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- PDB-6u07: Computational Stabilization of T Cell Receptor Constant Domains -

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Basic information

Entry
Database: PDB / ID: 6u07
TitleComputational Stabilization of T Cell Receptor Constant Domains
Components
  • Stabilized T cell receptor constant domain (Calpha)
  • Stabilized T cell receptor constant domain (Cbeta)
KeywordsIMMUNE SYSTEM / T cell receptor / TCR constant domains
Function / homology
Function and homology information


cell surface receptor signaling pathway / membrane / metal ion binding / plasma membrane
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Human nkt tcr beta chain / TRA@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsFroning, K. / Maguire, J. / Sereno, A. / Huang, F. / Chang, S. / Weichert, K. / Frommelt, A.J. / Dong, J. / Wu, X. / Austin, H. ...Froning, K. / Maguire, J. / Sereno, A. / Huang, F. / Chang, S. / Weichert, K. / Frommelt, A.J. / Dong, J. / Wu, X. / Austin, H. / Conner, E.M. / Fitchett, J.R. / Heng, A.R. / Balasubramaniam, D. / Hilgers, M.T. / Kuhlman, B. / Demarest, S.J.
CitationJournal: Nat Commun / Year: 2020
Title: Computational stabilization of T cell receptors allows pairing with antibodies to form bispecifics.
Authors: Froning, K. / Maguire, J. / Sereno, A. / Huang, F. / Chang, S. / Weichert, K. / Frommelt, A.J. / Dong, J. / Wu, X. / Austin, H. / Conner, E.M. / Fitchett, J.R. / Heng, A.R. / ...Authors: Froning, K. / Maguire, J. / Sereno, A. / Huang, F. / Chang, S. / Weichert, K. / Frommelt, A.J. / Dong, J. / Wu, X. / Austin, H. / Conner, E.M. / Fitchett, J.R. / Heng, A.R. / Balasubramaniam, D. / Hilgers, M.T. / Kuhlman, B. / Demarest, S.J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: 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 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stabilized T cell receptor constant domain (Calpha)
B: Stabilized T cell receptor constant domain (Cbeta)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0975
Polymers27,0242
Non-polymers733
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2770 Å2
ΔGint-24 kcal/mol
Surface area11450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.854, 59.852, 61.352
Angle α, β, γ (deg.)90.000, 110.240, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-301-

MG

21A-302-

MG

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Components

#1: Protein Stabilized T cell receptor constant domain (Calpha)


Mass: 12071.169 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q2YD82
#2: Protein Stabilized T cell receptor constant domain (Cbeta)


Mass: 14952.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: K7N5M4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.09 Å3/Da / Density % sol: 60.16 % / Description: Single, plate-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 23% PEG 4K, 300 mM magnesium sulfate, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2018 / Details: Kohzu HLD-4 with diamond 111 crystals
RadiationMonochromator: Kohzu HLD-4 with diamond 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.76→29.33 Å / Num. obs: 32373 / % possible obs: 99.2 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.04 / Rrim(I) all: 0.078 / Net I/σ(I): 5.6 / Num. measured all: 122769
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.76-1.863.81.1141791647000.5880.6581.2960.899.1
5.57-29.333.60.02367010210.9990.0130.02413.794.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.08 Å29.33 Å
Translation4.08 Å29.33 Å

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
XDSJanuary 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F53

2f53


Resolution: 1.76→29.33 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.307 / SU ML: 0.1 / SU R Cruickshank DPI: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1642 5.1 %RANDOM
Rwork0.2015 ---
obs0.2027 30717 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.38 Å2 / Biso mean: 30.088 Å2 / Biso min: 6.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å2-0.86 Å2
2--1.26 Å2-0 Å2
3----1.09 Å2
Refinement stepCycle: final / Resolution: 1.76→29.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 3 175 1896
Biso mean--35.9 37.61 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021777
X-RAY DIFFRACTIONr_bond_other_d0.0060.021592
X-RAY DIFFRACTIONr_angle_refined_deg1.241.932425
X-RAY DIFFRACTIONr_angle_other_deg0.73633674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8785217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35324.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18415274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.851510
X-RAY DIFFRACTIONr_chiral_restr0.0740.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212044
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
LS refinement shellResolution: 1.762→1.808 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 121 -
Rwork0.373 2237 -
all-2358 -
obs--98.41 %

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