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- PDB-1sys: Crystal structure of HLA, B*4403, and peptide EEPTVIKKY -

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Basic information

Entry
Database: PDB / ID: 1sys
TitleCrystal structure of HLA, B*4403, and peptide EEPTVIKKY
Components
  • Beta-2-microglobulin
  • Sorting nexin 5
  • leukocyte antigen (HLA) class I molecule
KeywordsIMMUNE SYSTEM / HLA / MHC / Class I / B44
Function / homology
Function and homology information


retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...retromer, tubulation complex / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / tubular endosome / macropinocytic cup / phosphatidylinositol-5-phosphate binding / retromer complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / regulation of interleukin-6 production / Golgi Associated Vesicle Biogenesis / dynactin binding / brush border / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / phagocytic cup / regulation of macroautophagy / D1 dopamine receptor binding / positive regulation of insulin receptor signaling pathway / detection of bacterium / ruffle / negative regulation of blood pressure / phosphatidylinositol binding / : / : / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / intracellular protein transport / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / cytoplasmic side of plasma membrane / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endosome / immune response / cadherin binding
Similarity search - Function
SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily ...SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsZernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. ...Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Bottomley, S.P. / Beddoe, T. / Peh, C.A. / Rossjohn, J. / McCluskey, J.
CitationJournal: J.Exp.Med. / Year: 2004
Title: Natural HLA class I polymorphism controls the pathway of antigen presentation and susceptibility to viral evasion
Authors: Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Bharadwaj, M. / Chang, L. / Tait, B.D. / Holdsworth, R. / Brooks, A. ...Authors: Zernich, D. / Purcell, A.W. / Macdonald, W.A. / Kjer-Nielsen, L. / Ely, L.K. / Laham, N. / Crockford, T. / Mifsud, N.A. / Bharadwaj, M. / Chang, L. / Tait, B.D. / Holdsworth, R. / Brooks, A.G. / Bottomley, S.P. / Beddoe, T. / Peh, C.A. / Rossjohn, J. / McCluskey, J.
History
DepositionApr 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: leukocyte antigen (HLA) class I molecule
B: Beta-2-microglobulin
C: Sorting nexin 5


Theoretical massNumber of molelcules
Total (without water)44,9663
Polymers44,9663
Non-polymers00
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-17 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.823, 81.985, 110.155
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein leukocyte antigen (HLA) class I molecule


Mass: 31978.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / HDCMA22P


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Sorting nexin 5


Mass: 1108.283 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q9Y5X3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG 4000, 0.2M Ammonium Acetate, 0.2M Sodium Citrate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→45 Å / Num. obs: 18236

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45 Å /
RfactorNum. reflection
Rfree0.271 -
Rwork0.241 -
obs-17688
Refinement stepCycle: LAST / Resolution: 2.4→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3162 0 0 186 3348

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