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- EMDB-51022: Mouse Teneurin2 dimer variant A0B0 -

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Basic information

Entry
Database: EMDB / ID: EMD-51022
TitleMouse Teneurin2 dimer variant A0B0
Map dataSharpened map
Sample
  • Complex: Dimeric complex of mouse Teneurin2 A0B0 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: 2.82 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 A0B0
Authors: Berbeira-Santana M / Zhou CJ / el Omari K / Baker L / Seiradake E
History
DepositionJul 12, 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_51022.png

Downloads & links

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Map

FileDownload / File: emd_51022.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened 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-0.016353885 - 1.7759044
Average (Standard dev.)0.0026363556 (±0.036118537)
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_51022_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_51022_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_51022_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 A0B0 variant

EntireName: Dimeric complex of mouse Teneurin2 A0B0 variant
Components
  • Complex: Dimeric complex of mouse Teneurin2 A0B0 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 A0B0 variant

SupramoleculeName: Dimeric complex of mouse Teneurin2 A0B0 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: 266.01164 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: 266.301906 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 NGEHCTIDGC PDLCNGNGRC TLGQNSWQCV CQTGWRGPGC NVAMETSCAD NKDNE GDGL VDCLDPDCCL QSACQNSLLC RGSRDPLDII QQGQTDWPAV KSFYDRIKLL AGKDSTHIIP GDNPFNSSLV SLIRGQ VVT MDGTPLVGVN VSFVKYPKYG YTITRQDGTF DLIANGGSAL TLHFERAPFM SQERTVWLPW NSFYAMDTLV MKTEENS IP SCDLSGFVRP DPIIISSPLS TFFSASPASN PIVPETQVLH EEIELPGTNV KLRYLSSRTA GYKSLLKITM TQSTVPLN L IRVHLMVAVE GHLFQKSFQA SPNLAYTFIW DKTDAYGQRV YGLSDAVVSV GFEYETCPSL ILWEKRTALL QGFELDPSN LGGWSLDKHH TLNVKSGILH KGTGENQFLT QQPAIITSIM GNGRRRSISC PSCNGLAEGN KLLAPVALAV GIDGSLFVGD FNYIRRIFP SRNVTSILEL RNSPGHKYYL AVDPVTGSLY VSDTNSRRIY RVKSLSGAKD LAGNSEVVAG TGEQCLPFDE A RCGDGGKA VDATLMSPRG IAVDKNGLMY FVDATMIRKV DQNGIISTLL GSNDLTAVRP LSCDSSMDVA QVRLEWPTDL AV NPMDNSL YVLENNVILR ITENHQVSII AGRPMHCQVP GIDYSLSKLA IHSALESASA IAISHTGVLY ITETDEKKIN RLR QVTTNG EICLLAGAAS DCDCKNDVNC ICYSGDDAYA TDAILNSPSS LAVAPDGTIY IADLGNIRIR AVSKNKPVLN AFNQ YEAAS PGEQELYVFN ADGIHQYTVS LVTGEYLYNF TYSADNDVTE LIDNNGNSLK IRRDSSGMPR HLLMPDNQII TLTVG TNGG LKAVSTQNLE LGLMTYDGNT GLLATKSDET GWTTFYDYDH EGRLTNVTRP TGVVTSLHRE MEKSITIDIE NSNRDD DVT VITNLSSVEA SYTVVQDQVR NSYQLCNNGT LRVMYANGMA VSFHSEPHVL AGTITPTIGR CNISLPMENG LNSIEWR LR KEQIKGKVTI FGRKLRVHGR NLLSIDYDRN IRTEKIYDDH RKFTLRIIYD QVGRPFLWLP SSGLAAVNVS YFFNGRLA G LQRGAMSERT DIDKQGRIVS RMFADGKVWS YSYLDKSMVL LLQSQRQYIF EYDSSDRLHA VTMPSVARHS MSTHTSIGY IRNIYNPPES NASVIFDYSD DGRILKTSFL GTGRQVFYKY GKLSKLSEIV YDSTAVTFGY DETTGVLKMV NLQSGGFSCT IRYRKVGPL VDKQIYRFSE EGMINARFDY TYHDNSFRIA SIKPVISETP LPVDLYRYDE ISGKVEHFGK FGVIYYDINQ I ITTAVMTL SKHFDTHGRI KEVQYEMFRS LMYWMTVQYD SMGRVIKREL KLGPYANTTK YTYDYDGDGQ LQSVAVNDRP TW RYSYDLN GNLHLLNPGN SARLMPLRYD LRDRITRLGD VQYKIDDDGY LCQRGSDIFE YNSKGLLTRA YNKASGWSVQ YRY DGVGRR ASYKTNLGHH LQYFYSDLHN PTRITHVYNH SNSEITSLYY DLQGHLFAME SSSGEEYYVA SDNTGTPLAV FSIN GLMIK QLQYTAYGEI YYDSNPDFQM VIGFHGGLYD PLTKLVHFTQ RDYDVLAGRW TSPDYTMWRN VGKEPAPFNL YMFKN NNPL SNELDLKNYV TDVKSWLVMF GFQLSNIIPG FPRAKMYFVP PPYELSESQA SENGQLITGV QQTTERHNQA FLALEG QVI TKKLHASIRE KAGHWFATTT PIIGKGIMFA IKEGRVTTGV SSIASEDSRK VASVLNNAYY LDKMHYSIEG KDTHYFV KI GAADGDLVTL GTTIGRKVLE SGVNVTVSQP TLLVNGRTRR FTNIEFQYST LLLSIRYGLT PDTLDEEKAR VLDQARQR A LGTAWAKEQQ KARDGREGSR LWTEGEKQQL LSTGRVQGYE GYYVLPVEQY PELADSSSNI QFLRQNEMGK RGT

UniProtKB: Teneurin-2

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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: 10 / 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

Concentration0.17 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
25.0 mMHEPES

Details: 25 mM HEPES, 300 mM NaCl, pH 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0001 kPa
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
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6108 / Average electron dose: 41.503 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: 4649892
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 38045
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 10 / Avg.num./class: 15000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g42:
Mouse Teneurin2 dimer variant A0B0

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