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- PDB-3kpp: Crystal Structure of HLA B*4405 in complex with EEYLQAFTY a self ... -

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Basic information

Entry
Database: PDB / ID: 3kpp
TitleCrystal Structure of HLA B*4405 in complex with EEYLQAFTY a self peptide from the ABCD3 protein
Components
  • Beta-2-microglobulinBeta-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*4405 / allorecognition / TCR recognition / self peptide / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane
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 / 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 / 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 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 / 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 / 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 / positive regulation of immune response / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Modulation by Mtb of host immune system / 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 / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / 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
DI(HYDROXYETHYL)ETHER / 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: 1.9 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3Sep 6, 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

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1525
Polymers44,9403
Non-polymers2122
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-13 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.640, 81.620, 109.650
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: 32028.348 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 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
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 / Date: Jan 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→65.51 Å / Num. obs: 36594 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.147 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 19.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-20.4156532785149100
2-2.10.3038.1434364205100
2.1-2.20.23810.1361603487100
2.2-2.30.211.9301152910100
2.3-2.50.1641446869451899.9
2.5-2.60.13416.8183821773100
2.6-2.70.1218.6156371517100
2.7-30.09122.3357403465100
3-40.05335.9553925423100
4-50.03846.3198391977100
5-60.04742.48613882100
6-100.05142.79323992100
100.04345.5239529697.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1syv


Resolution: 1.9→65.51 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.176 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.853 / SU B: 6.931 / SU ML: 0.106 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1830 5 %RANDOM
Rwork0.186 ---
obs0.188 36594 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.21 Å2 / Biso mean: 20.42 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.72 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 14 497 3682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213419
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9414658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0025411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.07123.085188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99815564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9081536
X-RAY DIFFRACTIONr_chiral_restr0.0840.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022744
X-RAY DIFFRACTIONr_nbd_refined0.190.21669
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22319
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2448
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.227
X-RAY DIFFRACTIONr_mcbond_it0.6141.52066
X-RAY DIFFRACTIONr_mcangle_it1.02523275
X-RAY DIFFRACTIONr_scbond_it1.48631564
X-RAY DIFFRACTIONr_scangle_it2.2644.51383
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 132 -
Rwork0.258 2554 -
all-2686 -
obs--100 %
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)
10.85660.1038-0.23180.34350.01450.15170.006-0.03310.00880.0527-0.0042-0.01960.0019-0.0084-0.0017-0.0318-0.0011-0.0011-0.0446-0.0023-0.0281-4.292-12.35530.542
20.10240.05550.54520.19920.40162.9689-0.03920.01650.0549-0.04740.02460.07820.0110.0480.0146-0.0424-0.018-0.0185-0.02550.0112-0.0376-25.334-15.2142.238
31.8495-0.61240.99791.3872-0.56160.872-0.0920.13820.1666-0.048-0.0170.095-0.00110.09370.109-0.0391-0.0162-0.0401-0.0580.036-0.0208-15.0912.24610.857
43.37290.4693-1.60820.0653-0.22081.95010.0023-0.0935-0.33980.2019-0.0598-0.05230.09250.05180.0574-0.00370.00660.0061-0.0840.0210.03630.572-13.82236.355
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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