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- PDB-6mng: 4738 TCR bound to IAb Padi4 -

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Basic information

Entry
Database: PDB / ID: 6mng
Title4738 TCR bound to IAb Padi4
Components
  • 4738 TCR alpha chain
  • 4738 TCR beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Padi4 (92-105) peptide and MHCII I-Ab 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 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity ...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 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / 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 / stem cell population maintenance / response to type II interferon / toxic substance binding / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / post-translational protein modification / nucleosome assembly / 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 / chromatin organization / adaptive immune response / lysosome / early endosome / chromatin remodeling / immune response / lysosomal membrane / external side of plasma membrane / innate immune response / ubiquitin protein ligase binding / calcium ion binding / protein-containing complex binding / Golgi apparatus / cell surface / protein-containing complex / membrane / identical protein binding / nucleus / 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 / 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 / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.662 Å
AuthorsBlevins, S.J. / Stadinski, B.D. / 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
DepositionOct 1, 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

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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 MHCII I-Ab beta chain
A: 4738 TCR alpha chain
B: 4738 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,2364
Polymers95,2364
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-57 kcal/mol
Surface area34600 Å2
Unit cell
Length a, b, c (Å)250.917, 69.163, 64.150
Angle α, β, γ (deg.)90.000, 91.480, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-202-

HOH

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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 MHCII I-Ab beta chain / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


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 4738 TCR alpha chain


Mass: 23208.652 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 4738 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)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 3.04 Å3/Da / Density % sol: 59.6 % / Mosaicity: 0.1 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 12% 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: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.66→29.66 Å / Num. obs: 31505 / % possible obs: 99.1 % / Redundancy: 6.9 % / Biso Wilson estimate: 56.95 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.044 / Rrim(I) all: 0.118 / Net I/σ(I): 11.6 / Num. measured all: 218095
Reflection shellResolution: 2.66→2.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.761 / Num. unique obs: 2074 / CC1/2: 0.878 / Rpim(I) all: 0.306 / Rrim(I) all: 0.821 / % possible all: 90.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimless0.5.21data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P23

4p23


Resolution: 2.662→29.66 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.67
RfactorNum. reflection% reflection
Rfree0.2693 1991 6.32 %
Rwork0.2296 --
obs0.2321 31481 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 118.6 Å2 / Biso mean: 50.2462 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.662→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6076 0 0 13 6089
Biso mean---39.94 -
Num. residues----805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046251
X-RAY DIFFRACTIONf_angle_d0.7088558
X-RAY DIFFRACTIONf_chiral_restr0.047951
X-RAY DIFFRACTIONf_plane_restr0.0051111
X-RAY DIFFRACTIONf_dihedral_angle_d16.492106
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6622-2.72870.35971290.31841911204092
2.7287-2.80240.37111460.3062105225199
2.8024-2.88480.38551350.299220982233100
2.8848-2.97780.34141330.295921142247100
2.9778-3.08420.39931470.292520802227100
3.0842-3.20750.33851440.279621282272100
3.2075-3.35330.31541460.253520902236100
3.3533-3.52980.31411430.24721192262100
3.5298-3.75060.28811420.23621212263100
3.7506-4.03950.24431460.227121162262100
4.0395-4.44480.22351450.196521112256100
4.4448-5.08520.18531440.174621462290100
5.0852-6.39620.23061440.213521502294100
6.3962-29.66450.26231470.211722012348100

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