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- PDB-3r08: Crystal structure of mouse cd3epsilon in complex with antibody 2C... -

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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 / PD-1 signaling / Generation of second messenger molecules / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / Downstream TCR signaling / CD4-positive, alpha-beta T cell proliferation ...lymphocyte activation / Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Generation of second messenger molecules / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / Downstream TCR signaling / 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 / positive thymic T cell selection / positive regulation of cell-matrix adhesion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / T cell receptor complex / smoothened signaling pathway / positive regulation of interleukin-4 production / dendrite development / immunological synapse / positive regulation of calcium-mediated signaling / T cell proliferation / negative regulation of smoothened signaling pathway / positive regulation of T cell proliferation / T cell costimulation / T cell activation / positive regulation of interleukin-2 production / cerebellum development / response to nutrient / calcium-mediated signaling / apoptotic signaling pathway / SH3 domain binding / transmembrane signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of type II interferon production / cell-cell junction / positive regulation of T cell activation / T cell receptor signaling pathway / cell body / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / Golgi apparatus / endoplasmic reticulum / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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 -

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