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- PDB-8f0l: Crystal Structure of the Human T cell Receptor CD3(EPSILON) N-Ter... -

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Basic information

Entry
Database: PDB / ID: 8f0l
TitleCrystal Structure of the Human T cell Receptor CD3(EPSILON) N-Terminal Peptide Complexed with ADI-26906 FAB
Components
  • ADI-26906 Fab Heavy Chain
  • ADI-26906 Fab Light Chain
  • T-cell surface glycoprotein CD3 epsilon chain
KeywordsIMMUNE SYSTEM / CD3 epsilon / antibody-antigen complex / MEMBRANE PROTEIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


gamma-delta T cell receptor complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / 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 ...gamma-delta T cell receptor complex / T cell anergy / positive regulation of T cell anergy / positive regulation of cell-cell adhesion mediated by integrin / gamma-delta T cell activation / 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 / signal complex assembly / positive regulation of cell-matrix adhesion / T cell receptor complex / smoothened signaling pathway / positive regulation of interleukin-4 production / 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 / PD-1 signaling / T cell receptor binding / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of T cell proliferation / negative regulation of smoothened signaling pathway / T cell costimulation / positive regulation of interleukin-2 production / positive regulation of calcium-mediated signaling / cerebellum development / T cell activation / apoptotic signaling pathway / calcium-mediated signaling / SH3 domain binding / positive regulation of type II interferon production / positive regulation of peptidyl-tyrosine phosphorylation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transmembrane signaling receptor activity / cell-cell junction / Downstream TCR signaling / signaling receptor complex adaptor activity / T cell receptor signaling pathway / cell body / protein-containing complex assembly / regulation of apoptotic process / adaptive immune response / dendritic spine / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / protein kinase binding / 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 / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell surface glycoprotein CD3 epsilon chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.81 Å
AuthorsBattles, M.B. / Welin, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2023
Title: Structure-based engineering of a novel CD3 epsilon-targeting antibody for reduced polyreactivity.
Authors: Liu, C.Y. / Ahonen, C.L. / Brown, M.E. / Zhou, L. / Welin, M. / Krauland, E.M. / Pejchal, R. / Widboom, P.F. / Battles, M.B.
History
DepositionNov 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: ADI-26906 Fab Heavy Chain
L: ADI-26906 Fab Light Chain
A: ADI-26906 Fab Heavy Chain
B: ADI-26906 Fab Light Chain
P: T-cell surface glycoprotein CD3 epsilon chain
Q: T-cell surface glycoprotein CD3 epsilon chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,68313
Polymers99,0386
Non-polymers6457
Water12,827712
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12950 Å2
ΔGint-45 kcal/mol
Surface area36430 Å2
Unit cell
Length a, b, c (Å)73.634, 53.084, 113.934
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ADI-26906 Fab Heavy Chain


Mass: 24121.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: N-terminal glutamine spontaniously converted to pyroglutamic acid
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody ADI-26906 Fab Light Chain


Mass: 24035.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide T-cell surface glycoprotein CD3 epsilon chain / T-cell surface antigen T3/Leu-4 epsilon chain


Mass: 1362.378 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: N-terminal glutamine spontaniously converted to pyroglutamic acid
Source: (synth.) Homo sapiens (human) / References: UniProt: P07766
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals of the ADI-26906 Fab complexed to CD3 epsilon N13 peptide were obtained by the sitting drop vapor diffusion method. The ADI-26906 Fab buffered in PBS, was first buffer-exchanged ...Details: Crystals of the ADI-26906 Fab complexed to CD3 epsilon N13 peptide were obtained by the sitting drop vapor diffusion method. The ADI-26906 Fab buffered in PBS, was first buffer-exchanged into 20 mM Bis-Tris pH 6.0 and 150 mM NaCl. The Fab (0.31 mM) was mixed with the N13 peptide (7.8 mM) at a Fab:peptide ratio of 1:25 and incubated on ice for 1.5 h. A BCS screen (Molecular Dimensions Ltd.) was set up using a mosquito crystallization robot (STP Labtech), with each drop consisting of 100 nL protein and 100 nL of reservoir solution, and left to equilibrate against a 40 uL reservoir solution at 293 K. After a few days, crystals were obtained in condition A6 (0.1 M MES pH 6.5, 25% w/v PEG Smear Broad).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.81→66.31 Å / Num. obs: 79385 / % possible obs: 99.9 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.03 / Rrim(I) all: 0.08 / Net I/σ(I): 13.8
Reflection shellResolution: 1.81→1.841 Å / Redundancy: 7 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3938 / CC1/2: 0.746 / Rpim(I) all: 0.352 / Rrim(I) all: 0.942 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.19.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IRZ

4irz


Resolution: 1.81→48.6 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.195 --
Rwork0.166 --
obs-79377 99.9 %
Refinement stepCycle: LAST / Resolution: 1.81→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 42 712 7457
LS refinement shellResolution: 1.81→1.88 Å /
RfactorNum. reflection
Rfree0.276 -
Rwork0.166 -
obs-7861
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.32665.4233-1.33615.591-0.73745.99970.2544-0.3144-0.18340.5449-0.1466-1.5227-0.55821.8296-0.11730.3854-0.1632-0.04510.650.00050.488232.61921.3451-35.0591
24.1922-3.6895-2.88875.21223.51764.6288-0.13820.1096-0.26550.0558-0.1910.28350.0754-0.17760.32010.1686-0.03710.02450.1599-0.01960.2044-6.9637-13.9081-13.1341
32.8777-0.45051.18333.1820.28173.85320.04560.334-0.0067-0.1585-0.09960.048-0.0364-0.34250.02550.17870.0058-0.02340.14-0.01540.1592-11.9001-3.0004-19.0357
43.4935-0.6803-0.98953.6905-0.36.85910.01340.2999-0.2807-0.209-0.0670.30850.3793-0.38080.03470.1784-0.026-0.04250.1862-0.05820.1955-15.2921-11.6541-18.5648
52.3389-1.0060.48340.7393-0.33740.582-0.02130.09530.04960.0188-0.0496-0.05310.02190.02930.06780.1862-0.01910.02080.1415-0.00330.16575.0232-10.0191-13.1913
61.91230.92391.51352.08971.68814.82970.0099-0.07730.12990.1055-0.0454-0.0923-0.09360.13210.04140.1722-0.00560.00410.1310.01170.204619.3195-11.5476-5.2999
78.90184.77895.96185.21223.79574.16490.4728-0.4695-0.40040.4554-0.2328-0.38910.4558-0.1388-0.20570.2633-0.0388-0.0040.24470.04450.197120.3814-18.35861.7289
83.39180.70111.40512.45730.65672.0791-0.00010.34990.1442-0.21570.0732-0.2129-0.13740.1372-0.06360.28920.00520.05250.16190.04360.2225-0.828115.6273-20.1311
92.38190.10090.38560.31240.11290.30740.04110.01710.0624-0.0198-0.0194-0.1756-0.10360.0062-0.02340.2523-0.01160.0060.15310.01480.2491.510611.6215-12.2731
102.01970.6091-0.20434.53671.02511.6289-0.00540.0915-0.0819-0.08370.0717-0.5919-0.0540.2411-0.06220.1344-0.022-0.01290.20140.01320.239630.9717-8.5761-14.5014
112.05620.56030.32542.3964-0.27211.52270.0250.2799-0.1382-0.0650.0323-0.17230.05790.4099-0.04270.20760.02050.00830.2768-0.03450.161319.8601-16.6324-40.4836
122.5018-0.28160.89642.2506-0.78574.83520.22490.5328-0.3927-0.4163-0.26960.19670.6358-0.01380.03790.30840.0563-0.00080.2927-0.09370.245-11.736-22.1483-51.0109
137.3808-0.56362.47121.530.18512.7208-0.18220.03070.55740.18310.0687-0.1532-0.48920.11460.15410.4432-0.06510.00790.17070.03010.251513.25056.7443-35.8269
143.5228-0.1440.60610.77240.05030.8422-0.09040.33080.3792-0.0543-0.00310.0191-0.35630.16160.06980.3476-0.05430.00130.20970.05970.19510.39393.0848-43.5038
154.17522.3212-0.35795.4558-1.03642.40280.1377-0.2159-0.23630.1908-0.24520.28140.067-0.40450.11050.19640.01850.0010.3112-0.04710.1984-20.1282-15.0139-38.9853
164.3295-4.3061-3.67684.32283.74773.33270.14241.0326-0.1692-1.1833-0.53831.3716-0.3452-1.13750.2930.35850.0142-0.13970.37660.02160.3538-19.560511.0793-23.5401
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'Q' and (resid 2 through 7 )Q2 - 7
2X-RAY DIFFRACTION2chain 'H' and (resid 2 through 25 )H2 - 25
3X-RAY DIFFRACTION3chain 'H' and (resid 26 through 64 )H26 - 64
4X-RAY DIFFRACTION4chain 'H' and (resid 65 through 83 )H65 - 83
5X-RAY DIFFRACTION5chain 'H' and (resid 84 through 151 )H84 - 151
6X-RAY DIFFRACTION6chain 'H' and (resid 152 through 194 )H152 - 194
7X-RAY DIFFRACTION7chain 'H' and (resid 195 through 219 )H195 - 219
8X-RAY DIFFRACTION8chain 'L' and (resid 1 through 38 )L1 - 38
9X-RAY DIFFRACTION9chain 'L' and (resid 39 through 118 )L39 - 118
10X-RAY DIFFRACTION10chain 'L' and (resid 119 through 216 )L119 - 216
11X-RAY DIFFRACTION11chain 'A' and (resid 2 through 125 )A2 - 125
12X-RAY DIFFRACTION12chain 'A' and (resid 126 through 219 )A126 - 219
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 38 )B1 - 38
14X-RAY DIFFRACTION14chain 'B' and (resid 39 through 118 )B39 - 118
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 218 )B119 - 218
16X-RAY DIFFRACTION16chain 'P' and (resid 2 through 7 )P2 - 7

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