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- PDB-7s8i: PHOSPHOPEPTIDE-SPECIFIC LC13 TCR, MONOCLINIC CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 7s8i
TitlePHOSPHOPEPTIDE-SPECIFIC LC13 TCR, MONOCLINIC 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: 1.66 Å
AuthorsPatskovsky, Y. / Nyovanie, S. / Patskovska, L. / Natarajan, A. / Joshi, B. / Morin, B. / Brittsan, C. / Huber, O. / Gordon, S. / Michelet, X. ...Patskovsky, Y. / Nyovanie, S. / Patskovska, L. / 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 Cancer Institute (NIH/NCI)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 6, 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)50,3323
Polymers50,2962
Non-polymers351
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-35 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.679, 77.228, 67.680
Angle α, β, γ (deg.)90.000, 104.380, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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 Å3/Da / Density % sol: 38.57 % / Description: plate
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20-28%PEG1000, 0.1M HEPES-NAOH, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 19, 2019 / Details: SI 111 CRYSTAL
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.66→33.71 Å / Num. obs: 46274 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2098 / % possible all: 89.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OGA

1oga


Resolution: 1.66→33.71 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.422 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1421 3.1 %RANDOM
Rwork0.1673 ---
obs0.1689 44804 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.21 Å2 / Biso mean: 33.156 Å2 / Biso min: 15.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.03 Å2
2--0.76 Å2-0 Å2
3----0.49 Å2
Refinement stepCycle: final / Resolution: 1.66→33.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3497 0 1 464 3962
Biso mean--38.17 40.2 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193710
X-RAY DIFFRACTIONr_bond_other_d0.0010.023381
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9455069
X-RAY DIFFRACTIONr_angle_other_deg0.75637825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08424.52177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.07215611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2691521
X-RAY DIFFRACTIONr_chiral_restr0.0860.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02881
LS refinement shellResolution: 1.66→1.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 81 -
Rwork0.252 3233 -
all-3314 -
obs--96.37 %
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)
11.08950.2049-1.10180.6171-1.3623.5094-0.0233-0.1607-0.0207-0.0451-0.0608-0.00930.02040.17420.08410.08320.055-0.0530.0636-0.04060.05136.111815.104925.5239
20.9623-0.0503-0.71410.1522-0.35262.0402-0.05560.0149-0.0001-0.04690.00780.02510.1487-0.10250.04780.0260.0043-0.01470.0147-0.01660.0291-10.39119.653616.573
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 201
2X-RAY DIFFRACTION2B0 - 241

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