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- PDB-4p23: J809.B5 TCR bound to IAb/3K -

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Basic information

Entry
Database: PDB / ID: 4p23
TitleJ809.B5 TCR bound to IAb/3K
Components
  • 3K peptide and MHC IAb beta chain,H-2 class II histocompatibility antigen, A beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • J809.B5 TCR V alpha chain (Va2.8)
  • J809.B5 TCR V beta chain (Vb8.2)
KeywordsIMMUNE SYSTEM / TCR MHC peptide
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / B cell affinity maturation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / B cell affinity maturation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / cellular response to type II interferon / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / Golgi apparatus / cell surface / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsStadinski, B.D. / Huseby, E.S. / Trenh, P. / Stern, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health United States
CitationJournal: J Immunol. / Year: 2014
Title: Effect of CDR3 Sequences and Distal V Gene Residues in Regulating TCR-MHC Contacts and Ligand Specificity.
Authors: Stadinski, B.D. / Trenh, P. / Duke, B. / Huseby, P.G. / Li, G. / Stern, L.J. / Huseby, E.S.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: J809.B5 TCR V alpha chain (Va2.8)
B: J809.B5 TCR V beta chain (Vb8.2)
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide and MHC IAb beta chain,H-2 class II histocompatibility antigen, A beta chain


Theoretical massNumber of molelcules
Total (without water)94,4094
Polymers94,4094
Non-polymers00
Water6,467359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-51 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)239.121, 73.514, 65.730
Angle α, β, γ (deg.)90.000, 90.580, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-215-

HOH

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Components

#1: Protein J809.B5 TCR V alpha chain (Va2.8)


Mass: 22311.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein J809.B5 TCR V beta chain (Vb8.2)


Mass: 26758.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20242.615 Da / Num. of mol.: 1 / Fragment: residues 27-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14434
#4: Protein 3K peptide and MHC IAb beta chain,H-2 class II histocompatibility antigen, A beta chain


Mass: 25095.957 Da / Num. of mol.: 1 / Fragment: residues 31-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P14483
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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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: 3.11 Å3/Da / Density % sol: 60.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100mM NaCitrate pH5.8 100mM NaCacodylate pH5.8 10% PEG4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.24→41 Å / Num. obs: 53984 / % possible obs: 97.8 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.082 / Χ2: 1.098 / Net I/av σ(I): 22.118 / Net I/σ(I): 9.6 / Num. measured all: 311303
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.24-2.285.30.46226080.58595.8
2.28-2.325.50.48426060.4994.9
2.32-2.365.40.4726290.50195.8
2.36-2.415.20.43626340.49396.6
2.41-2.475.70.3926510.52695.9
2.47-2.525.60.32326490.52697
2.52-2.595.60.28426270.55696.4
2.59-2.665.30.23326740.58796.5
2.66-2.735.50.20826780.60796.9
2.73-2.825.60.18126690.65797.3
2.82-2.925.40.1426690.76697.3
2.92-3.045.70.12226970.86598.5
3.04-3.185.90.127361.01698.9
3.18-3.355.80.08327351.28899
3.35-3.5660.06827511.54499.7
3.56-3.836.30.06127671.76599.9
3.83-4.216.50.05427551.97199.9
4.21-4.826.40.04327961.971100
4.82-6.076.30.04427991.944100
6.07-416.30.04128542.09299.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data scaling
HKLdata reduction
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RDT

3rdt


Resolution: 2.25→39.851 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2601 5.07 %Random selection
Rwork0.1643 ---
obs0.1668 51290 94.4 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.19 Å2 / Biso mean: 44.1886 Å2 / Biso min: 19.06 Å2
Refinement stepCycle: final / Resolution: 2.25→39.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6377 0 0 359 6736
Biso mean---47.43 -
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)
11.428-0.8086-0.32111.58120.58851.6983-0.1306-0.0748-0.20430.15430.1236-0.00960.16020.0811-0.00310.20780.00090.01320.17350.01330.272246.6258-41.9855-14.0334
22.4656-0.34730.07511.94740.46622.11640.1197-0.1947-0.26650.08630.024-0.0860.3170.1288-0.0960.35910.0058-0.03930.28430.0350.449676.3571-41.4048-32.0585
32.19290.4875-0.61921.24550.19221.31680.1171-0.13030.045-0.03010.0787-0.2554-0.18710.2042-0.15140.2572-0.03380.02760.2105-0.04140.300850.1348-19.5102-8.949
41.6704-0.57620.45952.58560.68131.5497-0.0029-0.06680.0865-0.12540.0452-0.063-0.055-0.0245-0.01490.2812-0.0281-0.02170.17070.00430.319772.175-25.0118-31.5621
51.48-0.2026-0.73321.09640.06372.11620.02060.2521-0.0862-0.0133-0.0584-0.0057-0.0597-0.31510.03540.20710.0379-0.0140.3249-0.01680.221322.978-26.26482.1496
61.5451-0.2324-0.68312.033-0.20522.08080.0769-0.20410.19840.2351-0.00550.0735-0.3949-0.0419-0.03690.27650.02880.01620.2946-0.04170.211218.7777-12.467125.526
72.3947-0.6093-0.08391.92950.31262.1649-0.2891-0.5741-0.22670.18690.11090.20770.32030.1830.17050.29380.05330.02860.39450.09250.29098.3136-33.043338.5084
81.9955-0.83720.96213.6266-3.416.1531-0.04550.29770.1085-0.1429-0.4405-0.47720.21440.01840.31210.24370.0570.00850.27390.00310.198428.6484-27.6864-2.1694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:110)A2 - 110
2X-RAY DIFFRACTION2chain 'A' and (resseq 113:201)A113 - 201
3X-RAY DIFFRACTION3chain 'B' and (resseq 1:109)B1 - 109
4X-RAY DIFFRACTION4chain 'B' and (resseq 115:238)B115 - 238
5X-RAY DIFFRACTION5chain 'C' and (resseq 1:81) or chain 'D' and (resseq 6:93)C0
6X-RAY DIFFRACTION6chain 'C' and (resseq 84:178)C84 - 178
7X-RAY DIFFRACTION7chain 'D' and (resseq 96:191)D96 - 191
8X-RAY DIFFRACTION8chain 'D' and (resseq -25:-13)D-25 - -13

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