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- PDB-1r5i: Crystal structure of the MAM-MHC complex -

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Basic information

Entry
Database: PDB / ID: 1r5i
TitleCrystal structure of the MAM-MHC complex
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Hemagglutinin peptide
  • superantigen
KeywordsIMMUNE SYSTEM / superantigen / MHC / MAM / 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 / 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 ...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 / 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 / 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 / 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 / endocytic vesicle membrane / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / host cell surface receptor binding / immune response / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / virion membrane / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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 / Hemagglutinin / Superantigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycoplasma arthritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 2.6 Å
AuthorsZhao, Y. / Li, Z. / Drozd, S.J. / Guo, Y. / Mourad, W. / Li, H.
CitationJournal: Structure / Year: 2004
Title: Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex.
Authors: Zhao, Y. / Li, Z. / Drozd, S.J. / Guo, Y. / Mourad, W. / Li, H.
History
DepositionOct 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: 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, DRB1-1 beta chain
C: Hemagglutinin peptide
D: superantigen
E: HLA class II histocompatibility antigen, DR alpha chain
F: HLA class II histocompatibility antigen, DRB1-1 beta chain
G: Hemagglutinin peptide
H: superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,18512
Polymers140,8058
Non-polymers3804
Water1,910106
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: Hemagglutinin peptide
D: superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5936
Polymers70,4034
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: HLA class II histocompatibility antigen, DR alpha chain
F: HLA class II histocompatibility antigen, DRB1-1 beta chain
G: Hemagglutinin peptide
H: superantigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5936
Polymers70,4034
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.286, 178.814, 179.554
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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 / MHC class II antigen DRA


Mass: 21225.512 Da / Num. of mol.: 2 / Fragment: alpha chain of class II MHC (residues 26-206)
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 / MHC class I antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: beta chain of class II MHC (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 Hemagglutinin peptide


Mass: 1506.807 Da / Num. of mol.: 2 / Fragment: haemagglutinin peptide (residues 306-318) / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in influenza virus.
References: UniProt: P11133
#4: Protein superantigen / Mycoplasma arthritidis-derived mitogen


Mass: 25589.617 Da / Num. of mol.: 2
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, 110 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.94 Å3/Da / Density % sol: 68.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: potassium sodium hosphate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.4 mg/mlprotein1drop
220 mMHEPES1droppH7.5
3100 mM1dropNaCl
41 mMdithiothreitol1drop
51 mM1dropZn(OAc)2
61.7 Mpotassium sodium phosphate1reservoir
70.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 8, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→43 Å / Num. all: 65311 / Num. obs: 65311 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.489 / % possible all: 80.4
Reflection
*PLUS
% possible obs: 95.9 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 80.4 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
SOLVEphasing
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: PDB entry 1DLH

1dlh


Resolution: 2.6→42.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3119994.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 4640 7.1 %RANDOM
Rwork0.238 ---
all0.238 65311 --
obs0.238 65311 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.9383 Å2 / ksol: 0.345188 e/Å3
Displacement parametersBiso mean: 45.7 Å2
Baniso -1Baniso -2Baniso -3
1--10.35 Å20 Å20 Å2
2--20.35 Å20 Å2
3----10 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.59 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9888 0 20 106 10014
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.86
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 651 7.1 %
Rwork0.394 8490 -
obs-9222 80.8 %
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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