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- PDB-1seb: COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BA... -

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Basic information

Entry
Database: PDB / ID: 1seb
TitleCOMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BACTERIAL SUPERANTIGEN SEB
Components
  • (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN) x 2
  • ENDOGENOUS PEPTIDE MODEL, POLY-ALA
  • ENTEROTOXIN TYPE B
KeywordsCOMPLEX (MHC II/PEPTIDE/TOXIN) / HISTOCOMPATIBILITY ANTIGEN / MHC II / SUPERANTIGEN / ENTEROTOXIN PEPTIDE / TOXIN / COMPLEX (MHC II-PEPTIDE-TOXIN) COMPLEX
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / autolysosome membrane / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / 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 memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / 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 / Generation of second messenger molecules / macrophage differentiation / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / negative regulation of T cell proliferation / T cell receptor binding / MHC class II antigen presentation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / negative regulation of inflammatory response to antigenic stimulus / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / structural constituent of cytoskeleton / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / cognition / positive regulation of T cell activation / Interferon gamma signaling / endocytic vesicle membrane / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / adaptive immune response / lysosome / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / cell surface / signal transduction / : / 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 / Ubiquitin-like (UB roll) - #120 / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / 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 / Ubiquitin-like (UB roll) - #120 / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / 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 / 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 / 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
Enterotoxin type B / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsJardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Chi, Y.I. / Stauffacher, C. / Strominger, J.L. / Wiley, D.C.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen.
Authors: Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Chi, Y.I. / Stauffacher, C. / Strominger, J.L. / Wiley, D.C.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystallographic Analysis of Endogenous Peptides Associated with Hla-Dr1 Suggests a Common, Polyproline II-Like Conformation for Bound Peptides
Authors: Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Strominger, J.L. / Wiley, D.C.
History
DepositionNov 26, 1995Processing site: BNL
Revision 1.0Jun 20, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
C: ENDOGENOUS PEPTIDE MODEL, POLY-ALA
D: ENTEROTOXIN TYPE B
E: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
F: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
G: ENDOGENOUS PEPTIDE MODEL, POLY-ALA
H: ENTEROTOXIN TYPE B


Theoretical massNumber of molelcules
Total (without water)144,6558
Polymers144,6558
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.000, 114.700, 149.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.331943, -0.93061, -0.154201), (-0.928817, -0.350985, 0.118781), (-0.164661, 0.103796, -0.980874)81.5667, 107.9656, 43.8542
2given(0.322613, -0.930674, -0.17253), (-0.932147, -0.344045, 0.112853), (-0.164388, 0.124417, -0.978518)82.1961, 107.7428, 42.7804
3given(0.335693, -0.931675, -0.138895), (-0.929209, -0.351715, 0.113436), (-0.154537, 0.090982, -0.983789)81.3957, 107.9864, 44.0986
4given(0.286918, -0.944051, -0.162622), (-0.942375, -0.308647, 0.1291), (-0.17207, 0.11621, -0.978206)83.9813, 107.261, 43.4628
5given(0.310564, -0.938287, -0.152211), (-0.933537, -0.331232, 0.137094), (-0.17905, 0.099518, -0.978794)83.1576, 107.1495, 44.9449
6given(0.300711, -0.941339, -0.153144), (-0.938962, -0.320353, 0.1254), (-0.167104, 0.106087, -0.980215)83.7429, 106.4834, 43.885
7given(0.331943, -0.93061, -0.154201), (-0.928817, -0.350985, 0.118781), (-0.164661, 0.103796, -0.980874)81.5667, 107.9656, 43.8542
DetailsTHE ASYMMETRIC UNIT CONTAINS A DIMER CONSISTING OF TWO HLA/DR-1 AND TWO SEB MOLECULES. THE DEPOSITORS PROVIDED A MONOMER AND THE TRANSFORMATIONS TO GENERATE THE OTHER MONOMER IN THE DIMER. THE PROTEIN DATA BANK GENERATED THE COMPLETE ASYMMETRIC UNIT USING THE TRANSFORMATIONS PROVIDED. CHAINS A, B, C, D WERE DEPOSITED AND CHAINS E, F, G, H WERE GENERATED USING THE TRANSFORMATIONS GIVEN ON MTRIX RECORDS BELOW. SEE REMARK 295 FOR ADDITIONAL DETAILS.

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Components

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / HLA-DR1


Mass: 21084.826 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: LG-2 / Cell line (production host): LG-2 cells / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / HLA-DR1


Mass: 22324.938 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: LG-2 / Cell line (production host): LG-2 cells / Production host: Homo sapiens (human) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide ENDOGENOUS PEPTIDE MODEL, POLY-ALA


Mass: 1124.378 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: SUPERPOSITION OF MANY DIFFERENT PEPTIDES / Source: (natural) Homo sapiens (human)
#4: Protein ENTEROTOXIN TYPE B / SEB


Mass: 27793.309 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Cell line: LG-2 / References: UniProt: P01552
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 mMTris1drop
310 mMsodium acetate1reservoir
410 %ethylene glycol1reservoir
512-20 %PEG40001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: KODAK / Detector: IMAGE PLATE / Date: Nov 1, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionNum. obs: 40627 / % possible obs: 86 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.7→6 Å / σ(F): 2
Details: THERE IS SOME EVIDENCE THAT THE SECOND SEB MOLECULE IS FOUND AT LOWER OCCUPANCY IN THE LATTICE. THE DR1:SEB STRUCTURE CONTAINS A BACKBONE MODEL (REFINED AS POLYALANINE) FOR ELECTRON DENSITY ...Details: THERE IS SOME EVIDENCE THAT THE SECOND SEB MOLECULE IS FOUND AT LOWER OCCUPANCY IN THE LATTICE. THE DR1:SEB STRUCTURE CONTAINS A BACKBONE MODEL (REFINED AS POLYALANINE) FOR ELECTRON DENSITY THAT CORRESPONDS TO A COMPLEX MIXTURE OF PEPTIDES THAT CO-PURIFY WITH THE HLA-DR1 MOLECULE (SEE REFERENCE 1 ABOVE FOR DETAILS). MHC CLASS II MOLECULES FORM VERY STABLE COMPLEXES WITH PEPTIDES AND, WHEN ISOLATED FROM HUMAN CELL LINES, HLA-DR1 MOLECULES HAVE BEEN SHOWN TO BE LOADED WITH A MIXTURE OF CELLULAR OR SERUM DERIVED PEPTIDES. THE NUMBER OF DIFFERENT PEPTIDES IS ESTIMATED TO BE ON THE ORDER OF THOUSANDS OF DIFFERENT SPECIES. IN THE CO-CRYSTAL OF HLA-DR1 WITH SEB, INTERPRETABLE ELECTRON DENSITY IS OBSERVED FOR THE BACKBONE OF A 13 AMINO ACID PEPTIDE WITH THE HLA-DR1 PEPTIDE-BINDING SITE. ALTHOUGH GOOD SIDE CHAIN DENSITY IS OBSERVED WITHIN THIS REGION, THE ELECTRON DENSITY COULD NOT BE UNAMBIGUOUSLY CORRELATED WITH ANY OF THE SEQUENCES DETERMINED FOR PEPTIDES ELUTED FROM PURIFIED HLA-DR1. THE ELECTRON DENSITY IS CONSISTENT WITH THE SUPERPOSITION OF MANY PEPTIDES WITH DIFFERENT SEQUENCES THAT ASSUME A COMMON CONFORMATION WITHIN THE HLA-DR1 PEPTIDE-BINDING SITE. THE POLYALANINE MODEL, THEREFORE, REPRESENTS A CONSENSUS CONFORMATION FOR PEPTIDE-BINDING TO HLA-DR1. IN THIS ENTRY THIS CHAIN IS PRESENTED AS CHAIN C (AND G) WITH THE RESIDUES NAMED "UNK".
RfactorNum. reflection
Rfree0.327 -
Rwork0.257 -
obs0.257 31557
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9400 0 0 0 9400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.16
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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