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- PDB-5iek: Structure of HLA-B*40:02 in complex with the endogenous peptide R... -

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Basic information

Entry
Database: PDB / ID: 5iek
TitleStructure of HLA-B*40:02 in complex with the endogenous peptide REFSKEPEL
Components
  • ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-40 alpha chain
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen system
Function / homology
Function and homology information


central element / meiotic spindle midzone / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / mitotic spindle midzone assembly / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter ...central element / meiotic spindle midzone / meiotic spindle midzone assembly / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / mitotic spindle midzone assembly / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / regulation of interleukin-12 production / regulation of dendritic cell differentiation / chromosome passenger complex / lateral element / regulation of T cell anergy / regulation of interleukin-6 production / protection from natural killer cell mediated cytotoxicity / mitotic cytokinesis / SUMOylation of DNA replication proteins / TAP binding / chromosome, centromeric region / mitotic spindle assembly / detection of bacterium / 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 / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / molecular function activator activity / Resolution of Sister Chromatid Cohesion / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / chromosome segregation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / defense response / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / RHO GTPases Activate Formins / 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 assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / kinetochore / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / spindle / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / positive regulation of cellular senescence / sensory perception of smell / tertiary granule lumen / Separation of Sister Chromatids / MHC class II protein complex binding / DAP12 signaling / T cell differentiation in thymus / late endosome membrane / mitotic cell cycle / negative regulation of neuron projection development / protein refolding / protein-folding chaperone binding / ER-Phagosome pathway / microtubule cytoskeleton / midbody / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / microtubule
Similarity search - Function
Chromosome passenger complex (CPC) protein INCENP N-terminal / Chromosome passenger complex (CPC) protein INCENP N terminal / Inner centromere protein, ARK-binding domain / Inner centromere protein, ARK binding region / 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 ...Chromosome passenger complex (CPC) protein INCENP N-terminal / Chromosome passenger complex (CPC) protein INCENP N terminal / Inner centromere protein, ARK-binding domain / Inner centromere protein, ARK binding region / 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 / Beta-2-microglobulin / HLA class I histocompatibility antigen, B alpha chain / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsAlpizar, A. / Marcilla, M. / Santiago, C.
CitationJournal: To Be Published
Title: Structure of HLA-B*40:02 in complex with the endogenous peptide REFSKEPEL
Authors: Alpizar, A. / Marcilla, M. / Santiago, C.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Oct 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-40 alpha chain
B: Beta-2-microglobulin
C: ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)45,1533
Polymers45,1533
Non-polymers00
Water9,476526
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-16 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.260, 82.201, 111.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-40 alpha chain / Bw-60 / MHC class I antigen B*40


Mass: 32137.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami pLys / References: UniProt: Q04826, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys / References: UniProt: P61769
#3: Protein/peptide ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU


Mass: 1136.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NQS7*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 150 mM Tris 8.5, 23% PEG8K, 70 mM potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00556 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00556 Å / Relative weight: 1
ReflectionNum. obs: 46622 / % possible obs: 99.9 % / Redundancy: 6.1 % / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→24.975 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.21
RfactorNum. reflection% reflection
Rfree0.1881 2211 5 %
Rwork0.1616 --
obs0.163 44245 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.34 Å2 / Biso mean: 26.2613 Å2 / Biso min: 6.52 Å2
Refinement stepCycle: final / Resolution: 1.8→24.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 0 526 3702
Biso mean---34.72 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093283
X-RAY DIFFRACTIONf_angle_d1.0364463
X-RAY DIFFRACTIONf_chiral_restr0.062455
X-RAY DIFFRACTIONf_plane_restr0.006590
X-RAY DIFFRACTIONf_dihedral_angle_d17.0521973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83910.30931420.265425572699
1.8391-1.88190.24051430.229225702713
1.8819-1.9290.25751270.202126072734
1.929-1.98110.22811190.178126292748
1.9811-2.03940.21131290.173925692698
2.0394-2.10510.21631340.172926152749
2.1051-2.18030.21281340.165526052739
2.1803-2.26760.2131300.155926172747
2.2676-2.37070.2141540.155825812735
2.3707-2.49560.19581390.163526242763
2.4956-2.65180.21111130.159926472760
2.6518-2.85630.16541530.166326332786
2.8563-3.14320.21261310.162526402771
3.1432-3.59690.17811660.153826352801
3.5969-4.52730.14351450.131126822827
4.5273-24.9770.15131520.155728232975

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