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- EMDB-50976: Mouse Teneurin2 dimer variant A1B0 -

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Basic information

Entry
Database: EMDB / ID: EMD-50976
TitleMouse Teneurin2 dimer variant A1B0
Map dataDeepEMhancer sharpened map
Sample
  • Complex: Dimeric complex of mouse Teneurin2 A1B0 variant
    • Protein or peptide: Teneurin transmembrane protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordscell adhesion molecule / complex / homodimer / CELL ADHESION
Function / homology
Function and homology information


filopodium / PML body / growth cone / dendritic spine / postsynaptic membrane / cell adhesion / endoplasmic reticulum / Golgi apparatus / signal transduction / protein homodimerization activity
Similarity search - Function
: / : / Teneurin intracellular, N-terminal / : / : / : / Teneurin Intracellular Region / Teneurin-3-like, galactose-binding domain-like / Teneurin antibiotic-binding-like domain / Teneurin 1-4, FN-plug domain ...: / : / Teneurin intracellular, N-terminal / : / : / : / Teneurin Intracellular Region / Teneurin-3-like, galactose-binding domain-like / Teneurin antibiotic-binding-like domain / Teneurin 1-4, FN-plug domain / Teneurin TTR-like domain / Teneurin NHL domain / Teneurin YD-shell / Teneurin N-terminal domain profile. / Tox-GHH domain / : / GHH signature containing HNH/Endo VII superfamily nuclease toxin / YD repeat / Teneurin EGF domain / Rhs repeat-associated core / Carboxypeptidase-like, regulatory domain superfamily / Six-bladed beta-propeller, TolB-like / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsBerbeira-Santana M / Zhou JC / el Omari K / Baker L / Seiradake E
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust226647/Z/22/Z United Kingdom
CitationJournal: To Be Published
Title: Mouse Teneurin2 dimer variant A1B0
Authors: Berbeira-Santana M / Zhou CJ / el Omari K / Baker L / Seiradake E
History
DepositionJul 10, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50976.png

Downloads & links

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Map

FileDownload / File: emd_50976.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.054678433 - 1.7899922
Average (Standard dev.)0.0018880647 (±0.030186232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw map

Fileemd_50976_additional_1.map
AnnotationRaw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_50976_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_50976_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric complex of mouse Teneurin2 A1B0 variant

EntireName: Dimeric complex of mouse Teneurin2 A1B0 variant
Components
  • Complex: Dimeric complex of mouse Teneurin2 A1B0 variant
    • Protein or peptide: Teneurin transmembrane protein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Dimeric complex of mouse Teneurin2 A1B0 variant

SupramoleculeName: Dimeric complex of mouse Teneurin2 A1B0 variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Dimeric complex purified by SEC after recombinant expression in HEK293T cells.
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 267.78383 KDa

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Macromolecule #1: Teneurin transmembrane protein 2

MacromoleculeName: Teneurin transmembrane protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 267.134719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGHHHHHHR GGLNDIFEAQ KIEWHEGGST GHLLGLNWQL QPADGHTFNN GVRTGLPGND DVATVPSGGK VPWSLKNSSI DSGEAEVGR RVTQEVPPGV FWRSQIHISQ PQFLKFNISL GKDALFGVYI RRGLPPSHAQ YDFMERLDGK EKWSVVESPR E RRSIQTLV ...String:
ETGHHHHHHR GGLNDIFEAQ KIEWHEGGST GHLLGLNWQL QPADGHTFNN GVRTGLPGND DVATVPSGGK VPWSLKNSSI DSGEAEVGR RVTQEVPPGV FWRSQIHISQ PQFLKFNISL GKDALFGVYI RRGLPPSHAQ YDFMERLDGK EKWSVVESPR E RRSIQTLV QNEAVFVQYL DVGLWHLAFY NDGKDKEMVS FNTVVLDSVQ DCPRNCHGNG ECVSGLCHCF PGFLGADCAK AA CPVLCSG NGQYSKGTCQ CYSGWKGAEC DVPMNQCIDP SCGGHGSCID GNCVCAAGYK GEHCEEVDCL DPTCSSHGVC VNG ECLCSP GWGGLNCELA RVQCPDQCSG HGTYLPDSGL CSCDPNWMGP DCSVEVCSVD CGTHGVCIGG ACRCEEGWTG AACD QRVCH PRCIEHGTCK DGKCECREGW NGEHCTIGRQ TAGTETDGCP DLCNGNGRCT LGQNSWQCVC QTGWRGPGCN VAMET SCAD NKDNEGDGLV DCLDPDCCLQ SACQNSLLCR GSRDPLDIIQ QGQTDWPAVK SFYDRIKLLA GKDSTHIIPG DNPFNS SLV SLIRGQVVTM DGTPLVGVNV SFVKYPKYGY TITRQDGTFD LIANGGSALT LHFERAPFMS QERTVWLPWN SFYAMDT LV MKTEENSIPS CDLSGFVRPD PIIISSPLST FFSASPASNP IVPETQVLHE EIELPGTNVK LRYLSSRTAG YKSLLKIT M TQSTVPLNLI RVHLMVAVEG HLFQKSFQAS PNLAYTFIWD KTDAYGQRVY GLSDAVVSVG FEYETCPSLI LWEKRTALL QGFELDPSNL GGWSLDKHHT LNVKSGILHK GTGENQFLTQ QPAIITSIMG NGRRRSISCP SCNGLAEGNK LLAPVALAVG IDGSLFVGD FNYIRRIFPS RNVTSILELS NSPGHKYYLA VDPVTGSLYV SDTNSRRIYR VKSLSGAKDL AGNSEVVAGT G EQCLPFDE ARCGDGGKAV DATLMSPRGI AVDKNGLMYF VDATMIRKVD QNGIISTLLG SNDLTAVRPL SCDSSMDVAQ VR LEWPTDL AVNPMDNSLY VLENNVILRI TENHQVSIIA GRPMHCQVPG IDYSLSKLAI HSALESASAI AISHTGVLYI TET DEKKIN RLRQVTTNGE ICLLAGAASD CDCKNDVNCI CYSGDDAYAT DAILNSPSSL AVAPDGTIYI ADLGNIRIRA VSKN KPVLN AFNQYEAASP GEQELYVFNA DGIHQYTVSL VTGEYLYNFT YSADNDVTEL IDNNGNSLKI RRDSSGMPRH LLMPD NQII TLTVGTNGGL KAVSTQNLEL GLMTYDGNTG LLATKSDETG WTTFYDYDHE GRLTNVTRPT GVVTSLHREM EKSITI DIE NSNRDDDVTV ITNLSSVEAS YTVVQDQVRN SYQLCNNGTL RVMYANGMAV SFHSEPHVLA GTITPTIGRC NISLPME NG LNSIEWRLRK EQIKGKVTIF GRKLRVHGRN LLSIDYDRNI RTEKIYDDHR KFTLRIIYDQ VGRPFLWLPS SGLAAVNV S YFFNGRLAGL QRGAMSERTD IDKQGRIVSR MFADGKVWSY SYLDKSMVLL LQSQRQYIFE YDSSDRLHAV TMPSVARHS MSTHTSIGYI RNIYNPPESN ASVIFDYSDD GRILKTSFLG TGRQVFYKYG KLSKLSEIVY DSTAVTFGYD ETTGVLKMVN LQSGGFSCT IRYRKVGPLV DKQIYRFSEE GMINARFDYT YHDNSFRIAS IKPVISETPL PVDLYRYDEI SGKVEHFGKF G VIYYDINQ IITTAVMTLS KHFDTHGRIK EVQYEMFRSL MYWMTVQYDS MGRVIKRELK LGPYANTTKY TYDYDGDGQL QS VAVNDRP TWRYSYDLNG NLHLLNPGNS ARLMPLRYDL RDRITRLGDV QYKIDDDGYL CQRGSDIFEY NSKGLLTRAY NKA SGWSVQ YRYDGVGRRA SYKTNLGHHL QYFYSDLHNP TRITHVYNHS NSEITSLYYD LQGHLFAMES SSGEEYYVAS DNTG TPLAV FSINGLMIKQ LQYTAYGEIY YDSNPDFQMV IGFHGGLYDP LTKLVHFTQR DYDVLAGRWT SPDYTMWRNV GKEPA PFNL YMFKNNNPLS NELDLKNYVT DVKSWLVMFG FQLSNIIPGF PRAKMYFVPP PYELSESQAS ENGQLITGVQ QTTERH NQA FLALEGQVIT KKLHASIREK AGHWFATTTP IIGKGIMFAI KEGRVTTGVS SIASEDSRKV ASVLNNAYYL DKMHYSI EG KDTHYFVKIG AADGDLVTLG TTIGRKVLES GVNVTVSQPT LLVNGRTRRF TNIEFQYSTL LLSIRYGLTP DTLDEEKA R VLDQARQRAL GTAWAKEQQK ARDGREGSRL WTEGEKQQLL STGRVQGYEG YYVLPVEQYP ELADSSSNIQ FLRQNEMGK RGT

UniProtKB: Teneurin-2

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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

Concentration0.27 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
25.0 mMHEPES

Details: 25 mM HEPES, 300 mM NaCl, pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8975 / Average electron dose: 42.303 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3672845
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 167798
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: SWISSMODEL
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g2h:
Mouse Teneurin2 dimer variant A1B0

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