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- PDB-3vri: HLA-B*57:01-RVAQLENVYI in complex with abacavir -

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Basic information

Entry
Database: PDB / ID: 3vri
TitleHLA-B*57:01-RVAQLENVYI 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


U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex ...U7 snRNA binding / histone pre-mRNA DCP binding / U7 snRNP / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / protein methylation / U12-type spliceosomal complex / methylosome / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / SMN-Sm protein complex / U2-type spliceosomal complex / telomerase RNA binding / telomerase holoenzyme complex / regulation of interleukin-12 production / U2-type precatalytic spliceosome / regulation of dendritic cell differentiation / U2-type prespliceosome assembly / commitment complex / U2-type catalytic step 2 spliceosome / U4 snRNP / regulation of T cell anergy / U2 snRNP / RNA Polymerase II Transcription Termination / U1 snRNP / regulation of interleukin-6 production / precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / spliceosomal snRNP assembly / TAP binding / U4/U6 x U5 tri-snRNP complex / 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 / catalytic step 2 spliceosome / detection of bacterium / mRNA Splicing - Major Pathway / RNA splicing / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / spliceosomal complex / 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 / defense response / 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 / cellular response to iron ion / mRNA splicing, via spliceosome / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / snRNP Assembly / positive regulation of protein binding / ER-Phagosome pathway
Similarity search - Function
Small nuclear ribonucleoprotein Sm D3 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Small nuclear ribonucleoprotein Sm D3 / Like-Sm (LSM) domain containing protein, LSm4/SmD1/SmD3 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-1KX / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Small nuclear ribonucleoprotein Sm D3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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)45,2175
Polymers44,8353
Non-polymers3822
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-26 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.279, 49.061, 71.027
Angle α, β, γ (deg.)90.00, 99.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide 10-mer peptide


Mass: 1219.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesised peptide / References: UniProt: P62318*PLUS

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Non-polymers , 3 types, 579 molecules

#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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 50.09 %
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: Oct 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: 1.6→60 Å / Num. obs: 57626 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.5
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8389 / % possible all: 99.6

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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: 1.6→40.19 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8718 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2920 5.07 %random
Rwork0.1853 ---
obs0.187 57609 99.52 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.952 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 81.5 Å2 / Biso mean: 21.925 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.8217 Å2-0 Å20.4246 Å2
2---0.2362 Å20 Å2
3----0.5855 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 26 577 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063312
X-RAY DIFFRACTIONf_angle_d1.1484514
X-RAY DIFFRACTIONf_chiral_restr0.071466
X-RAY DIFFRACTIONf_plane_restr0.005592
X-RAY DIFFRACTIONf_dihedral_angle_d15.9151239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62620.3171350.289625992734100
1.6262-1.65430.29881480.271925832731100
1.6543-1.68440.3071500.26552590274099
1.6844-1.71680.29571280.243225512679100
1.7168-1.75180.26531440.22826122756100
1.7518-1.78990.24061400.21662580272099
1.7899-1.83150.27421260.20342615274199
1.8315-1.87730.25351380.19925972735100
1.8773-1.92810.24941340.193625692703100
1.9281-1.98480.22631420.18632574271699
1.9848-2.04890.23171270.19382613274099
2.0489-2.12210.21071280.1912588271699
2.1221-2.20710.22771520.18612580273299
2.2071-2.30750.22531440.184926102754100
2.3075-2.42920.19841160.18042600271699
2.4292-2.58130.21481380.188226422780100
2.5813-2.78060.20781400.18452587272799
2.7806-3.06030.21581660.18542588275499
3.0603-3.50290.20931350.163826472782100
3.5029-4.41240.1671440.14526562800100
4.4124-40.2030.20291450.179127082853100

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