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- PDB-3vrj: HLA-B*57:01-LTTKLTNTNI in complex with abacavir -

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Basic information

Entry
Database: PDB / ID: 3vrj
TitleHLA-B*57:01-LTTKLTNTNI in complex with abacavir
Components
  • 10-mer peptide
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
KeywordsIMMUNE SYSTEM / Human leukocyte antigen / antigen presentation / T-cell receptor
Function / homology
Function and homology information


respiratory chain complex IV / Respiratory electron transport / mitochondrial respiratory chain complex IV / regulation of interleukin-12 production / regulation of dendritic cell differentiation / cytochrome-c oxidase / cellular respiration / regulation of T cell anergy / mitochondrial electron transport, cytochrome c to oxygen / regulation of interleukin-6 production ...respiratory chain complex IV / Respiratory electron transport / mitochondrial respiratory chain complex IV / regulation of interleukin-12 production / regulation of dendritic cell differentiation / cytochrome-c oxidase / cellular respiration / regulation of T cell anergy / mitochondrial electron transport, cytochrome c to oxygen / regulation of interleukin-6 production / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / 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 / lactation / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / mitochondrial membrane / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / TP53 Regulates Metabolic Genes / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / Cytoprotection by HMOX1 / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / mitochondrial inner membrane / adaptive immune response / learning or memory / response to hypoxia / immune response / copper ion binding / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase subunit II, periplasmic domain ...Cytochrome c oxidase subunit 2, C-terminal / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / 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 / Cupredoxin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1KX / Cytochrome c oxidase subunit 2 / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVivian, J.P. / Illing, P.T. / McCluskey, J. / Rossjohn, J.
CitationJournal: Nature / Year: 2012
Title: Immune self-reactivity triggered by drug-modified HLA-peptide repertoire
Authors: Illing, P.T. / Vivian, J.P. / Dudek, N.L. / Kostenko, L. / Chen, Z. / Bharadwaj, M. / Miles, J.J. / Kjer-Nielsen, L. / Gras, S. / Williamson, N.A. / Burrows, S.R. / Purcell, A.W. / Rossjohn, J. / McCluskey, J.
History
DepositionApr 11, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 10-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0214
Polymers44,7353
Non-polymers2861
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-20 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.291, 49.005, 70.875
Angle α, β, γ (deg.)90.00, 99.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-57 alpha chain / HLA-B*5701 / Bw-57 / MHC class I antigen B*57


Mass: 31736.172 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide 10-mer peptide


Mass: 1119.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesised peptide / References: UniProt: P00403*PLUS
#4: Chemical ChemComp-1KX / {(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]cyclopent-2-en-1-yl}methanol / Abacavir / Abacavir


Mass: 286.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N6O / Comment: medication, inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25
Details: 28% PEG 8000, 0.2M ammonium sulfate, 0.1M cacodylate, pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 5, 2011
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 34469 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 13.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1157 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFX

2rfx


Resolution: 1.9→43.511 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.875 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.47 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1706 4.95 %random
Rwork0.1748 ---
obs0.1767 34451 99.54 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.369 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 86.18 Å2 / Biso mean: 21.5099 Å2 / Biso min: 3.32 Å2
Baniso -1Baniso -2Baniso -3
1-4.8451 Å2-0 Å21.985 Å2
2---1.3419 Å20 Å2
3----3.5032 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3139 0 21 419 3579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053288
X-RAY DIFFRACTIONf_angle_d1.1434471
X-RAY DIFFRACTIONf_chiral_restr0.067462
X-RAY DIFFRACTIONf_plane_restr0.004587
X-RAY DIFFRACTIONf_dihedral_angle_d16.3521230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.95590.24221370.198527422879100
1.9559-2.0190.24171490.183526972846100
2.019-2.09120.22451410.183527182859100
2.0912-2.17490.23621350.178727052840100
2.1749-2.27390.24391230.180727452868100
2.2739-2.39380.20861500.171627282878100
2.3938-2.54380.20881480.182127072855100
2.5438-2.74010.21481540.18782697285199
2.7401-3.01580.25391420.18982720286299
3.0158-3.45210.21061300.16922744287499
3.4521-4.34860.18171550.1472697285299
4.3486-43.52270.18781420.175228452987100

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