[English] 日本語
Yorodumi
- EMDB-25892: Full-length human E-cadherin bound to blocking Fab 67G8 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25892
TitleFull-length human E-cadherin bound to blocking Fab 67G8
Map datacisTEM generate3D full map
Sample
  • Complex: Complex of human E-cadherin monomer with blocking Fab 67G8
    • Complex: Full length E-cadherin with Twin-Strep tag
      • Protein or peptide: E-cadherin (CDH1) with C-terminal Twin-Strep tag
    • Complex: Blocking antibody fragment 67G8 Fab
      • Protein or peptide: Blocking antibody fragment 67G8 Fab heavy chain
      • Protein or peptide: Blocking antibody fragment 67G8 Fab light chain
KeywordsE-cadherin / Fab / CDH1 / functional antibody / CELL ADHESION
Function / homology
Function and homology information


response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion ...response to heparin / desmosome assembly / response to Gram-positive bacterium / pituitary gland development / gamma-catenin binding / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / negative regulation of axon extension / desmosome / cellular response to indole-3-methanol / calcium-dependent cell-cell adhesion / flotillin complex / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / cell-cell adhesion mediated by cadherin / adherens junction organization / Formation of definitive endoderm / catenin complex / Apoptotic cleavage of cell adhesion proteins / cell-cell junction assembly / Adherens junctions interactions / GTPase activating protein binding / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / apical junction complex / homophilic cell-cell adhesion / lateral plasma membrane / Integrin cell surface interactions / RHO GTPases activate IQGAPs / synapse assembly / cell adhesion molecule binding / positive regulation of protein localization / Degradation of the extracellular matrix / Transcriptional and post-translational regulation of MITF-M expression and activity / InlA-mediated entry of Listeria monocytogenes into host cells / protein tyrosine kinase binding / negative regulation of cell migration / protein localization to plasma membrane / adherens junction / trans-Golgi network / cell-cell adhesion / beta-catenin binding / positive regulation of protein import into nucleus / response to toxic substance / cytoplasmic side of plasma membrane / cell morphogenesis / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / neuron projection development / cell junction / cell migration / lamellipodium / actin cytoskeleton / regulation of gene expression / postsynapse / endosome / cadherin binding / response to xenobiotic stimulus / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.53 Å
AuthorsMaker A / Gumbiner BM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122467 United States
CitationJournal: Protein Expr Purif / Year: 2022
Title: Reconstitution of the full transmembrane cadherin-catenin complex.
Authors: Allison Maker / Barry M Gumbiner /
Abstract: The dynamic regulation of epithelial adherens junctions relies on all components of the E-cadherin-catenin complex. Previously, the complexes have been partially reconstituted and composed only of α- ...The dynamic regulation of epithelial adherens junctions relies on all components of the E-cadherin-catenin complex. Previously, the complexes have been partially reconstituted and composed only of α-catenin, β-catenin, and the E-cadherin cytoplasmic domain. However, p120-catenin and the full-length E-cadherin including the extracellular, transmembrane, and intra-cellular domains are vital to the understanding of the relationship between extracellular adhesion and intracellular signaling. Here, we reconstitute the complete and full-length cadherin-catenin complex, including full-length E-cadherin, α-catenin, β-catenin, and p120-catenin, into nanodiscs. We are able to observe the cadherin in nanodiscs by cryo-EM. We also reconstitute α-catenin, β-catenin, and p120-catenin with the E-cadherin cytoplasmic tail alone in order to analyze the affinities of their binding interactions. We find that p120-catenin does not associate strongly with α- or β-catenin and binds much more transiently to the cadherin cytoplasmic tail than does β-catenin. Overall, this work creates many new possibilities for biochemical studies understanding transmembrane signaling of cadherins and the role of p120-catenin in adhesion activation.
History
DepositionJan 10, 2022-
Header (metadata) releaseJan 19, 2022-
Map releaseJan 19, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25892.png

Downloads & links

-
Map

FileDownload / File: emd_25892.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcisTEM generate3D full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 320 pix.
= 537.6 Å		1.68 Å/pix.
x 320 pix.
= 537.6 Å		1.68 Å/pix.
x 320 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0 / Movie #1: 6
Minimum - Maximum-7.9065113 - 17.433605
Average (Standard dev.)0.0012349988 (±0.32979113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-7.90717.4340.001

-
Supplemental data

-
Half map: cisTEM generate3D half map 1

Fileemd_25892_half_map_1.map
AnnotationcisTEM generate3D half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: cisTEM generate3D half map 2

Fileemd_25892_half_map_2.map
AnnotationcisTEM generate3D half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of human E-cadherin monomer with blocking Fab 67G8

EntireName: Complex of human E-cadherin monomer with blocking Fab 67G8
Components
  • Complex: Complex of human E-cadherin monomer with blocking Fab 67G8
    • Complex: Full length E-cadherin with Twin-Strep tag
      • Protein or peptide: E-cadherin (CDH1) with C-terminal Twin-Strep tag
    • Complex: Blocking antibody fragment 67G8 Fab
      • Protein or peptide: Blocking antibody fragment 67G8 Fab heavy chain
      • Protein or peptide: Blocking antibody fragment 67G8 Fab light chain

-
Supramolecule #1: Complex of human E-cadherin monomer with blocking Fab 67G8

SupramoleculeName: Complex of human E-cadherin monomer with blocking Fab 67G8
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cadherin was embedded in MSP1D1 nanodisc not visible in final map.
Molecular weightTheoretical: 130 KDa

-
Supramolecule #2: Full length E-cadherin with Twin-Strep tag

SupramoleculeName: Full length E-cadherin with Twin-Strep tag / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80 KDa

-
Supramolecule #3: Blocking antibody fragment 67G8 Fab

SupramoleculeName: Blocking antibody fragment 67G8 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 / Details: His tagged recombinant Fab fragment
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 50 KDa

-
Macromolecule #1: E-cadherin (CDH1) with C-terminal Twin-Strep tag

MacromoleculeName: E-cadherin (CDH1) with C-terminal Twin-Strep tag / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: DWVIPPISCP ENEKGPFPKN LVQIKSNKDK EGKVFYSITG QGADTPPVGV FIIERETGWL KVTEPLDRER IATYTLFSHA VSSNGNAVED PMEILITVTD QNDNKPEFTQ EVFKGSVMEG ALPGTSVMEV TATDADDDVN TYNAAIAYTI LSQDPELPDK NMFTINRNTG ...String:
DWVIPPISCP ENEKGPFPKN LVQIKSNKDK EGKVFYSITG QGADTPPVGV FIIERETGWL KVTEPLDRER IATYTLFSHA VSSNGNAVED PMEILITVTD QNDNKPEFTQ EVFKGSVMEG ALPGTSVMEV TATDADDDVN TYNAAIAYTI LSQDPELPDK NMFTINRNTG VISVVTTGLD RESFPTYTLV VQAADLQGEG LSTTATAVIT VTDTNDNPPI FNPTTYKGQV PENEANVVIT TLKVTDADAP NTPAWEAVYT ILNDDGGQFV VTTNPVNNDG ILKTAKGLDF EAKQQYILHV AVTNVVPFEV SLTTSTATVT VDVLDVNEAP IFVPPEKRVE VSEDFGVGQE ITSYTAQEPD TFMEQKITYR IWRDTANWLE INPDTGAIST RAELDREDFE HVKNSTYTAL IIATDNGSPV ATGTGTLLLI LSDVNDNAPI PEPRTIFFCE RNPKPQVINI IDADLPPNTS PFTAELTHGA SANWTIQYND PTQESIILKP KMALEVGDYK INLKLMDNQN KDQVTTLEVS VCDCEGAAGV CRKAQPVEAG LQIPAILGIL GGILALLILI LLLLLFLRRR AVVKEPLLPP EDDTRDNVYY YDEEGGGEED QDFDLSQLHR GLDARPEVTR NDVAPTLMSV PRYLPRPANP DEIGNFIDEN LKAADTDPTA PPYDSLLVFD YEGSGSEAAS LSSLNSSESD KDQDYDYLNE WGNRFKKLAD MYGGGEDHSA WSHPQFEKGG GSGGGSGGSA WSHPQFEK

-
Macromolecule #2: Blocking antibody fragment 67G8 Fab heavy chain

MacromoleculeName: Blocking antibody fragment 67G8 Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDWSWVFLFL LSVNEGVYCQ VQLQQSGNDL VKPGASVKLS CKASGYTFTS YWINWIKQRP GQGLEWIGRV VPGSGNTYYN EIFKGKATLT VDTSSRSAYI QLSSLSSEDS AVYFCVRYGG HYFDYWGQGT TLTVSSAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP ...String:
MDWSWVFLFL LSVNEGVYCQ VQLQQSGNDL VKPGASVKLS CKASGYTFTS YWINWIKQRP GQGLEWIGRV VPGSGNTYYN EIFKGKATLT VDTSSRSAYI QLSSLSSEDS AVYFCVRYGG HYFDYWGQGT TLTVSSAKTT PPSVYPLAPG SAAQTNSMVT LGCLVKGYFP EPVTVTWNSG SLSSGVHTFP AVLQSDLYTL SSSVTVPSSP RPSETVTCNV AHPASSTKVD KKIVPRDCHH HHHH

-
Macromolecule #3: Blocking antibody fragment 67G8 Fab light chain

MacromoleculeName: Blocking antibody fragment 67G8 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MDFQVQIFSF LLISASVIMS RGQIVLSQSP AILSASPGEM VTMTCRASSS VSYMHWNQQK PGSSPKPWIY ATSNLASGVP ARFSGSGSGT SYSLTISRVE AEDAATYYCQ QWSSNPPTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK ...String:
MDFQVQIFSF LLISASVIMS RGQIVLSQSP AILSASPGEM VTMTCRASSS VSYMHWNQQK PGSSPKPWIY ATSNLASGVP ARFSGSGSGT SYSLTISRVE AEDAATYYCQ QWSSNPPTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV LNSWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.10 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClsodium chloride
1.0 mMCaCl2calcium chloride
GridMaterial: GOLD / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsNanodiscs averaged out in final reconstruction.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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

+
Image processing

Particle selectionNumber selected: 356986
Startup modelType of model: INSILICO MODEL / In silico model: De novo model created in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0) / Number images used: 97712
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.14)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more