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- PDB-7s8j: PHOSPHOPEPTIDE-SPECIFIC LC13 TCR, ORTHORHOMBIC CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 7s8j
TitlePHOSPHOPEPTIDE-SPECIFIC LC13 TCR, ORTHORHOMBIC CRYSTAL FORM
Components
  • TRAV27_LC13 TCR ALPHA CHAIN
  • TRBV27_LC13 TCR BETA CHAIN
KeywordsIMMUNE SYSTEM / HLA / MLL PEPTIDE / HLA-B*07:02 / HLA-B7 / IMMUNITY / PHOSPHOPEPTIDE / CANCER / NEOANTIGEN / TCR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsPatskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovska, L. / Patskovsky, Y. / Nyovanie, S. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R. / Findeis, M. / Hurwitz, A. / Van Dijk, M. / Buell, J. / Underwood, D. / Krogsgaard, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124489 United States
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of phosphopeptide neoantigen immunogenicity.
Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. ...Authors: Patskovsky, Y. / Natarajan, A. / Patskovska, L. / Nyovanie, S. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. / Schmitzberger, F. / Stein, R.B. / Findeis, M.A. / Hurwitz, A. / Van Dijk, M. / Chantzoura, E. / Yague, A.S. / Pollack Smith, D. / Buell, J.S. / Underwood, D. / Krogsgaard, M.
History
DepositionSep 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
Revision 1.2Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 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
A: TRAV27_LC13 TCR ALPHA CHAIN
B: TRBV27_LC13 TCR BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4386
Polymers50,2962
Non-polymers1424
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-63 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.549, 73.334, 110.031
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRAV27_LC13 TCR ALPHA CHAIN


Mass: 22647.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30A / Production host: Escherichia coli BL21 (bacteria)
#2: Protein TRBV27_LC13 TCR BETA CHAIN


Mass: 27649.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET30A / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.48 % / Description: PLATE
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20-25% PEG4000, 0.2M AMMONIUM, SULFATE, 0.1M SODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 4, 2020 / Details: SI 111 CRYSTAL
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.92→29.21 Å / Num. obs: 37831 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2424 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7S8I

7s8i


Resolution: 1.92→29.21 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.535 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1156 3.1 %RANDOM
Rwork0.1681 ---
obs0.1695 36615 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 139.53 Å2 / Biso mean: 34.962 Å2 / Biso min: 16.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å20 Å2
2--0.24 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.92→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 4 426 3888
Biso mean--42.55 42.06 -
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133607
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173150
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.6464925
X-RAY DIFFRACTIONr_angle_other_deg1.3011.5727355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145456
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08223.315184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77915572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6731517
X-RAY DIFFRACTIONr_chiral_restr0.0630.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
LS refinement shellResolution: 1.924→1.974 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 88 -
Rwork0.233 2557 -
all-2645 -
obs--95.8 %

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