCATWDGY YKKLFGSGTT LVVTDKQLDA DVSPKPTIFL PSIAETKLQK A GTYLCLLE ...String:
MQWALAVLLA FLSPASQKSS NLEGRTKSVI RQTGSSAEIT CDLAEGSTGY IHWYLHQEGK APQRLLYYDS YTSSVVLESG ISPGKYDTY GSTRKNLRMI LRNLIENDSG VYYCATWDGY YKKLFGSGTT LVVTDKQLDA DVSPKPTIFL PSIAETKLQK A GTYLCLLE KFFPDIIKIH WQEKKSNTIL GSQEGNTMKT NDTYMKFSWL TVPEESLDKE HRCIVRHENN KNGIDQEIIF PP IKTDVTT VDPKYNYSKD ANDVITMDPK DNWSKDANDT LLLQLTNTSA YYTYLLLLLK SVVYFAIITC CLLRRTAFCC NGE KS

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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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 548003
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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