[English] 日本語
Yorodumi
- PDB-3r08: Crystal structure of mouse cd3epsilon in complex with antibody 2C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r08
TitleCrystal structure of mouse cd3epsilon in complex with antibody 2C11 Fab
Components
  • Mouse anti-mouse CD3epsilon antibody 2C11 heavy chain
  • Mouse anti-mouse CD3epsilon antibody 2C11 light chain
  • T-cell surface glycoprotein CD3 epsilon chain
KeywordsIMMUNE SYSTEM / CD3epsilon / antibody / T-cell receptor / signalling
Function / homology
Function and homology information


lymphocyte activation / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation ...lymphocyte activation / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of T cell anergy / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / alpha-beta T cell receptor complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of cell-matrix adhesion / smoothened signaling pathway / T cell receptor complex / positive regulation of interleukin-4 production / dendrite development / immunological synapse / T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / T cell activation / cerebellum development / negative regulation of smoothened signaling pathway / apoptotic signaling pathway / calcium-mediated signaling / positive regulation of T cell activation / SH3 domain binding / positive regulation of type II interferon production / cell-cell junction / transmembrane signaling receptor activity / T cell receptor signaling pathway / cell body / dendritic spine / adaptive immune response / cell surface receptor signaling pathway / negative regulation of gene expression / external side of plasma membrane / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane
Similarity search - Function
Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ig-like domain profile. / Immunoglobulin-like domain ...Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain / CD3 protein, epsilon/gamma/delta subunit / Immunoreceptor tyrosine-based activation motif / Phosphorylated immunoreceptor signalling ITAM / ITAM motif mammalian type profile. / Immunoreceptor tyrosine-based activation motif / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesCricetulus migratorius (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsShore, D.A. / Zhu, X. / Wilson, I.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: T cell receptors are structures capable of initiating signaling in the absence of large conformational rearrangements.
Authors: Fernandes, R.A. / Shore, D.A. / Vuong, M.T. / Yu, C. / Zhu, X. / Pereira-Lopes, S. / Brouwer, H. / Fennelly, J.A. / Jessup, C.M. / Evans, E.J. / Wilson, I.A. / Davis, S.J.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Mouse anti-mouse CD3epsilon antibody 2C11 light chain
H: Mouse anti-mouse CD3epsilon antibody 2C11 heavy chain
E: T-cell surface glycoprotein CD3 epsilon chain


Theoretical massNumber of molelcules
Total (without water)56,2593
Polymers56,2593
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)263.177, 263.177, 263.177
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

-
Components

#1: Antibody Mouse anti-mouse CD3epsilon antibody 2C11 light chain


Mass: 23646.154 Da / Num. of mol.: 1 / Fragment: UNP residues 22-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma
#2: Antibody Mouse anti-mouse CD3epsilon antibody 2C11 heavy chain


Mass: 23149.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Cell: hybridoma
#3: Protein T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 9463.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cricetulus migratorius (Armenian hamster)
Gene: Cd3e / Cell (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22646
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 6.75 Å3/Da / Density % sol: 81.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.2
Details: 0.1 M Mes, ammonium sulfate, dioxane, pH 5.2, VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 24, 2006
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 4.1→50 Å / Num. obs: 12153 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 116.64 Å2
Reflection shellResolution: 4.1→4.25 Å / % possible all: 98.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3R06, 1SY6

3r06

1sy6


Resolution: 4.1→33.15 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 582 4.81 %RANDOM
Rwork0.222 ---
obs0.224 12110 --
Displacement parametersBiso mean: 180.73 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 1.274 Å
Refinement stepCycle: LAST / Resolution: 4.1→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3944 0 0 0 3944
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.0140402
X-RAY DIFFRACTIONt_angle_deg1.4455032
X-RAY DIFFRACTIONt_dihedral_angle_d13462
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes982
X-RAY DIFFRACTIONt_gen_planes5805
X-RAY DIFFRACTIONt_it404020
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.82
X-RAY DIFFRACTIONt_other_torsion25.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion5405
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact46454
LS refinement shellResolution: 4.1→4.49 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3605 144 5.01 %
Rwork0.2777 2732 -
all0.2815 2876 -

+
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