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- PDB-1pyw: Human class II MHC protein HLA-DR1 bound to a designed peptide re... -

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Entry
Database: PDB / ID: 1pyw
TitleHuman class II MHC protein HLA-DR1 bound to a designed peptide related to influenza virus hemagglutinin, FVKQNA(MAA)AL, in complex with staphylococcal enterotoxin C3 variant 3B2 (SEC3-3B2)
Components
  • 9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL
  • Enterotoxin type C-3
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DR-1 beta chain
KeywordsIMMUNE SYSTEM/PROTEIN BINDING/TOXIN / MHC class II / Major histocompatibility protein complex / HLA-DR1 / Influenza / Hemagglutinin / Superantigen / Antigen / IMMUNE SYSTEM-PROTEIN BINDING-TOXIN COMPLEX
Function / homology
Function and homology information


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 / positive regulation of T cell mediated immune response to tumor cell / MHC class II receptor 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 / positive regulation of T cell mediated immune response to tumor cell / 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 / CD4 receptor binding / positive regulation of monocyte differentiation / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / T-helper 1 type immune response / polysaccharide binding / transport vesicle membrane / 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 / macrophage differentiation / humoral immune response / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / epidermis development / PD-1 signaling / trans-Golgi network membrane / 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 / viral budding from plasma membrane / cognition / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / 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 / positive regulation of immune response / Interferon gamma signaling / endocytic vesicle membrane / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / toxin activity / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of viral entry into host cell / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / Golgi membrane / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane
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. / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 / Enterotoxin / MHC class II, alpha/beta chain, N-terminal / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / 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 / Hemagglutinin / Enterotoxin type C-3 / HLA class II histocompatibility antigen, DRB1 beta chain / Enterotoxin type C-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZavala-Ruiz, Z. / Sundberg, E.J. / Stone, J.D. / DeOliveira, D.B. / Chan, I.C. / Svendsen, J. / Mariuzza, R.A. / Stern, L.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Exploration of the P6/P7 region of the peptide-binding site of the human class II Major Histocompatability Complex Protein HLA-DR1
Authors: Zavala-Ruiz, Z. / Sundberg, E.J. / Stone, J.D. / DeOliveira, D.B. / Chan, I.C. / Svendsen, J. / Mariuzza, R.A. / Stern, L.J.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_residues ...database_2 / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Aug 16, 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

Downloads & links

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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: 9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL
D: Enterotoxin type C-3


Theoretical massNumber of molelcules
Total (without water)71,9604
Polymers71,9604
Non-polymers00
Water7,458414
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.507, 172.507, 121.652
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain


Mass: 21155.904 Da / Num. of mol.: 1 / Fragment: Extracellular domain of HLA-DRA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA / 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, DR-1 beta chain


Mass: 22080.664 Da / Num. of mol.: 1 / Fragment: Extracellular domain of HLA-DRB1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB / Plasmid: pLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13758, UniProt: P01911*PLUS
#3: Protein/peptide 9-residue influenza virus hemagglutinin related peptide FVKQNA(MAA)AL


Mass: 1002.187 Da / Num. of mol.: 1 / Mutation: Y308F, T313A, L314(MAA), K315A / Source method: obtained synthetically
Details: Synthetic peptide based on the central region of a natural occuring peptide derived from the influenza virus hemagglutinin. Amino terminus is acetylated, alanine at position 7 is N- ...Details: Synthetic peptide based on the central region of a natural occuring peptide derived from the influenza virus hemagglutinin. Amino terminus is acetylated, alanine at position 7 is N-methylated, and carboxy terminus is amidated.
References: GenBank: 3212739, UniProt: P03437*PLUS
#4: Protein Enterotoxin type C-3 / SEC3


Mass: 27721.068 Da / Num. of mol.: 1 / Fragment: residues 28-266 / Mutation: K43S, L45F, A46K, H47W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Species: Staphylococcus aureus / Strain: Mu50/ATCC 700699 / Gene: ENTC3 OR SAV2009 OR SA1817 / Production host: Escherichia coli (E. coli) / Strain (production host): HB 2151 / References: UniProt: P23313, UniProt: P0A0L3*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 4.84 Å3/Da / Density % sol: 74.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: PEG 4000, Ethylene Glycol, Mangesium Acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / PH range low: 5.6 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12-6 %PEG40001reservoir
210 %ethylene glycol1reservoir
3100 Msodium acetate1reservoirpH5.2-5.6
48 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 14, 2002 / 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: 2.1→20 Å / Num. all: 81140 / Num. obs: 79802 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.075 / Net I/σ(I): 11.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7968 / Rsym value: 0.394 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % possible obs: 100 % / Num. measured all: 366342 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 7968 / Num. measured obs: 32165 / Rmerge(I) obs: 0.394

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1KLU

1klu


Resolution: 2.1→20 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 7813 9.9 %Random
Rwork0.209 ---
obs0.212 69514 98.3 %-
all-77327 --
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å22.58 Å20 Å2
2--1.02 Å20 Å2
3----2.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4982 0 0 414 5396
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.4411.5
X-RAY DIFFRACTIONc_scbond_it1.9992
X-RAY DIFFRACTIONc_mcangle_it2.3562
X-RAY DIFFRACTIONc_scangle_it2.9612.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008
RfactorNum. reflection% reflection
Rfree0.304 1288 -
Rwork0.273 --
obs-11495 97.6 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3ligands.param
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72
LS refinement shell
*PLUS
Lowest resolution: 2.17 Å / Rfactor Rfree: 0.312 / Rfactor Rwork: 0.284

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