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- EMDB-21205: Human Teneurin-2 and human Latrophilin-3 binary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-21205
TitleHuman Teneurin-2 and human Latrophilin-3 binary complex
Map dataTeneurin-Latrophilin complex containing domain 1-5 of human Teneurine-2 and Lectin domain of human Latrophilin-3
Sample
  • Complex: Binary complex of human Teneurin-2 with human Latrophilin-3 extracellular domain
    • Protein or peptide: Teneurin-2Teneurin
    • Protein or peptide: Adhesion G protein-coupled receptor L3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


retrograde trans-synaptic signaling by trans-synaptic protein complex / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / cell adhesion molecule binding / synapse assembly / filopodium / G protein-coupled receptor activity ...retrograde trans-synaptic signaling by trans-synaptic protein complex / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / : / neuron development / cell adhesion molecule binding / synapse assembly / filopodium / G protein-coupled receptor activity / axon guidance / neuron migration / adenylate cyclase-activating G protein-coupled receptor signaling pathway / PML body / cell-cell adhesion / cell-cell junction / cell junction / growth cone / postsynaptic membrane / carbohydrate binding / dendritic spine / cell surface receptor signaling pathway / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / axon / signaling receptor binding / synapse / glutamatergic synapse / dendrite / calcium ion binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / membrane / nucleus / plasma membrane
Similarity search - Function
Teneurin-2 / Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily ...Teneurin-2 / Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / GPCR, family 2, latrophilin, C-terminal / GPCR, family 2, latrophilin / Latrophilin Cytoplasmic C-terminal region / D-galactoside/L-rhamnose binding SUEL lectin domain superfamily / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / D-galactoside/L-rhamnose binding SUEL lectin domain / Galactose binding lectin domain / SUEL-type lectin domain profile. / YD repeat / Olfactomedin-like domain / Olfactomedin-like domain / Olfactomedin-like domain profile. / Olfactomedin-like domains / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Quinoprotein amine dehydrogenase, beta chain-like / Hormone receptor domain / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / Six-bladed beta-propeller, TolB-like / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain
Similarity search - Domain/homology
Adhesion G protein-coupled receptor L3 / Teneurin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsXie Y / Li J / Arac D / Zhao M
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM120322 United States
American Heart Association19POST34380439/Jingxian Li/2019-2020 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM134035-01 United States
CitationJournal: Nat Commun / Year: 2020
Title: Alternative splicing controls teneurin-latrophilin interaction and synapse specificity by a shape-shifting mechanism.
Authors: Jingxian Li / Yuan Xie / Shaleeka Cornelius / Xian Jiang / Richard Sando / Szymon P Kordon / Man Pan / Katherine Leon / Thomas C Südhof / Minglei Zhao / Demet Araç /
Abstract: The trans-synaptic interaction of the cell-adhesion molecules teneurins (TENs) with latrophilins (LPHNs/ADGRLs) promotes excitatory synapse formation when LPHNs simultaneously interact with FLRTs. ...The trans-synaptic interaction of the cell-adhesion molecules teneurins (TENs) with latrophilins (LPHNs/ADGRLs) promotes excitatory synapse formation when LPHNs simultaneously interact with FLRTs. Insertion of a short alternatively-spliced region within TENs abolishes the TEN-LPHN interaction and switches TEN function to specify inhibitory synapses. How alternative-splicing regulates TEN-LPHN interaction remains unclear. Here, we report the 2.9 Å resolution cryo-EM structure of the TEN2-LPHN3 complex, and describe the trimeric TEN2-LPHN3-FLRT3 complex. The structure reveals that the N-terminal lectin domain of LPHN3 binds to the TEN2 barrel at a site far away from the alternatively spliced region. Alternative-splicing regulates the TEN2-LPHN3 interaction by hindering access to the LPHN-binding surface rather than altering it. Strikingly, mutagenesis of the LPHN-binding surface of TEN2 abolishes the LPHN3 interaction and impairs excitatory but not inhibitory synapse formation. These results suggest that a multi-level coincident binding mechanism mediated by a cryptic adhesion complex between TENs and LPHNs regulates synapse specificity.
History
DepositionJan 9, 2020-
Header (metadata) releaseJun 3, 2020-
Map releaseJun 3, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface view colored by radius
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  • Surface view with fitted model
  • Atomic models: PDB-6vhh
  • Surface level: 0.01
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21205.png

Downloads & links

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Map

FileDownload / File: emd_21205.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTeneurin-Latrophilin complex containing domain 1-5 of human Teneurine-2 and Lectin domain of human Latrophilin-3
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.026192531 - 0.058946915
Average (Standard dev.)-0.00001958588 (±0.0018373288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0260.059-0.000

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Supplemental data

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Additional map: Refined map focusing on Domain 3

Fileemd_21205_additional_1.map
AnnotationRefined map focusing on Domain 3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Postprocessed map (sharpened and filtered)

Fileemd_21205_additional_2.map
AnnotationPostprocessed map (sharpened and filtered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map for main entry

Fileemd_21205_additional_3.map
AnnotationSharpened map for main entry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_21205_half_map_1.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_21205_half_map_2.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of human Teneurin-2 with human Latrophilin-3 extra...

EntireName: Binary complex of human Teneurin-2 with human Latrophilin-3 extracellular domain
Components
  • Complex: Binary complex of human Teneurin-2 with human Latrophilin-3 extracellular domain
    • Protein or peptide: Teneurin-2Teneurin
    • Protein or peptide: Adhesion G protein-coupled receptor L3
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Binary complex of human Teneurin-2 with human Latrophilin-3 extra...

SupramoleculeName: Binary complex of human Teneurin-2 with human Latrophilin-3 extracellular domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: The binary complex includes human Teneurin2 (TENM2) (Teneurin without alternative splice sequence NKEFKHS) and human Latrophilin3 (LPHN3/ADGRL3) with an alternative splice sequence KVEQK ...Details: The binary complex includes human Teneurin2 (TENM2) (Teneurin without alternative splice sequence NKEFKHS) and human Latrophilin3 (LPHN3/ADGRL3) with an alternative splice sequence KVEQK between lectin domain and olfactomedin domain.
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: Hi5
Molecular weightExperimental: 314 KDa

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Macromolecule #1: Teneurin-2

MacromoleculeName: Teneurin-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 216.254578 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TSCADNKDNE GDGLVDCLDP DCCLQSACQN SLLCRGSRDP LDIIQQGQTD WPAVKSFYDR IKLLAGKDST HIIPGENPFN SSLVSLIRG QVVTTDGTPL VGVNVSFVKY PKYGYTITRQ DGTFDLIANG GASLTLHFER APFMSQERTV WLPWNSFYAM D TLVMKTEE ...String:
TSCADNKDNE GDGLVDCLDP DCCLQSACQN SLLCRGSRDP LDIIQQGQTD WPAVKSFYDR IKLLAGKDST HIIPGENPFN SSLVSLIRG QVVTTDGTPL VGVNVSFVKY PKYGYTITRQ DGTFDLIANG GASLTLHFER APFMSQERTV WLPWNSFYAM D TLVMKTEE NSIPSCDLSG FVRPDPIIIS SPLSTFFSAA PGQNPIVPET QVLHEEIELP GSNVKLRYLS SRTAGYKSLL KI TMTQSTV PLNLIRVHLM VAVEGHLFQK SFQASPNLAY TFIWDKTDAY GQRVYGLSDA VVSVGFEYET CPSLILWEKR TAL LQGFEL DPSNLGGWSL DKHHILNVKS GILHKGTGEN QFLTQQPAII TSIMGNGRRR SISCPSCNGL AEGNKLLAPV ALAV GIDGS LYVGDFNYIR RIFPSRNVTS ILELRNNPAH KYYLAVDPVS GSLYVSDTNS RRIYRVKSLS GTKDLAGNSE VVAGT GEQC LPFDEARCGD GGKAIDATLM SPRGIAVDKN GLMYFVDATM IRKVDQNGII STLLGSNDLT AVRPLSCDSS MDVAQV RLE WPTDLAVNPM DNSLYVLENN VILRITENHQ VSIIAGRPMH CQVPGIDYSL SKLAIHSALE SASAIAISHT GVLYITE TD EKKINRLRQV TTNGEICLLA GAASDCDCKN DVNCNCYSGD DAYATDAILN SPSSLAVAPD GTIYIADLGN IRIRAVSK N KPVLNAFNQY EAASPGEQEL YVFNADGIHQ YTVSLVTGEY LYNFTYSTDN DVTELIDNNG NSLKIRRDSS GMPRHLLMP DNQIITLTVG TNGGLKVVST QNLELGLMTY DGNTGLLATK SDETGWTTFY DYDHEGRLTN VTRPTGVVTS LHREMEKSIT IDIENSNRD DDVTVITNLS SVEASYTVVQ DQVRNSYQLC NNGTLRVMYA NGMGISFHSE PHVLAGTITP TIGRCNISLP M ENGLNSIE WRLRKEQIKG KVTIFGRKLR VHGRNLLSID YDRSIRTEKI YDDHRKFTLR IIYDQVGRPF LWLPSSGLAA VN VSYFFNG RLAGLQRGAM SERTDIDKQG RIVSRMFADG KVWSYSYLDK SMVLLLQSQR QYIFEYDSSD RLLAVTMPSV ARH SMSTHT SIGYIRNIYN PPESNASVIF DYSDDGRILK TSFLGTGRQV FYKYGKLSKL SEIVYDSTAV TFGYDETTGV LKMV NLQSG GFSCTIRYRK IGPLVDKQIY RFSEEGMVNA RFDYTYHDNS FRIASIKPVI SETPLPVDLY RYDEISGKVE HFGKF GVIY YDINQIITTA VMTLSKHFDT HGRIKEVQYE MFRSLMYWMT VQYDSMGRVI KRELKLGPYA NTTKYTYDYD GDGQLQ SVA VNDRPTWRYS YDLNGNLHLL NPGNSVRLMP LRYDLRDRIT RLGDVQYKID DDGYLCQRGS DIFEYNSKGL LTRAYNK AS GWSVQYRYDG VGRRASYKTN LGHHLQYFYS DLHNPTRITH VYNHSNSEIT SLYYDLQGHL FAMESSSGEE YYVASDNT G TPLAVFSING LMIKQLQYTA YGEIYYDSNP DFQMVIGFHG GLYDPLTKLV HFTQRDYDVL AGRWTSPDYT MWKNVGKEP APFNLYMFKS NNPLSSELGL KNYVTDVKSW LVMFGFQLSN IIPGFPRAKM YFVPPPYELS ESQASENGQL ITGVQQKTER HNQAFMALE GQVITKKLHA SIREKAGHWF ATTTPIIGKG IMFAIKEGRV TTGVSSIASE DSRKVASVLN NAYYLDKMHY S IEGKDTHY FVKIGSADGD LVTLGTTIGR KVLESGVNVT VSQPTLLVNG RTRRFTNIEF QYSTLLLSIR YGLTPDTLDE EK ARVLDQA RQRALGTAWA KEQQKARDGR EGSRLWTEGE KQQLLSTGRV QGYEGYYVLP VEQYPELADS SSNIQFLRQN EMG KRHHHH HH

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Macromolecule #2: Adhesion G protein-coupled receptor L3

MacromoleculeName: Adhesion G protein-coupled receptor L3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 95.209586 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SRAPIPMAVV RRELSCESYP IELRCPGTDV IMIESANYGR TDDKICDSDP AQMENIRCYL PDAYKIMSQR CNNRTQCAVV AGPDVFPDP CPGTYKYLEV QYECVPYKVE QKVFLCPGLL KGVYQSEHLF ESDHQSGAWC KDPLQASDKI YYMPWTPYRT D TLTEYSSK ...String:
SRAPIPMAVV RRELSCESYP IELRCPGTDV IMIESANYGR TDDKICDSDP AQMENIRCYL PDAYKIMSQR CNNRTQCAVV AGPDVFPDP CPGTYKYLEV QYECVPYKVE QKVFLCPGLL KGVYQSEHLF ESDHQSGAWC KDPLQASDKI YYMPWTPYRT D TLTEYSSK DDFIAGRPTT TYKLPHRVDG TGFVVYDGAL FFNKERTRNI VKFDLRTRIK SGEAIIANAN YHDTSPYRWG GK SDIDLAV DENGLWVIYA TEQNNGKIVI SQLNPYTLRI EGTWDTAYDK RSASNAFMIC GILYVVKSVY EDDDNEATGN KID YIYNTD QSKDSLVDVP FPNSYQYIAA VDYNPRDNLL YVWNNYHVVK YSLDFGPLDS RSGQAHHGQV SYISPPIHLD SELE RPSVK DISTTGPLGM GSTTTSTTLR TTTLSPGRST TPSVSGRRNR STSTPSPAVE VLDDMTTHLP SASSQIPALE ESCEA VEAR EIMWFKTRQG QIAKQPCPAG TIGVSTYLCL APDGIWDPQG PDLSNCSSPW VNHITQKLKS GETAANIARE LAEQTR NHL NAGDITYSVR AMDQLVGLLD VQLRNLTPGG KDSAARSLNK AMVETVNNLL QPQALNAWRD LTTSDQLRAA TMLLHTV EE SAFVLADNLL KTDIVRENTD NIKLEVARLS TEGNLEDLKF PENMGHGSTI QLSANTLKQN GRNGEIRVAF VLYNNLGP Y LSTENASMKL GTEALSTNHS VIVNSPVITA AINKEFSNKV YLADPVVFTV KHIKQSEENF NPNCSFWSYS KRTMTGYWS TQGCRLLTTN KTHTTCSCNH LTNFAVLMAH VEVKHSDAVH DLLLDVHHHH HH

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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

Concentration2.2 mg/mL
BufferpH: 8.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 5402 / Average exposure time: 4.2 sec. / Average electron dose: 60.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4475958
CTF correctionSoftware - Name: RELION (ver. 3.0.8) / Details: CTF correction was done in Relion reconstruction
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6cmx

Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationSoftware - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 436208
FSC plot (resolution estimation)

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