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- PDB-3tfk: 42F3-p4B10/H2-Ld -

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Basic information

Entry
Database: PDB / ID: 3tfk
Title42F3-p4B10/H2-Ld
Components
  • 42F3 alpha
  • 42F3 beta
  • H2-Ld SBM2
  • p4B10 peptide
KeywordsIMMUNE SYSTEM / Ig MHC / Antigen recognition / TCR-pMHC / chimera protein / Membrane Receptor
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / 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: 2.753 Å
AuthorsAdams, J.J. / 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 15, 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 ...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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H2-Ld SBM2
B: p4B10 peptide
C: 42F3 alpha
D: 42F3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7845
Polymers72,7224
Non-polymers621
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: H2-Ld SBM2
B: p4B10 peptide
C: 42F3 alpha
D: 42F3 beta
hetero molecules

A: H2-Ld SBM2
B: p4B10 peptide
C: 42F3 alpha
D: 42F3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,56710
Polymers145,4438
Non-polymers1242
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area19760 Å2
ΔGint-69 kcal/mol
Surface area53180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.090, 102.090, 323.081
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 2 types, 2 molecules AD

#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
#4: Protein 42F3 beta


Mass: 27248.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mouse-human chimera beta chain / Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pet28a / Production host: Escherichia coli (E. coli)

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Protein/peptide / Antibody , 2 types, 2 molecules BC

#2: Protein/peptide p4B10 peptide


Mass: 1017.154 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: GenScript
#3: Antibody 42F3 alpha


Mass: 23383.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Mouse-human chimera alpha chain / Source: (gene. exp.) Mus musculus, Homo sapiens / Plasmid: pet28a / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 7 molecules

#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.34 Å3/Da / Density % sol: 63.19 %
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: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→80.77 Å / Num. all: 26925 / Num. obs: 26909 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.75→2.9 Å / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TF7

3tf7


Resolution: 2.753→50.42 Å / SU ML: 0.51 / σ(F): 0.12 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.291 1348 5.04 %Random
Rwork0.2473 ---
all0.2496 28109 --
obs0.2496 26761 99.77 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.159 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.8826 Å20 Å2-0 Å2
2--1.8826 Å20 Å2
3----3.7652 Å2
Refinement stepCycle: LAST / Resolution: 2.753→50.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4972 0 4 6 4982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025109
X-RAY DIFFRACTIONf_angle_d0.6216930
X-RAY DIFFRACTIONf_dihedral_angle_d13.2981841
X-RAY DIFFRACTIONf_chiral_restr0.045721
X-RAY DIFFRACTIONf_plane_restr0.002910
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.753-2.85140.50921140.45652488X-RAY DIFFRACTION100
2.8514-2.96550.40711420.36752462X-RAY DIFFRACTION100
2.9655-3.10050.37611380.32792475X-RAY DIFFRACTION100
3.1005-3.26390.35371340.30792474X-RAY DIFFRACTION100
3.2639-3.46840.32831310.27532507X-RAY DIFFRACTION100
3.4684-3.73610.32031240.25772516X-RAY DIFFRACTION100
3.7361-4.11190.27111430.24562539X-RAY DIFFRACTION100
4.1119-4.70650.24691610.20012524X-RAY DIFFRACTION100
4.7065-5.92830.28031180.20222638X-RAY DIFFRACTION100
5.9283-50.4280.24391430.22392790X-RAY DIFFRACTION99

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