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- PDB-2oje: Mycoplasma arthritidis-derived mitogen complexed with class II MH... -

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Basic information

Entry
Database: PDB / ID: 2oje
TitleMycoplasma arthritidis-derived mitogen complexed with class II MHC molecule HLA-DR1/HA complex in the presence of EDTA
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Superantigen
  • haemagglutinin peptide 306-318
KeywordsIMMUNE SYSTEM / superantigen / MHC
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / 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 / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / 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 / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / apical plasma membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
mam-mhc complex, Chain D, Domain 2 / Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 / Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / 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 ...mam-mhc complex, Chain D, Domain 2 / Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 / Mycoplasma arthritidis-derived mitogen / Superantigen MAM / Mycoplasma arthritidis-derived mitogen, C-terminal / Mycoplasma arthritidis-derived mitogen / 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 / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Arc Repressor Mutant, subunit A / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / Superantigen / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycoplasma arthritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3 Å
AuthorsLi, H. / Zhao, Y. / Guo, Y. / Li, Z. / Eisele, L. / Mourad, W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Zinc induces dimerization of the class II major histocompatibility complex molecule that leads to cooperative binding to a superantigen.
Authors: Li, H. / Zhao, Y. / Guo, Y. / Li, Z. / Eisele, L. / Mourad, W.
History
DepositionJan 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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 precursor
B: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
C: haemagglutinin peptide 306-318
D: Superantigen
E: HLA class II histocompatibility antigen, DR alpha chain precursor
F: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
G: haemagglutinin peptide 306-318
H: Superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,61812
Polymers140,2388
Non-polymers3804
Water2,126118
1
A: HLA class II histocompatibility antigen, DR alpha chain precursor
B: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
C: haemagglutinin peptide 306-318
D: Superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3096
Polymers70,1194
Non-polymers1902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-57 kcal/mol
Surface area28050 Å2
MethodPISA
2
E: HLA class II histocompatibility antigen, DR alpha chain precursor
F: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
G: haemagglutinin peptide 306-318
H: Superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3096
Polymers70,1194
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10060 Å2
ΔGint-67 kcal/mol
Surface area28050 Å2
MethodPISA
3
A: HLA class II histocompatibility antigen, DR alpha chain precursor
B: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
C: haemagglutinin peptide 306-318
D: Superantigen
hetero molecules

A: HLA class II histocompatibility antigen, DR alpha chain precursor
B: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
C: haemagglutinin peptide 306-318
D: Superantigen
hetero molecules

E: HLA class II histocompatibility antigen, DR alpha chain precursor
F: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
G: haemagglutinin peptide 306-318
H: Superantigen
hetero molecules

E: HLA class II histocompatibility antigen, DR alpha chain precursor
F: HLA class II histocompatibility antigen, DRB1-1 beta chain precursor
G: haemagglutinin peptide 306-318
H: Superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)281,23724
Polymers280,47716
Non-polymers7608
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_445x-1/2,-y-1/2,-z+1/21
Buried area49680 Å2
ΔGint-267 kcal/mol
Surface area103020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.735, 179.555, 179.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-200-

HOH

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 4 molecules AEBF

#1: Protein HLA class II histocompatibility antigen, DR alpha chain precursor / MHC class II antigen DRA


Mass: 21112.354 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 27-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain precursor / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: extracellular domain, residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide / Protein , 2 types, 4 molecules CGDH

#3: Protein/peptide haemagglutinin peptide 306-318


Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: residues 306-318 / Source method: obtained synthetically / Details: This sequence occurs naturally in influenza virus / References: UniProt: Q91LS8*PLUS
#4: Protein Superantigen / / MYCOPLASMA ARTHRITIDIS-DERIVED MITOGEN


Mass: 25419.404 Da / Num. of mol.: 2 / Fragment: residues 25-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma arthritidis (bacteria) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q48898

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Non-polymers , 2 types, 122 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 3.97 Å3/Da / Density % sol: 68.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.7M potassium sodium phosphate, 0.1M HEPES, 2 mM EDTA, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→40.22 Å / Num. obs: 40345 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rmerge(I) obs: 0.124 / Rsym value: 12.4 / Net I/σ(I): 17
Reflection shellResolution: 3→3.19 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6761 / Rsym value: 56.3 / % possible all: 91.5

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Processing

Software
NameVersionClassification
CNS1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5I

1r5i


Resolution: 3→40.22 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2671296.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2850 7.1 %RANDOM
Rwork0.211 ---
all0.211 ---
obs0.211 40345 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.6402 Å2 / ksol: 0.34148 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1--6.73 Å20 Å20 Å2
2--13.74 Å20 Å2
3----7.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 3→40.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9872 0 20 118 10010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.992.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.398 443 6.6 %
Rwork0.333 6318 -
obs--91.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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