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- PDB-1klu: Crystal structure of HLA-DR1/TPI(23-37) complexed with staphyloco... -

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Basic information

Entry
Database: PDB / ID: 1klu
TitleCrystal structure of HLA-DR1/TPI(23-37) complexed with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2)
Components
  • ENTEROTOXIN TYPE C-3
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
  • HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN
  • Triosephosphate isomerase peptide
KeywordsIMMUNE SYSTEM/TOXIN / HLA-DR1/TPI / enterotoxin C3 / human melanoma antigen / CD4+ T cells / IMMUNE SYSTEM-TOXIN COMPLEX
Function / homology
Function and homology information


methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation ...methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / triose-phosphate isomerase / triose-phosphate isomerase activity / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / Gluconeogenesis / CD4 receptor binding / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / Glycolysis / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / glycolytic process / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / Downstream TCR signaling / T cell receptor signaling pathway / toxin activity / early endosome membrane / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / cell surface / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Superantigen toxin, C-terminal / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / 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 / Enterotoxin / MHC classes I/II-like antigen recognition protein / : / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aldolase-type TIM barrel / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Enterotoxin type C-3 / Triosephosphate isomerase
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsSundberg, E.J. / Sawicki, M.W. / Andersen, P.S. / Sidney, J. / Sette, A. / Mariuzza, R.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Minor structural changes in a mutated human melanoma antigen correspond to dramatically enhanced stimulation of a CD4+ tumor-infiltrating lymphocyte line.
Authors: Sundberg, E.J. / Sawicki, M.W. / Southwood, S. / Andersen, P.S. / Sette, A. / Mariuzza, R.A.
#1: Journal: J.Exp.Med. / Year: 1999
Title: Biochemical identification of a mutated human melanoma antigen recognized by CD4+ T cells
Authors: Pieper, R. / Christian, R.E. / Gonzales, M.I. / Nishimura, M.I. / Gupta, G. / Settlage, R.E. / Shabanowitz, J. / Rosenberg, S.A. / Hunt, D.F. / Topalian, S.L.
History
DepositionDec 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN
C: Triosephosphate isomerase peptide
D: ENTEROTOXIN TYPE C-3


Theoretical massNumber of molelcules
Total (without water)72,0564
Polymers72,0564
Non-polymers00
Water7,296405
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.296, 171.296, 121.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3

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Components

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN / HLA-DR1 alpha subunit / hla-dr antigen alpha chain


Mass: 20784.455 Da / Num. of mol.: 1 / Fragment: residues 29-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR-1 BETA CHAIN / HLA-DR1 beta subunit / HLA-DR beta 1 chain


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide Triosephosphate isomerase peptide


Mass: 1469.659 Da / Num. of mol.: 1 / Fragment: residues 23-37 / Source method: obtained synthetically / Details: peptide synthesis / References: UniProt: P60174*PLUS
#4: Protein ENTEROTOXIN TYPE C-3 / enterotoxin C3 / SEC3


Mass: 27721.068 Da / Num. of mol.: 1 / Fragment: residues 29-266
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Variant: 3B2 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0L5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O
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: 4.74 Å3/Da / Density % sol: 74.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: PEG 4000, sodium acetate, ethylene glycol, pH 5.2, VAPOR DIFFUSION, HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 Msodium acetate1reservoirpH5.2
310 %(w/v)ethylene glycol1reservoir
42-4 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.93→100 Å / Num. all: 99361 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 7.8 Å2 / Rsym value: 0.095
Reflection
*PLUS
Lowest resolution: 100 Å / Num. obs: 99361 / % possible obs: 99.8 % / Num. measured all: 311680 / Rmerge(I) obs: 0.095
Reflection shell
*PLUS
Highest resolution: 1.93 Å / Lowest resolution: 1.96 Å / % possible obs: 98.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 1.93→14.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 152684.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4246 5.1 %RANDOM
Rwork0.208 ---
obs0.208 83852 84.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6737 Å2 / ksol: 0.37004 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å22.25 Å20 Å2
2--1.36 Å20 Å2
3----2.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.93→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5010 0 0 405 5415
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 521 5.3 %
Rwork0.238 9277 -
obs--59.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Num. reflection Rfree: 4240 / % reflection Rfree: 4.3 % / Rfactor Rfree: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.519
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Lowest resolution: 1.96 Å / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.254

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