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- PDB-2fo4: Enhanced MHC class I binding and immune responses through anchor ... -

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Basic information

Entry
Database: PDB / ID: 2fo4
TitleEnhanced MHC class I binding and immune responses through anchor modification of the non-canonical tumor associated MUC1-8 peptide
Components
  • 8-mer from Mucin-1
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
KeywordsIMMUNE SYSTEM / anchor modifications / H-2Kb / MUC1 / non-canonical peptide / MUC1-8 / vaccine design
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / negative regulation of cell adhesion mediated by integrin / negative regulation of transcription by competitive promoter binding / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / Dectin-2 family / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / mitotic G1 DNA damage checkpoint signaling / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / transcription coregulator activity / DNA damage response, signal transduction by p53 class mediator / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / Golgi lumen / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / p53 binding / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / Interleukin-4 and Interleukin-13 signaling / protein homotetramerization / vesicle / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / apical plasma membrane / RNA polymerase II cis-regulatory region sequence-specific DNA binding / external side of plasma membrane / chromatin / structural molecule activity / Golgi apparatus / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / nucleus / plasma membrane / cytosol
Similarity search - Function
Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains ...Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Mucin-1 / Mucin-1 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLazoura, E. / Ramsland, P.A.
CitationJournal: Immunology / Year: 2006
Title: Enhanced major histocompatibility complex class I binding and immune responses through anchor modification of the non-canonical tumour-associated mucin 1-8 peptide
Authors: Lazoura, E. / Lodding, J. / Farrugia, W. / Ramsland, P.A. / Stevens, J. / Wilson, I.A. / Pietersz, G.A. / Apostolopoulos, V.
History
DepositionJan 12, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, K-B alpha chain
B: Beta-2-microglobulin
P: 8-mer from Mucin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,50711
Polymers44,2563
Non-polymers1,2518
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-75 kcal/mol
Surface area18550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.260, 87.890, 45.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 31648.322 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS, RESIDUES 1-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01901, UniProt: Q3UBW0*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): SC2 cells / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide 8-mer from Mucin-1 / MUCIN 1 / TRANSMEMBRANE / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor- ...MUCIN 1 / TRANSMEMBRANE / MUC-1 / Polymorphic epithelial mucin / PEM / PEMT / Episialin / Tumor-associated mucin / Carcinoma-associated mucin / Tumor-associated epithelial membrane antigen / EMA / H23AG / Peanut- reactive urinary mucin / PUM / Breast carcinoma-associated antigen DF3 / CD227 antigen


Mass: 903.014 Da / Num. of mol.: 1 / Mutation: T5F, A8L / Source method: obtained synthetically
Details: The 8-residue peptide of mucin 1 was chemically synthesized.
References: UniProt: Q16615, UniProt: P15941*PLUS

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Sugars , 2 types, 2 molecules

#4: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 109 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 1.9M sodium/potasium phosphate, 2% MPD, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Feb 17, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 14860 / Num. obs: 14860 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1448 / % possible all: 96.2

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G7Q

1g7q


Resolution: 2.7→41.8 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1449 -random
Rwork0.193 ---
all-14860 --
obs-14860 94.3 %-
Displacement parametersBiso mean: 37.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→41.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 80 103 3300
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.347 181 -
Rwork0.285 --
obs-1782 78.1 %

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