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- EMDB-43644: Structure of mCELSR1 extracellular region containing CADH9-GAIN d... -

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Basic information

Entry
Database: EMDB / ID: EMD-43644
TitleStructure of mCELSR1 extracellular region containing CADH9-GAIN domains
Map datalocally filtered using cryoSPARC. used for manual building.
Sample
  • Complex: Extracellular region of mCELSR1
    • Protein or peptide: Cadherin EGF LAG seven-pass G-type receptor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCELSR / adhesion / GPCR / planar cell polarity / SIGNALING PROTEIN
Function / homology
Function and homology information


orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / protein localization involved in establishment of planar polarity / establishment of body hair planar orientation / establishment of planar polarity of embryonic epithelium / establishment of planar polarity / motor neuron migration / apical protein localization / anterior/posterior pattern specification ...orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis / planar dichotomous subdivision of terminal units involved in lung branching morphogenesis / lateral sprouting involved in lung morphogenesis / protein localization involved in establishment of planar polarity / establishment of body hair planar orientation / establishment of planar polarity of embryonic epithelium / establishment of planar polarity / motor neuron migration / apical protein localization / anterior/posterior pattern specification / inner ear morphogenesis / homophilic cell adhesion via plasma membrane adhesion molecules / hair follicle development / Rho protein signal transduction / locomotory behavior / regulation of actin cytoskeleton organization / neural tube closure / wound healing / G protein-coupled receptor activity / cell surface receptor signaling pathway / calcium ion binding / nucleoplasm / membrane / plasma membrane
Similarity search - Function
: / CELSR2-like, ninth cadherin domain / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain ...: / CELSR2-like, ninth cadherin domain / GAIN domain, N-terminal / GPCR-Autoproteolysis INducing (GAIN) domain / Laminin-type EGF-like (LE) domain profile. / Laminin-type EGF-like (LE) domain signature. / Laminin-type epidermal growth factor-like domai / Laminin EGF domain / Laminin-type EGF domain / Laminin G domain / GAIN domain superfamily / GPCR proteolysis site, GPS, motif / Laminin G domain profile. / GPS motif / GAIN-B domain profile. / G-protein-coupled receptor proteolytic site domain / Laminin G domain / Laminin G domain / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Cadherin EGF LAG seven-pass G-type receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBandekar SJ / Arac D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM148412 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM142266 United States
CitationJournal: To Be Published
Title: Title: Structure of the extracellular region of the adhesion GPCR CELSR1 reveals a compact module which regulates G protein-coupling
Authors: Bandekar SJ / Arac D
History
DepositionFeb 6, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43644.png

Downloads & links

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Map

FileDownload / File: emd_43644.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocally filtered using cryoSPARC. used for manual building.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å		1.1 Å/pix.
x 288 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.6703563 - 4.302973
Average (Standard dev.)0.0043549496 (±0.06229689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_43644_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_43644_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Extracellular region of mCELSR1

EntireName: Extracellular region of mCELSR1
Components
  • Complex: Extracellular region of mCELSR1
    • Protein or peptide: Cadherin EGF LAG seven-pass G-type receptor 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Extracellular region of mCELSR1

SupramoleculeName: Extracellular region of mCELSR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 262 KDa

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Macromolecule #1: Cadherin EGF LAG seven-pass G-type receptor 1

MacromoleculeName: Cadherin EGF LAG seven-pass G-type receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 245.638281 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ASTSPQFPLP SYQVSVPENE PAGTAVIELR AHDPDEGDAG RLSYQMEALF DERSNGYFLI DAATGAVTTA RSLDRETKDT HVLKVSAVD HGSPRRSAAT YLTVTVSDTN DHSPVFEQSE YRERIRENLE VGYEVLTIRA TDGDAPSNAN MRYRLLEGAG G VFEIDARS ...String:
ASTSPQFPLP SYQVSVPENE PAGTAVIELR AHDPDEGDAG RLSYQMEALF DERSNGYFLI DAATGAVTTA RSLDRETKDT HVLKVSAVD HGSPRRSAAT YLTVTVSDTN DHSPVFEQSE YRERIRENLE VGYEVLTIRA TDGDAPSNAN MRYRLLEGAG G VFEIDARS GVVRTRAVVD REEAAEYQLL VEANDQGRNP GPLSASATVH IVVEDENDNY PQFSEKRYVV QVPEDVAVNT AV LRVQATD RDQGQNAAIH YSIVSGNLKG QFYLHSLSGS LDVINPLDFE AIREYTLRIK AQDGGRPPLI NSSGLVSVQV LDV NDNAPI FVSSPFQAAV LENVPLGHSV LHIQAVDADA GENARLQYRL VDTASTIVGG SSVDSENPAS APDFPFQIHN SSGW ITVCA ELDREEVEHY SFGVEAVDHG SPAMSSSASV SITVLDVNDN DPMFTQPVYE LRLNEDAAVG SSVLTLRARD RDANS VITY QLTGGNTRNR FALSSQSGGG LITLALPLDY KQERQYVLAV TASDGTRSHT AQVFINVTDA NTHRPVFQSS HYTVSV SED RPVGTSIATI SATDEDTGEN ARITYVLEDP VPQFRIDPDT GTIYTMTELD YEDQAAYTLA ITAQDNGIPQ KSDTTSL EI LILDANDNAP RFLRDFYQGS VFEDAPPSTS VLQVSATDRD SGPNGRLLYT FQGGDDGDGD FYIEPTSGVI RTQRRLDR E NVAVYNLWAL AVDRGSPNPL SASVGIQVSV LDINDNPPVF EKDELELFVE ENSPVGSVVA RIRANDPDEG PNAQIMYQI VEGNVPEVFQ LDLLSGDLRA LVELDFEVRR DYMLVVQATS APLVSRATVH IRLLDQNDNP PELPDFQILF NNYVTNKSNS FPSGVIGRI PAHDPDLSDS LNYTFLQGNE LSLLLLDPAT GELQLSRDLD NNRPLEALME VSVSDGIHSV TALCTLRVTI I TDDMLTNS ITVRLENMSQ EKFLSPLLSL FVEGVATVLS TTKDDIFVFN IQNDTDVSSN ILNVTFSALL PGGTRGRFFP SE DLQEQIY LNRTLLTTIS AQRVLPFDDN ICLREPCENY MKCVSVLRFD SSAPFISSTT VLFRPIHPIT GLRCRCPPGF TGD YCETEI DLCYSNPCGA NGRCRSREGG YTCECFEDFT GEHCQVNVRS GRCASGVCKN GGTCVNLLIG GFHCVCPPGE YEHP YCEVS TRSFPPQSFV TFRGLRQRFH FTVSLAFATQ DRNALLLYNG RFNEKHDFIA LEIVEEQLQL TFSAGETTTT VTPQV PGGV SDGRWHSVLV QYYNKPNIGH LGLPHGPSGE KVAVVTVDDC DAAVAVHFGS YVGNYSCAAQ GTQSGSKKSL DLTGPL LLG GVPNLPEDFP VHSRQFVGCM RNLSIDGRIV DMAAFIANNG TRAGCASQRN FCDGTSCQNG GTCVNRWNTY LCECPLR FG GKNCEQAMPH PQRFTGESVV LWSDLDITIS VPWYLGLMFR TRKEDGVLME ATAGTSSRLH LQILNSYIRF EVSYGPSD V ASMQLSKSRI TDGGWHHLLI ELRSAKEGKD IKYLAVMTLD YGMDQSTVQI GNQLPGLKMR TIVIGGVTED KVSVRHGFR GCMQGVRMGE TSTNIATLNM NDALKVRVKD GCDVEDPCAS SPCPPHSHCR DTWDSYSCIC DRGYFGKKCV DACLLNPCKH VAACVRSPN TPRGYSCECG PGHYGQYCEN KVDLPCPKGW WGNPVCGPCH CAVSQGFDPD CNKTNGQCQC KENYYKPPAQ D ACLPCDCF PHGSHSRACD MDTGQCACKP GVIGRQCNRC DNPFAEVTSL GCEVIYNGCP RAFEAGIWWP QTKFGQPAAV PC PKGSVGN AVRHCSGEKG WLPPELFNCT SGSFVDLKAL NEKLNRNETR MDGNRSLRLA KALRNATQGN STLFGNDVRT AYQ LLARIL QHESRQQGFD LAATREANFH EDVVHTGSAL LAPATEASWE QIQRSEAGAA QLLRHFEAYF SNVARNVKRT YLRP FVIVT ANMILAVDIF DKLNFTGAQV PRFEDIQEEL PRELESSVSF PADTFKPPEK KEGPVVRLTN RRTTPLTAQP EPRAE RETS SSRRRRHPDE PGQFAVALVV IYRTLGQLLP EHYDPDHRSL RLPNRPVINT PVVSAMVYSE GTPLPSSLQR PILVEF SLL ETEERSKPVC VFWNHSLDTG GTGGWSAKGC ELLSRNRTHV TCQCSHSASC AVLMDISRRE HHHHHHHHH

UniProtKB: Cadherin EGF LAG seven-pass G-type receptor 1

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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: 6 / 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

Concentration3.0 mg/mL
BufferpH: 8.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
10.0 mM(HOCH2)3CNH2Tris
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Detailsmostly monodispserse with small aggregates present

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171416
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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