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- PDB-6bxp: Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn -

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Basic information

Entry
Database: PDB / ID: 6bxp
TitleCrystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
Components
  • Beta-2-microglobulin
  • HIV peptide RKV-Kyn
  • HLA class I histocompatibility antigen, B-57 alpha chain
KeywordsIMMUNE SYSTEM / Immunopeptidome / kynurenine / HIV / PTM / HLA-B*57:01
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / regulation of interleukin-12 production / positive regulation of establishment of T cell polarity / regulation of dendritic cell differentiation / Alpha-defensins / regulation of T cell anergy / regulation of interleukin-6 production / Dectin-2 family / TAP binding ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / regulation of interleukin-12 production / positive regulation of establishment of T cell polarity / regulation of dendritic cell differentiation / Alpha-defensins / regulation of T cell anergy / regulation of interleukin-6 production / Dectin-2 family / 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 / Binding and entry of HIV virion / detection of bacterium / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / secretory granule membrane / negative regulation of receptor binding / actin filament organization / host cell endosome membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / 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 / ER to Golgi transport vesicle membrane / Assembly Of The HIV Virion / 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 / defense response / Budding and maturation of HIV virion / 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 / specific granule lumen / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / immune response / receptor ligand activity / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / fusion of virus membrane with host plasma membrane / innate immune response / external side of plasma membrane / focal adhesion / fusion of virus membrane with host endosome membrane / viral envelope / Neutrophil degranulation / symbiont entry into host cell / virion attachment to host cell
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / Envelope glycoprotein gp160 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsGras, S. / Rossjohn, J.
CitationJournal: Proteomics / Year: 2018
Title: Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics.
Authors: Ramarathinam, S.H. / Gras, S. / Alcantara, S. / Yeung, A.W.S. / Mifsud, N.A. / Sonza, S. / Illing, P.T. / Glaros, E.N. / Center, R.J. / Thomas, S.R. / Kent, S.J. / Ternette, N. / Purcell, D. ...Authors: Ramarathinam, S.H. / Gras, S. / Alcantara, S. / Yeung, A.W.S. / Mifsud, N.A. / Sonza, S. / Illing, P.T. / Glaros, E.N. / Center, R.J. / Thomas, S.R. / Kent, S.J. / Ternette, N. / Purcell, D.F.J. / Rossjohn, J. / Purcell, A.W.
History
DepositionDec 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 20, 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 I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: HIV peptide RKV-Kyn
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9384
Polymers44,8793
Non-polymers591
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-19 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.446, 82.051, 110.434
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-57 alpha chain / Bw-57 / MHC class I antigen B*57


Mass: 31736.172 Da / Num. of mol.: 1 / Fragment: residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide HIV peptide RKV-Kyn


Mass: 1394.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.56 Å3/Da / Density % sol: 52 % / Mosaicity: 0.13 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18%PEG4000, 0.2M NH4 Ac, 0.1M NaCitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.45→27.96 Å / Num. obs: 79286 / % possible obs: 97.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.45-1.483.70.6111492340800.716299
7.81-27.963.60.04413923870.99219.367

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.3.6data scaling
PHASERphasing
BUSTER2.10.0refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G9D

4g9d


Resolution: 1.45→21.23 Å / Cor.coef. Fo:Fc: 0.9635 / Cor.coef. Fo:Fc free: 0.9539 / SU R Cruickshank DPI: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.066 / SU Rfree Blow DPI: 0.066 / SU Rfree Cruickshank DPI: 0.063
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 4018 5.07 %RANDOM
Rwork0.1696 ---
obs0.1708 79250 96.72 %-
Displacement parametersBiso max: 100.32 Å2 / Biso mean: 23.03 Å2 / Biso min: 6.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.2771 Å20 Å20 Å2
2--1.5002 Å20 Å2
3----1.7773 Å2
Refine analyzeLuzzati coordinate error obs: 0.153 Å
Refinement stepCycle: final / Resolution: 1.45→21.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 0 22 573 3699
Biso mean--28.47 36.67 -
Num. residues----379
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1200SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes517HARMONIC5
X-RAY DIFFRACTIONt_it3414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4409SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3414HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4672HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion14.66
LS refinement shellResolution: 1.45→1.49 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2473 281 4.76 %
Rwork0.2156 5627 -
all0.2171 5908 -
obs--96.72 %

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