[English] 日本語
Yorodumi
- EMDB-16279: Structure of CEACAM5 A3-B3 domain in Complex with Tusamitamab Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16279
TitleStructure of CEACAM5 A3-B3 domain in Complex with Tusamitamab Fab
Map dataCryo EM map for the complex
Sample
  • Complex: hCEACAM5-A3B3-Tusamitamab Fab complex
    • Protein or peptide: Tusamitamab Fab heavy Chain
    • Protein or peptide: Tusamitamab Light Chain
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCEACAM5 / Tusamitamab / Cancer / cell adhesion / cryo-EM / small molecular weight / Fab / A3-B3 / human membrane protein
Function / homology
Function and homology information


GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / regulation of immune system process / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / protein tyrosine kinase binding ...GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / regulation of immune system process / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / protein tyrosine kinase binding / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 5
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus sp. (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsKumar A / Bertrand T / Rapisarda C / Rak A
Funding support France, 1 items
OrganizationGrant numberCountry
Other private France
CitationJournal: Res Sq / Year: 2023
Title: Structural insights into epitope-paratope interactions of monoclonal antibody targeting CEACAM5-expressing tumors
Authors: Rak A / Kumar A / Duffi F / Gagnaire M / Rapisarda C / Bertrand T
History
DepositionDec 6, 2022-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16279.png

Downloads & links

-
Map

FileDownload / File: emd_16279.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo EM map for the complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å		1.16 Å/pix.
x 256 pix.
= 296.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-34.901577000000003 - 77.238235000000003
Average (Standard dev.)0.000000000002839 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 296.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A

Fileemd_16279_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B

Fileemd_16279_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : hCEACAM5-A3B3-Tusamitamab Fab complex

EntireName: hCEACAM5-A3B3-Tusamitamab Fab complex
Components
  • Complex: hCEACAM5-A3B3-Tusamitamab Fab complex
    • Protein or peptide: Tusamitamab Fab heavy Chain
    • Protein or peptide: Tusamitamab Light Chain
    • Protein or peptide: Carcinoembryonic antigen-related cell adhesion molecule 5
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: hCEACAM5-A3B3-Tusamitamab Fab complex

SupramoleculeName: hCEACAM5-A3B3-Tusamitamab Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Human CEACAM5 a3-B3 domain in the comlex with the Tusamitamab Fab
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70 KDa

-
Macromolecule #1: Tusamitamab Fab heavy Chain

MacromoleculeName: Tusamitamab Fab heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 24.833652 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQESGPG LVKPGGSLSL SCAASGFVFS SYDMSWVRQT PERGLEWVAY ISSGGGITYA PSTVKGRFTV SRDNAKNTLY LQMNSLTSE DTAVYYCAAH YFGSSGPFAY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String:
EVQLQESGPG LVKPGGSLSL SCAASGFVFS SYDMSWVRQT PERGLEWVAY ISSGGGITYA PSTVKGRFTV SRDNAKNTLY LQMNSLTSE DTAVYYCAAH YFGSSGPFAY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT HHHHHH

-
Macromolecule #2: Tusamitamab Light Chain

MacromoleculeName: Tusamitamab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus sp. (mice)
Molecular weightTheoretical: 23.497072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPAS LSASVGDRVT ITCRASENIF SYLAWYQQKP GKSPKLLVYN TRTLAEGVPS RFSGSGSGTD FSLTISSLQP EDFATYYCQ HHYGTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS LSASVGDRVT ITCRASENIF SYLAWYQQKP GKSPKLLVYN TRTLAEGVPS RFSGSGSGTD FSLTISSLQP EDFATYYCQ HHYGTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: Carcinoembryonic antigen-related cell adhesion molecule 5

MacromoleculeName: Carcinoembryonic antigen-related cell adhesion molecule 5
type: protein_or_peptide / ID: 3 / Details: A3-B3 domain / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.883041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ELPKPSISSN NSKPVEDKDA VAFTCEPEAQ NTTYLWWVNG QSLPVSPRLQ LSNGNRTLTL FNVTRNDARA YVCGIQNSVS ANRSDPVTL DVLYGPDTPI ISPPDSSYLS GANLNLSCHS ASNPSPQYSW RINGIPQQHT QVLFIAKITP NNNGTYACFV S NLATGRNN ...String:
ELPKPSISSN NSKPVEDKDA VAFTCEPEAQ NTTYLWWVNG QSLPVSPRLQ LSNGNRTLTL FNVTRNDARA YVCGIQNSVS ANRSDPVTL DVLYGPDTPI ISPPDSSYLS GANLNLSCHS ASNPSPQYSW RINGIPQQHT QVLFIAKITP NNNGTYACFV S NLATGRNN SIVKSITVSA SGTSPGLSAH HHHHH

UniProtKB: Carcinoembryonic antigen-related cell adhesion molecule 5

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.87 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Name: D-PBS / Details: Dulbeccos phosphate buffered saline
GridModel: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5072 / Average exposure time: 4.72 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 240000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 2614488 / Details: Picked using blob picker
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 213470
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 3.2)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8bw0:
Structure of CEACAM5 A3-B3 domain in Complex with Tusamitamab Fab

+
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://pdbjlvh1.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