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- PDB-1qew: HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WIT... -

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Entry
Database: PDB / ID: 1qew
TitleHUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WITH A NONAMERIC PEPTIDE FROM MELANOMA-ASSOCIATED ANTIGEN 3 (RESIDUES 271-279)
Components
  • PROTEIN (BETA-2-MICROGLOBULIN)
  • PROTEIN (HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B* 3501 ALPHA CHAIN)
  • PROTEIN (MELANOMA-ASSOCIATED ANTIGEN 3)
KeywordsCOMPLEX (MHC PROTEINTIGEN) / HISTOCOMPATIBILITY ANTIGEN
Function / homology
Function and homology information


: / : / : / : / : / caspase binding / regulation of membrane depolarization / retina homeostasis / negative regulation of protein processing / positive regulation of memory T cell activation ...: / : / : / : / : / caspase binding / regulation of membrane depolarization / retina homeostasis / negative regulation of protein processing / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / positive regulation of protein binding / detection of bacterium / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / T cell receptor binding / negative regulation of autophagy / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / 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 / histone deacetylase binding / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / antimicrobial humoral immune response mediated by antimicrobial peptide / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / cellular response to lipopolysaccharide / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / 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
Beta-2-microglobulin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Melanoma-associated antigen 3 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOrth, P. / Alings, C. / Saenger, W. / Ziegler, A.
CitationJournal: To be Published
Title: HUMAN CLASS I HISTOCOMPATIBILITY ANTIGEN (HLA-A 0201) COMPLEX WITH A NONAMERIC PEPTIDE FROM MELANOMA-ASSOCIATED ANTIGEN 3 (RESIDUES 271-279)
Authors: Orth, P. / Alings, C. / Saenger, W. / Ziegler, A.
History
DepositionApr 2, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 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: PROTEIN (HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B* 3501 ALPHA CHAIN)
B: PROTEIN (BETA-2-MICROGLOBULIN)
C: PROTEIN (MELANOMA-ASSOCIATED ANTIGEN 3)


Theoretical massNumber of molelcules
Total (without water)44,7933
Polymers44,7933
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-23 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.990, 54.520, 76.380
Angle α, β, γ (deg.)90.00, 105.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, B-35 B* 3501 ALPHA CHAIN)


Mass: 31854.203 Da / Num. of mol.: 1 / Fragment: residues 25-299,SWS P01892
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI XA90 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein PROTEIN (BETA-2-MICROGLOBULIN)


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: residues 21-199, SWS P01884
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): E. COLI XA90 / References: UniProt: P01884, UniProt: P61769*PLUS
#3: Protein/peptide PROTEIN (MELANOMA-ASSOCIATED ANTIGEN 3)


Mass: 1059.283 Da / Num. of mol.: 1 / Fragment: residues 271-280, SWS P43357 / Source method: isolated from a natural source / Details: SYNTHETIC / Source: (natural) Homo sapiens (human) / References: UniProt: P43357
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.6
Details: 20 % POLYETHYLENGLYCOL 8000, SODIUM CITRATE, PH 5.6

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 22410 / % possible obs: 95.9 % / Redundancy: 2 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.078 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.3 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.193 / % possible all: 86.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0G

1b0g


Resolution: 2.2→20 Å / Data cutoff high rms absF: 100000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1091 4.6 %RANDOM
Rwork0.204 ---
obs-22410 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 294 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.50.985
X-RAY DIFFRACTIONc_mcangle_it21.646
X-RAY DIFFRACTIONc_scbond_it21.575
X-RAY DIFFRACTIONc_scangle_it2.52.428
LS refinement shellResolution: 2.2→2.3 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.296 107
Rwork0.249 1942
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3WATER.TOP

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