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- PDB-3upr: HLA-B*57:01 complexed to pep-V and Abacavir -

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Basic information

Entry
Database: PDB / ID: 3upr
TitleHLA-B*57:01 complexed to pep-V and Abacavir
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • pep-V
KeywordsIMMUNE SYSTEM / HLA-B*57:01 / MHC / antigen presenting cell / T-cell receptor / human leukocyte antigen / drug hypersensitivity / abacavir hypersensitivity / repertoire-altering small molecule / immune response / Immunoglobulin-like beta-sandwich
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / 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 / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å
AuthorsPompeu, Y.A. / Ostrov, D.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire.
Authors: Ostrov, D.A. / Grant, B.J. / Pompeu, Y.A. / Sidney, J. / Harndahl, M. / Southwood, S. / Oseroff, C. / Lu, S. / Jakoncic, J. / de Oliveira, C.A. / Yang, L. / Mei, H. / Shi, L. / Shabanowitz, ...Authors: Ostrov, D.A. / Grant, B.J. / Pompeu, Y.A. / Sidney, J. / Harndahl, M. / Southwood, S. / Oseroff, C. / Lu, S. / Jakoncic, J. / de Oliveira, C.A. / Yang, L. / Mei, H. / Shi, L. / Shabanowitz, J. / English, A.M. / Wriston, A. / Lucas, A. / Phillips, E. / Mallal, S. / Grey, H.M. / Sette, A. / Hunt, D.F. / Buus, S. / Peters, B.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2012Group: Database references
Revision 1.2Sep 13, 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
P: pep-V
B: Beta-2-microglobulin
Q: pep-V
C: HLA class I histocompatibility antigen, B-57 alpha chain
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,96110
Polymers89,3186
Non-polymers6444
Water7,782432
1
A: HLA class I histocompatibility antigen, B-57 alpha chain
P: pep-V
B: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9815
Polymers44,6593
Non-polymers3222
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-27 kcal/mol
Surface area18800 Å2
MethodPISA
2
Q: pep-V
C: HLA class I histocompatibility antigen, B-57 alpha chain
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9815
Polymers44,6593
Non-polymers3222
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-25 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.751, 131.412, 88.340
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE MAIN BIOLOGICAL UNIT IS COMPOSED BY A HETERODIMER CONSISTING OF A SINGLE HEAVY CHAIN (HLA-B*57-01) AND A SINGLE LIGHT CHAIN (BETA2-MICROGLOBULIN)

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 31867.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P18465, UniProt: P01889*PLUS
#3: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules PQ

#2: Protein/peptide pep-V


Mass: 1043.236 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 3 types, 436 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.: 2 / Source method: obtained synthetically / Formula: C14H18N6O / Comment: medication, inhibitor*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M NaCacodylate, 0.1MNaAcetate, 25%PEG 8,000, 15% Glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 15, 2011
RadiationMonochromator: Si(111) with Toroidal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 68342 / Num. obs: 64925 / % possible obs: 95 % / Observed criterion σ(I): 1 / Rsym value: 0.09 / Net I/σ(I): 22.84
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2605 / Rsym value: 0.48 / % possible all: 77

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2rfx

2rfx


Resolution: 1.999→28.534 Å / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 31.06 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2278 3069 5.15 %
Rwork0.1874 --
obs0.1894 64671 96.85 %
all-66775 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.612 Å2 / ksol: 0.363 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.3752 Å2-0 Å2-2.755 Å2
2--6.7064 Å2-0 Å2
3----2.3312 Å2
Refinement stepCycle: LAST / Resolution: 1.999→28.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6272 0 44 432 6748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046516
X-RAY DIFFRACTIONf_angle_d0.7958855
X-RAY DIFFRACTIONf_dihedral_angle_d13.9092411
X-RAY DIFFRACTIONf_chiral_restr0.058911
X-RAY DIFFRACTIONf_plane_restr0.0041157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9992-2.03370.33721240.29142467X-RAY DIFFRACTION73
2.0337-2.07070.28111320.27732633X-RAY DIFFRACTION80
2.0707-2.11050.33221540.27082912X-RAY DIFFRACTION87
2.1105-2.15350.34491540.26253005X-RAY DIFFRACTION91
2.1535-2.20040.27071600.25673143X-RAY DIFFRACTION95
2.2004-2.25150.27841660.25713151X-RAY DIFFRACTION95
2.2515-2.30780.31641670.23983148X-RAY DIFFRACTION95
2.3078-2.37020.30531640.24453184X-RAY DIFFRACTION95
2.3702-2.43990.24891690.23893140X-RAY DIFFRACTION95
2.4399-2.51860.26241660.23913158X-RAY DIFFRACTION95
2.5186-2.60850.27291640.22453173X-RAY DIFFRACTION95
2.6085-2.71290.26911630.22583125X-RAY DIFFRACTION95
2.7129-2.83620.32381640.21153185X-RAY DIFFRACTION95
2.8362-2.98560.24271690.20183169X-RAY DIFFRACTION95
2.9856-3.17240.23731640.18493158X-RAY DIFFRACTION95
3.1724-3.4170.21071680.16483146X-RAY DIFFRACTION94
3.417-3.76010.21251680.14383143X-RAY DIFFRACTION94
3.7601-4.30250.17361660.12873124X-RAY DIFFRACTION94
4.3025-5.41410.15651680.12543156X-RAY DIFFRACTION94
5.4141-27.88710.19691690.18233125X-RAY DIFFRACTION92

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