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- PDB-1t5x: HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and... -

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Basic information

Entry
Database: PDB / ID: 1t5x
TitleHLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen SEC3-3B2
Components
  • 15-mer peptide fragment of Regulatory protein MIG1
  • Enterotoxin type C-3
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / MHC class II / major histocompatibiloty complex protein / HLA-DR1 / superantigen / antigen / peptide
Function / homology
Function and homology information


negative regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / 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 / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation ...negative regulation of transcription from RNA polymerase II promoter by glucose / positive regulation of filamentous growth of a population of unicellular organisms in response to starvation / carbon catabolite repression of transcription from RNA polymerase II promoter by glucose / 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 / positive regulation of T cell mediated immune response to tumor cell / 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 memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / nuclear envelope lumen / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / sequence-specific DNA binding / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm
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/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / 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 / 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 / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / 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 / Regulatory protein MIG1
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZavala-Ruiz, Z. / Strug, I. / Anderson, M.W. / Gorski, J. / Stern, L.J.
CitationJournal: Chem.Biol. / Year: 2004
Title: A Polymorphic Pocket at the P10 Position Contributes to Peptide Binding Specificity in Class II MHC Proteins
Authors: Zavala-Ruiz, Z. / Strug, I. / Anderson, M.W. / Gorski, J. / Stern, L.J.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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, DRB1-1 beta chain
C: 15-mer peptide fragment of Regulatory protein MIG1
D: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)72,4484
Polymers72,4484
Non-polymers00
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.208, 173.208, 121.543
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 / MHC class II antigen DRA


Mass: 21042.748 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA*0101 / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class I antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1*0101 / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide 15-mer peptide fragment of Regulatory protein MIG1 / Regulatory protein CAT4


Mass: 1603.795 Da / Num. of mol.: 1 / Fragment: Synthetic peptide / Source method: obtained synthetically
Details: Synthetic peptide desinged to study the P10 side chain specificity of HLA-DR1
References: UniProt: P27705
#4: Protein Enterotoxin type C-3 / SEC3 / enterotoxin typeC3


Mass: 27721.068 Da / Num. of mol.: 1 / Fragment: SEC3 variant 3B2 / Mutation: K43S, L45F, A46K, H47W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: SEC3 / Production host: Escherichia coli (E. coli) / Strain (production host): HB 2151 / References: UniProt: P0A0L5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 4.39 Å3/Da / Density % sol: 71.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, Ethylene Glycol, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 20, 2003 / Details: Confocal Mirrors
RadiationMonochromator: Confocal Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.39→29.8 Å / Num. all: 53191 / Num. obs: 53191 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.114 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2 / Num. unique all: 5392 / Rsym value: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PBB entrt 1PYW

1pyw


Resolution: 2.5→29.8 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4691 -Random
Rwork0.208 ---
all0.211 46471 --
obs0.2081 46471 98.8 %-
Displacement parametersBiso mean: 43.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å25.49 Å20 Å2
2--1.66 Å20 Å2
3----3.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5005 0 0 221 5226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.328 779 -
Rwork0.297 --
obs-7051 100 %

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