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- PDB-1xiw: Crystal structure of human CD3-e/d dimer in complex with a UCHT1 ... -

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Basic information

Entry
Database: PDB / ID: 1xiw
TitleCrystal structure of human CD3-e/d dimer in complex with a UCHT1 single-chain antibody fragment
Components
  • T-cell surface glycoprotein CD3 delta chain
  • T-cell surface glycoprotein CD3 epsilon chain
  • immunoglobulin heavy chain variable region
  • immunoglobulin light chain variable region
Keywordsmembrane protein/Immune System / CD3-epsilon / CD3-delta / UCHT1-scFv / immunoglobulin fold / antibody-antigen complex / membrane protein-Immune System COMPLEX
Function / homology
Function and homology information


gamma-delta T cell activation / positive regulation of cell-cell adhesion mediated by integrin / positive thymic T cell selection / signal complex assembly / alpha-beta T cell receptor complex / T cell receptor complex / positive regulation of cell-matrix adhesion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development ...gamma-delta T cell activation / positive regulation of cell-cell adhesion mediated by integrin / positive thymic T cell selection / signal complex assembly / alpha-beta T cell receptor complex / T cell receptor complex / positive regulation of cell-matrix adhesion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / dendrite development / alpha-beta T cell activation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / cerebellum development / positive regulation of T cell proliferation / cell surface receptor protein tyrosine kinase signaling pathway / T cell activation / clathrin-coated endocytic vesicle membrane / SH3 domain binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / transmembrane signaling receptor activity / T cell receptor signaling pathway / Downstream TCR signaling / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / signaling receptor complex adaptor activity / protein-containing complex assembly / cell body / regulation of apoptotic process / dendritic spine / adaptive immune response / protein-macromolecule adaptor activity / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / 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 ...CD3 gamma/delta subunit, Ig-like domain / T-cell surface glycoprotein CD3 delta chain / 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 / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / T-cell surface glycoprotein CD3 delta chain / T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArnett, K.L. / Harrison, S.C. / Wiley, D.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.
Authors: Arnett, K.L. / Harrison, S.C. / Wiley, D.C.
History
DepositionSep 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Aug 23, 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The chimera protein consists of immunoglobulin light chain variable region (chains C, G), ...SEQUENCE The chimera protein consists of immunoglobulin light chain variable region (chains C, G), a linker GGGGSGGGGSGGGGS, and immunoglobulin heavy chain variable region (chains D, H). However, the linker GGGGSGGGGSGGGGS are not modeled due to disorder. The conflicts are due to immunoglobulin domain variable region (v)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell surface glycoprotein CD3 epsilon chain
B: T-cell surface glycoprotein CD3 delta chain
C: immunoglobulin light chain variable region
D: immunoglobulin heavy chain variable region
E: T-cell surface glycoprotein CD3 epsilon chain
F: T-cell surface glycoprotein CD3 delta chain
G: immunoglobulin light chain variable region
H: immunoglobulin heavy chain variable region


Theoretical massNumber of molelcules
Total (without water)93,2888
Polymers93,2888
Non-polymers00
Water5,747319
1
A: T-cell surface glycoprotein CD3 epsilon chain
B: T-cell surface glycoprotein CD3 delta chain
C: immunoglobulin light chain variable region
D: immunoglobulin heavy chain variable region


Theoretical massNumber of molelcules
Total (without water)46,6444
Polymers46,6444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: T-cell surface glycoprotein CD3 epsilon chain
F: T-cell surface glycoprotein CD3 delta chain
G: immunoglobulin light chain variable region
H: immunoglobulin heavy chain variable region


Theoretical massNumber of molelcules
Total (without water)46,6444
Polymers46,6444
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.874, 79.326, 150.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 11893.056 Da / Num. of mol.: 2 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3E, T3E / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07766
#2: Protein T-cell surface glycoprotein CD3 delta chain / T-cell receptor T3 delta chain


Mass: 9106.425 Da / Num. of mol.: 2 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD3D, T3D / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04234
#3: Antibody immunoglobulin light chain variable region


Mass: 11994.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: UCHT1 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: PH0888
#4: Antibody immunoglobulin heavy chain variable region


Mass: 13650.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: UCHT1 / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: PIR: PH0887
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, sodium chloride, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 22K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2003
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 62308 / Num. obs: 60988 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 6134 / Rsym value: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6FAB

6fab


Resolution: 1.9→49.17 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2409958.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3068 5 %RANDOM
Rwork0.204 ---
all0.214 60759 --
obs0.204 60759 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2681 Å2 / ksol: 0.361556 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---4.74 Å20 Å2
3---5.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-50 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6044 0 0 319 6363
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.421.5
X-RAY DIFFRACTIONc_mcangle_it4.592
X-RAY DIFFRACTIONc_scbond_it4.982
X-RAY DIFFRACTIONc_scangle_it6.642.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 508 5 %
Rwork0.206 9690 -
obs-9690 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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