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- PDB-3kpl: Crystal Structure of HLA B*4402 in complex with EEYLQAFTY a self ... -

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Basic information

Entry
Database: PDB / ID: 3kpl
TitleCrystal Structure of HLA B*4402 in complex with EEYLQAFTY a self peptide from the ABCD3 protein
Components
  • Beta-2-microglobulin
  • EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3
  • HLA class I histocompatibility antigen, B-44 alpha chain
KeywordsIMMUNE SYSTEM / HLA B*4402 / allorecognition / TCR recognition / self peptide / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I
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 / 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 / detection of bacterium / : ...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 / 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 / detection of bacterium / : / : / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / protein-folding chaperone binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma membrane / signaling receptor binding / innate immune response / focal adhesion / 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 / identical protein binding / membrane / 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 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 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsMacdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. ...Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / Jackson, D. / Brooks, A.G. / Purcell, A.W. / Kappler, J.W. / Burrows, S.R. / Rossjohn, J. / McCluskey, J.
CitationJournal: Immunity / Year: 2009
Title: T cell allorecognition via molecular mimicry.
Authors: Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / ...Authors: Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / Jackson, D. / Brooks, A.G. / Purcell, A.W. / Kappler, J.W. / Burrows, S.R. / Rossjohn, J. / McCluskey, J.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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-44 alpha chain
B: Beta-2-microglobulin
C: EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3


Theoretical massNumber of molelcules
Total (without water)44,8923
Polymers44,8923
Non-polymers00
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-18 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.790, 81.700, 109.900
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-44 alpha chain / MHC class I antigen B*44 / Bw-44


Mass: 31980.258 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, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


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 EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3


Mass: 1163.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M ammonium acetate, 20-28% PEG 4000, 0.1M Na-citrate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→46.109 Å / Num. obs: 29968 / % possible obs: 87.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.883 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 11.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.11461486165668.4
2-2.10.1256.46455396293.4
2.1-2.20.1126.95708330893.9
2.2-2.30.1057.44841275494
2.3-2.40.0978.14127231993.6
2.4-2.50.0868.83436192293
2.5-30.06511.411343618090.6
3-40.04117.38839463584.9
4-60.031214685231280.1
6-100.02322160473372.9
100.01922.640018759.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYV

1syv


Resolution: 1.96→15 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 9.143 / SU ML: 0.132 / SU R Cruickshank DPI: 0.217 / SU Rfree: 0.192 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 3001 10 %RANDOM
Rwork0.2 ---
obs0.205 29906 89.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 35.27 Å2 / Biso mean: 11.86 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.96→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 270 3437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213273
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9394450
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1725385
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.75123.352179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.64915537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1571531
X-RAY DIFFRACTIONr_chiral_restr0.080.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022595
X-RAY DIFFRACTIONr_nbd_refined0.1950.21387
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22182
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2277
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.214
X-RAY DIFFRACTIONr_mcbond_it0.6051.51998
X-RAY DIFFRACTIONr_mcangle_it0.90123131
X-RAY DIFFRACTIONr_scbond_it1.2831494
X-RAY DIFFRACTIONr_scangle_it1.9424.51319
LS refinement shellResolution: 1.96→2.009 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 195 -
Rwork0.283 1870 -
all-2065 -
obs--85.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25080.17030.4520.7672-0.03850.2793-0.0022-0.0896-0.00620.0985-0.00090.043-0.01720.01030.0031-0.0253-0.00030.0049-0.0444-0.0006-0.08344.23112.18530.741
20.28660.072-0.9150.43740.04784.93340.05650.046-0.0386-0.07860.0365-0.0711-0.2314-0.0199-0.093-0.0485-0.00590.0267-0.0222-0.0112-0.068825.54415.3572.175
32.9448-0.8782-1.11022.3110.8041.1635-0.09310.0988-0.2079-0.14410.0474-0.15780.0227-0.0760.0457-0.0274-0.02760.043-0.0772-0.0254-0.061715.327-2.65610.702
411.1027-0.68954.49030.76170.86263.62830.0684-0.6040.13070.2662-0.0990.1999-0.1979-0.19040.03060.034-0.01370.0227-0.06190.0323-0.0882-0.789513.652636.4517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION2A181 - 276
3X-RAY DIFFRACTION3B1 - 99
4X-RAY DIFFRACTION4C1 - 9

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