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- PDB-3kpo: Crystal Structure of HLA B*4403 in complex with EEYLKAWTF, a mimotope -

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Basic information

Entry
Database: PDB / ID: 3kpo
TitleCrystal Structure of HLA B*4403 in complex with EEYLKAWTF, a mimotope
Components
  • Beta-2-microglobulin
  • EEYLKAWTF, mimotope peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / HLA B*4403 / allorecognition / TCR recognition / mimotope peptide / Immune response / MHC I / Membrane / 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 / antigen processing and presentation / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / antigen processing and presentation / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / 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 / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / innate immune response / signaling receptor binding / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / HLA class I histocompatibility antigen B alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 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: MHC class I antigen
B: Beta-2-microglobulin
C: EEYLKAWTF, mimotope peptide


Theoretical massNumber of molelcules
Total (without water)45,0453
Polymers45,0453
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-22 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 81.850, 109.960
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 MHC class I antigen / Major histocompatibility complex / class I / B


Mass: 31978.328 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, DAMA-387C9.2-001 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2L6G2, UniProt: P01889*PLUS
#2: Protein 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, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#3: Protein/peptide EEYLKAWTF, mimotope peptide


Mass: 1187.319 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 51.59 %
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: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40.93 Å / Num. obs: 21033 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.328 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 18.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.40.4254.917529246699.7
2.4-2.50.3435.914785208299.7
2.5-2.60.292712794179699.8
2.6-2.70.2518.410879155399.9
2.7-30.17511.224882348799.9
3-40.0772438341546199.8
4-50.03742.214082199799.9
5-60.03839.66238895100
6-100.031436755998100
100.02150168629897.1

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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: 2.3→40.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.18 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.819 / SU B: 14.499 / SU ML: 0.183 / SU R Cruickshank DPI: 0.345 / SU Rfree: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1028 4.9 %RANDOM
Rwork0.2 ---
obs0.203 21030 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 45.47 Å2 / Biso mean: 23 Å2 / Biso min: 7.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---1.13 Å20 Å2
3---1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3177 0 0 203 3380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213316
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.9394510
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.875392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9323.128179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.50215551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5911533
X-RAY DIFFRACTIONr_chiral_restr0.0970.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022627
X-RAY DIFFRACTIONr_nbd_refined0.1990.21335
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.213
X-RAY DIFFRACTIONr_mcbond_it0.6311.52021
X-RAY DIFFRACTIONr_mcangle_it1.07723172
X-RAY DIFFRACTIONr_scbond_it1.59531518
X-RAY DIFFRACTIONr_scangle_it2.4514.51338
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 77 -
Rwork0.255 1441 -
all-1518 -
obs--99.48 %
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)
10.891-0.1270.26860.55560.02550.215-0.01610.0444-0.0012-0.05610.0127-0.0306-0.0189-0.00530.0034-0.0171-0.00060.0137-0.0515-0.0028-0.023-4.21912.368-30.768
20.40820.1379-0.46120.16910.39042.95620.0123-0.0198-0.065-0.00430.01950.0088-0.1526-0.0178-0.0318-0.02530.02870.0211-0.05580.0152-0.0008-25.56315.265-2.424
31.59580.5837-0.44771.3361-0.47350.6653-0.0565-0.0324-0.10630.0990.06030.0260.0074-0.0006-0.0039-0.0290.01560.0321-0.06370.0251-0.0167-15.131-2.219-10.845
49.59852.06973.4590.53630.19874.5717-0.31870.39580.3061-0.01010.3804-0.2567-0.140.1316-0.06170.01650.01-0.0084-0.115-0.09320.13320.117214.1956-37.002
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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