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- PDB-2rfx: Crystal Structure of HLA-B*5701, presenting the self peptide, LSS... -

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Basic information

Entry
Database: PDB / ID: 2rfx
TitleCrystal Structure of HLA-B*5701, presenting the self peptide, LSSPVTKSF
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • LSSPVTKSF
KeywordsIMMUNE SYSTEM / alpha beta sandwich-immunologlobulin like / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


regulation of interleukin-12 production / CD22 mediated BCR regulation / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Fc epsilon receptor (FCERI) signaling / IgG immunoglobulin complex / Classical antibody-mediated complement activation / immunoglobulin mediated immune response / protection from natural killer cell mediated cytotoxicity ...regulation of interleukin-12 production / CD22 mediated BCR regulation / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Fc epsilon receptor (FCERI) signaling / IgG immunoglobulin complex / Classical antibody-mediated complement activation / immunoglobulin mediated immune response / protection from natural killer cell mediated cytotoxicity / FCGR activation / TAP binding / Role of LAT2/NTAL/LAB on calcium mobilization / detection of bacterium / Role of phospholipids in phagocytosis / 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 / Scavenging of heme from plasma / antigen binding / beta-2-microglobulin binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of T cell mediated cytotoxicity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / secretory granule membrane / B cell receptor signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / Cell surface interactions at the vascular wall / Endosomal/Vacuolar pathway / FCGR3A-mediated phagocytosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / defense response / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / Regulation of actin dynamics for phagocytic cup formation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / FCERI mediated NF-kB activation / sensory perception of smell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / blood microparticle / Potential therapeutics for SARS / amyloid fibril formation / protein homotetramerization / Initial triggering of complement / intracellular iron ion homeostasis / adaptive immune response / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / signaling receptor binding / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
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, 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
Immunoglobulin kappa constant / 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: 2.5 Å
AuthorsArchbold, J.K. / Macdonald, W.A. / Rossjohn, J. / McCluskey, J.
CitationJournal: Immunity / Year: 2008
Title: Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity
Authors: Chessman, D. / Kostenko, L. / Lethborg, T. / Purcell, A.W. / Williamson, N.A. / Chen, Z. / Kjer-Nielsen, L. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Almeida, C.A. / Nolan, D. / ...Authors: Chessman, D. / Kostenko, L. / Lethborg, T. / Purcell, A.W. / Williamson, N.A. / Chen, Z. / Kjer-Nielsen, L. / Mifsud, N.A. / Tait, B.D. / Holdsworth, R. / Almeida, C.A. / Nolan, D. / Macdonald, W.A. / Archbold, J.K. / Kellerher, A.D. / Marriott, D. / Mallal, S. / Bharadwaj, M. / Rossjohn, J. / McCluskey, J.
History
DepositionOct 2, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-57 alpha chain
B: Beta-2-microglobulin
C: LSSPVTKSF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7227
Polymers44,3533
Non-polymers3684
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-21 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.844, 49.029, 70.666
Angle α, β, γ (deg.)90.00, 100.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, B-57 alpha chain / HLA-B*5701 heavy chain / MHC class I antigen B*57 / Bw-57


Mass: 31639.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide LSSPVTKSF


Mass: 966.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / References: UniProt: P01834*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.49 Å3/Da / Density % sol: 50.57 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→60 Å / Num. obs: 15096 / % possible obs: 94.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.1 / % possible all: 89.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2H6P

2h6p


Resolution: 2.5→27.48 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 19.763 / SU ML: 0.229 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.794 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26845 735 5 %RANDOM
Rwork0.20948 ---
obs0.21239 13978 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.131 Å2
Baniso -1Baniso -2Baniso -3
1-2.64 Å20 Å20.86 Å2
2---1.52 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 24 185 3336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9414523
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55323.073179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54915549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1781534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2461
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022634
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1810.21365
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.22173
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2711.52018
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.46523176
X-RAY DIFFRACTIONr_scbond_it0.68331520
X-RAY DIFFRACTIONr_scangle_it1.1594.51338
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 41 -
Rwork0.243 961 -
obs--89.07 %
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)
12.05761.11280.64553.81670.56165.0736-0.10680.1063-0.0095-0.10010.1320.29490.2584-0.3302-0.0251-0.2841-0.02140.076-0.17410.0361-0.119310.0843-13.816937.3513
25.99561.5833-5.96872.0635-1.09419.1327-0.1871-0.2221-0.53470.0705-0.162-0.35320.46660.26140.3491-0.01860.031-0.0434-0.17060.0211-0.113523.3569-16.87853.8958
32.2388-0.26732.55093.4106-0.648410.2808-0.0680.32670.1737-0.59370.08960.4727-0.3258-0.3968-0.0216-0.063-0.0289-0.0127-0.10380.0621-0.060111.1741-0.91313.8619
44.6599-2.44181.02852.3265-2.4383.6716-0.16050.05780.39230.41050.17350.3050.2534-0.1531-0.013-0.0742-0.00390.0843-0.0761-0.0322-0.06988.8824-14.211444.5448
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION2AA181 - 275181 - 275
3X-RAY DIFFRACTION3BB1 - 991 - 99
4X-RAY DIFFRACTION4CC1 - 91 - 9

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