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- EMDB-7526: Human Teneurin 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-7526
TitleHuman Teneurin 2
Map dataHuman Teneurin 2 ECR
Sample
  • Organelle or cellular component: Teneurin 2 extra-cellular region
    • Protein or peptide: Teneurin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose
KeywordsTeneurin / Membrane protein / CNS
Function / homology
Function and homology information


retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron development / cell adhesion molecule binding / filopodium / PML body / cell-cell adhesion / cell-cell junction / cell junction ...retrograde trans-synaptic signaling by trans-synaptic protein complex / positive regulation of filopodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / neuron development / cell adhesion molecule binding / filopodium / PML body / cell-cell adhesion / cell-cell junction / cell junction / growth cone / postsynaptic membrane / dendritic spine / neuron projection / protein heterodimerization activity / signaling receptor binding / dendrite / calcium ion binding / synapse / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / protein homodimerization activity / nucleus / plasma membrane
Similarity search - Function
Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / : / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Quinoprotein amine dehydrogenase, beta chain-like ...Teneurin intracellular, N-terminal / Teneurin Intracellular Region / Teneurin N-terminal domain profile. / Tox-GHH domain / GHH signature containing HNH/Endo VII superfamily nuclease toxin / : / YD repeat / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Quinoprotein amine dehydrogenase, beta chain-like / EGF-like domain, extracellular / EGF-like domain / Six-bladed beta-propeller, TolB-like / 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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsShalev-Benami M / Li J
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120322 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01 DK090165 United States
CitationJournal: Cell / Year: 2018
Title: Structural Basis for Teneurin Function in Circuit-Wiring: A Toxin Motif at the Synapse.
Authors: Jingxian Li / Moran Shalev-Benami / Richard Sando / Xian Jiang / Amanuel Kibrom / Jie Wang / Katherine Leon / Christopher Katanski / Olha Nazarko / Yue C Lu / Thomas C Südhof / Georgios ...Authors: Jingxian Li / Moran Shalev-Benami / Richard Sando / Xian Jiang / Amanuel Kibrom / Jie Wang / Katherine Leon / Christopher Katanski / Olha Nazarko / Yue C Lu / Thomas C Südhof / Georgios Skiniotis / Demet Araç /
Abstract: Teneurins (TENs) are cell-surface adhesion proteins with critical roles in tissue development and axon guidance. Here, we report the 3.1-Å cryoelectron microscopy structure of the human TEN2 ...Teneurins (TENs) are cell-surface adhesion proteins with critical roles in tissue development and axon guidance. Here, we report the 3.1-Å cryoelectron microscopy structure of the human TEN2 extracellular region (ECR), revealing a striking similarity to bacterial Tc-toxins. The ECR includes a large β barrel that partially encapsulates a C-terminal domain, which emerges to the solvent through an opening in the mid-barrel region. An immunoglobulin (Ig)-like domain seals the bottom of the barrel while a β propeller is attached in a perpendicular orientation. We further show that an alternatively spliced region within the β propeller acts as a switch to regulate trans-cellular adhesion of TEN2 to latrophilin (LPHN), a transmembrane receptor known to mediate critical functions in the central nervous system. One splice variant activates trans-cellular signaling in a LPHN-dependent manner, whereas the other induces inhibitory postsynaptic differentiation. These results highlight the unusual structural organization of TENs giving rise to their multifarious functions.
History
DepositionMar 6, 2018-
Header (metadata) releaseApr 11, 2018-
Map releaseJul 25, 2018-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6cmx
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7526.png

Downloads & links

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Map

FileDownload / File: emd_7526.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Teneurin 2 ECR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 260 pix.
= 260. Å		1 Å/pix.
x 260 pix.
= 260. Å		1 Å/pix.
x 260 pix.
= 260. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.2499995 - 0.37338814
Average (Standard dev.)-0.000032754604 (±0.009909255)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 260.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z260.000260.000260.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.2500.373-0.000

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Supplemental data

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Sample components

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Entire : Teneurin 2 extra-cellular region

EntireName: Teneurin 2 extra-cellular region
Components
  • Organelle or cellular component: Teneurin 2 extra-cellular region
    • Protein or peptide: Teneurin-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Teneurin 2 extra-cellular region

SupramoleculeName: Teneurin 2 extra-cellular region / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 215 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: 224.005812 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: HHHHHHHHAS DTYKLVIVLN GTTFTYTTEA VDAATAEKVF KQYANDAGVD GEWTYDAATK TFTVTEASEN LYFQSGSTSC ADNKDNEGD GLVDCLDPDC CLQSACQNSL LCRGSRDPLD IIQQGQTDWP AVKSFYDRIK LLAGKDSTHI IPGENPFNSS L VSLIRGQV ...String:
HHHHHHHHAS DTYKLVIVLN GTTFTYTTEA VDAATAEKVF KQYANDAGVD GEWTYDAATK TFTVTEASEN LYFQSGSTSC ADNKDNEGD GLVDCLDPDC CLQSACQNSL LCRGSRDPLD IIQQGQTDWP AVKSFYDRIK LLAGKDSTHI IPGENPFNSS L VSLIRGQV VTTDGTPLVG VNVSFVKYPK YGYTITRQDG TFDLIANGGA SLTLHFERAP FMSQERTVWL PWNSFYAMDT LV MKTEENS IPSCDLSGFV RPDPIIISSP LSTFFSAAPG QNPIVPETQV LHEEIELPGS NVKLRYLSSR TAGYKSLLKI TMT QSTVPL NLIRVHLMVA VEGHLFQKSF QASPNLAYTF IWDKTDAYGQ RVYGLSDAVV SVGFEYETCP SLILWEKRTA LLQG FELDP SNLGGWSLDK HHILNVKSGI LHKGTGENQF LTQQPAIITS IMGNGRRRSI SCPSCNGLAE GNKLLAPVAL AVGID GSLY VGDFNYIRRI FPSRNVTSIL ELRNNPAHKY YLAVDPVSGS LYVSDTNSRR IYRVKSLSGT KDLAGNSEVV AGTGEQ CLP FDEARCGDGG KAIDATLMSP RGIAVDKNGL MYFVDATMIR KVDQNGIIST LLGSNDLTAV RPLSCDSSMD VAQVRLE WP TDLAVNPMDN SLYVLENNVI LRITENHQVS IIAGRPMHCQ VPGIDYSLSK LAIHSALESA SAIAISHTGV LYITETDE K KINRLRQVTT NGEICLLAGA ASDCDCKNDV NCNCYSGDDA YATDAILNSP SSLAVAPDGT IYIADLGNIR IRAVSKNKP VLNAFNQYEA ASPGEQELYV FNADGIHQYT VSLVTGEYLY NFTYSTDNDV TELIDNNGNS LKIRRDSSGM PRHLLMPDNQ IITLTVGTN GGLKVVSTQN LELGLMTYDG NTGLLATKSD ETGWTTFYDY DHEGRLTNVT RPTGVVTSLH REMEKSITID I ENSNRDDD VTVITNLSSV EASYTVVQDQ VRNSYQLCNN GTLRVMYANG MGISFHSEPH VLAGTITPTI GRCNISLPME NG LNSIEWR LRKEQIKGKV TIFGRKLRVH GRNLLSIDYD RSIRTEKIYD DHRKFTLRII YDQVGRPFLW LPSSGLAAVN VSY FFNGRL AGLQRGAMSE RTDIDKQGRI VSRMFADGKV WSYSYLDKSM VLLLQSQRQY IFEYDSSDRL LAVTMPSVAR HSMS THTSI GYIRNIYNPP ESNASVIFDY SDDGRILKTS FLGTGRQVFY KYGKLSKLSE IVYDSTAVTF GYDETTGVLK MVNLQ SGGF SCTIRYRKIG PLVDKQIYRF SEEGMVNARF DYTYHDNSFR IASIKPVISE TPLPVDLYRY DEISGKVEHF GKFGVI YYD INQIITTAVM TLSKHFDTHG RIKEVQYEMF RSLMYWMTVQ YDSMGRVIKR ELKLGPYANT TKYTYDYDGD GQLQSVA VN DRPTWRYSYD LNGNLHLLNP GNSVRLMPLR YDLRDRITRL GDVQYKIDDD GYLCQRGSDI FEYNSKGLLT RAYNKASG W SVQYRYDGVG RRASYKTNLG HHLQYFYSDL HNPTRITHVY NHSNSEITSL YYDLQGHLFA MESSSGEEYY VASDNTGTP LAVFSINGLM IKQLQYTAYG EIYYDSNPDF QMVIGFHGGL YDPLTKLVHF TQRDYDVLAG RWTSPDYTMW KNVGKEPAPF NLYMFKSNN PLSSELGLKN YVTDVKSWLV MFGFQLSNII PGFPRAKMYF VPPPYELSES QASENGQLIT GVQQKTERHN Q AFMALEGQ VITKKLHASI REKAGHWFAT TTPIIGKGIM FAIKEGRVTT GVSSIASEDS RKVASVLNNA YYLDKMHYSI EG KDTHYFV KIGSADGDLV TLGTTIGRKV LESGVNVTVS QPTLLVNGRT RRFTNIEFQY STLLLSIRYG LTPDTLDEEK ARV LDQARQ RALGTAWAKE QQKARDGREG SRLWTEGEKQ QLLSTGRVQG YEGYYVLPVE QYPELADSSS NIQFLRQNEM GKR

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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: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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

Concentration0.15 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 44.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 426107
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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