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- PDB-6mkd: 4699 TCR bound to I-Ab Padi4 -

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Basic information

Entry
Database: PDB / ID: 6mkd
Title4699 TCR bound to I-Ab Padi4
Components
  • 4699 TCR alpha chain
  • 4699 TCR beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Major Histocompatibility Complex
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / positive regulation of T-helper 1 type immune response ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / stem cell population maintenance / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / post-translational protein modification / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / nucleosome assembly / chromatin organization / adaptive immune response / early endosome / lysosome / immune response / chromatin remodeling / innate immune response / external side of plasma membrane / calcium ion binding / ubiquitin protein ligase binding / Golgi apparatus / protein-containing complex / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / 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 / Cupredoxin / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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 / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsStadinski, B.D. / Blevins, S.J. / Huseby, E.S.
CitationJournal: Nat.Immunol. / Year: 2019
Title: A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development.
Authors: Stadinski, B.D. / Blevins, S.J. / Spidale, N.A. / Duke, B.R. / Huseby, P.G. / Stern, L.J. / Huseby, E.S.
History
DepositionSep 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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
Revision 1.3Nov 6, 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
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain
A: 4699 TCR alpha chain
B: 4699 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,2584
Polymers95,2584
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-59 kcal/mol
Surface area35350 Å2
Unit cell
Length a, b, c (Å)255.448, 73.643, 64.566
Angle α, β, γ (deg.)90.000, 90.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20242.615 Da / Num. of mol.: 1
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
#2: Protein Padi4 (92-105) peptide and MHC Class II I-Ab beta chain,H-2 class II histocompatibility antigen, A beta chain / P


Mass: 25027.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Padi4, Pad4, Pdi4, H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Z183, UniProt: P14483, protein-arginine deiminase
#3: Protein 4699 TCR alpha chain


Mass: 23230.615 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein 4699 TCR beta chain


Mass: 26756.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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: 3.36 Å3/Da / Density % sol: 63.39 % / Mosaicity: 0.52 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 14% PEG 4000, 100mM NaCacodylate, 100 mM NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.2→29.39 Å / Num. obs: 19627 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 68.58 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.081 / Rrim(I) all: 0.159 / Net I/σ(I): 6.7 / Num. measured all: 73637 / Scaling rejects: 18
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.695 / Num. unique obs: 3564 / CC1/2: 0.887 / Rpim(I) all: 0.409 / Rrim(I) all: 0.808 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.67 Å29.24 Å
Translation7.67 Å29.24 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASER2.6.0phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P23

4p23


Resolution: 3.2→29.242 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.1
RfactorNum. reflection% reflection
Rfree0.2779 973 4.97 %
Rwork0.2329 --
obs0.2351 19581 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.95 Å2 / Biso mean: 65.8062 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.2→29.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 0 0 5916
Num. residues----799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086084
X-RAY DIFFRACTIONf_angle_d1.1528348
X-RAY DIFFRACTIONf_chiral_restr0.06940
X-RAY DIFFRACTIONf_plane_restr0.0091088
X-RAY DIFFRACTIONf_dihedral_angle_d14.2052012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.36850.3211360.312655279198
3.3685-3.57920.34311320.28992597272997
3.5792-3.8550.3341400.26292625276598
3.855-4.24190.31741410.23892634277597
4.2419-4.85330.24051390.1942676281599
4.8533-6.10540.24361420.21482701284399
6.1054-29.24350.24921430.21352720286397

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