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- PDB-3tjh: 42F3-p3A1/H2-Ld complex -

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Basic information

Entry
Database: PDB / ID: 3tjh
Title42F3-p3A1/H2-Ld complex
Components
  • 42F3 alpha
  • 42F3 beta
  • H2-Ld SBM2
  • p3A1
KeywordsIMMUNE SYSTEM / IG MHC / Antigen Recognition / TCR-pMHC / Membrane Receptor
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell mediated cytotoxicity ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / T cell receptor binding / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / antibacterial humoral response / protein-folding chaperone binding / adaptive immune response / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class I histocompatibility antigen, L-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsAdams, J.J. / Kruse, A. / Kranz, D.M. / Garcia, K.C.
CitationJournal: Immunity / Year: 2011
Title: T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex.
Authors: Adams, J.J. / Narayanan, S. / Liu, B. / Birnbaum, M.E. / Kruse, A.C. / Bowerman, N.A. / Chen, W. / Levin, A.M. / Connolly, J.M. / Zhu, C. / Kranz, D.M. / Garcia, K.C.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: H2-Ld SBM2
B: p3A1
C: 42F3 alpha
D: 42F3 beta


Theoretical massNumber of molelcules
Total (without water)75,5384
Polymers75,5384
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-37 kcal/mol
Surface area28560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.190, 61.670, 69.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-371-

HOH

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Components

#1: Protein H2-Ld SBM2


Mass: 21072.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P01897*PLUS
#2: Protein/peptide p3A1


Mass: 1116.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GenScript
#3: Antibody 42F3 alpha


Mass: 24917.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pAcGP67a/BD BaculoGold / Production host: Trichoplusia ni (cabbage looper)
#4: Protein 42F3 beta


Mass: 28431.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pAcGP67a/BD BaculoGold / Production host: Trichoplusia ni (cabbage looper)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.6
Details: 16% PEG 3350, 0.2M ammonium nitrate and 0.1M Bis-Tris pH 6.6 in a 1:1 (v/v) drop with the TCR-pMHC complex. Crystals were soaked stepwise into well solution with 20% ethylene glycol and ...Details: 16% PEG 3350, 0.2M ammonium nitrate and 0.1M Bis-Tris pH 6.6 in a 1:1 (v/v) drop with the TCR-pMHC complex. Crystals were soaked stepwise into well solution with 20% ethylene glycol and flash frozen in liquid nitrogen, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 31, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→58.86 Å / Num. all: 49357 / Num. obs: 49259 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.12→2.23 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TF7

3tf7


Resolution: 2.12→29.735 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 2000 4.07 %Random
Rwork0.2061 ---
all0.2076 49259 --
obs0.2074 49112 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.882 Å2 / ksol: 0.345 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.6554 Å2-0 Å2-0 Å2
2---1.0815 Å20 Å2
3----5.5739 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4987 0 0 382 5369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035162
X-RAY DIFFRACTIONf_angle_d0.677005
X-RAY DIFFRACTIONf_dihedral_angle_d14.8741854
X-RAY DIFFRACTIONf_chiral_restr0.047728
X-RAY DIFFRACTIONf_plane_restr0.002915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.19580.2731950.23334584X-RAY DIFFRACTION99
2.1958-2.28360.30591960.23614634X-RAY DIFFRACTION99
2.2836-2.38750.27951980.22794645X-RAY DIFFRACTION100
2.3875-2.51330.26011970.22054665X-RAY DIFFRACTION100
2.5133-2.67070.26572000.22414683X-RAY DIFFRACTION100
2.6707-2.87680.2781980.22754673X-RAY DIFFRACTION100
2.8768-3.1660.26412000.22274716X-RAY DIFFRACTION100
3.166-3.62340.21522010.19554744X-RAY DIFFRACTION100
3.6234-4.56250.19782030.16984779X-RAY DIFFRACTION100
4.5625-29.73840.19752120.18944989X-RAY DIFFRACTION100

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