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- PDB-3x11: Crystal structure of HLA-B*57:01.I80N.L82R.R83G -

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Basic information

Entry
Database: PDB / ID: 3x11
TitleCrystal structure of HLA-B*57:01.I80N.L82R.R83G
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-57 alpha chain
  • Ig kappa chain C region
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Immunity / Antigen presentation / Immune receptors LILRs / TCRs / KIRs / plasma membrane
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / regulation of interleukin-6 production / Classical antibody-mediated complement activation / Initial triggering of complement / TAP binding / immunoglobulin mediated immune response / protection from natural killer cell mediated cytotoxicity / FCGR activation / 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 / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / detection of bacterium / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / secretory granule membrane / negative regulation of receptor binding / Regulation of Complement cascade / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Cell surface interactions at the vascular wall / Endosomal/Vacuolar pathway / B cell receptor signaling pathway / lumenal side of endoplasmic reticulum membrane / FCGR3A-mediated phagocytosis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / FCERI mediated MAPK activation / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / Regulation of actin dynamics for phagocytic cup formation / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / FCERI mediated NF-kB activation / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / blood microparticle / amyloid fibril formation / Potential therapeutics for SARS / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation
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 / Resolution: 2.15 Å
AuthorsVivian, J.P. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2015
Title: The interaction of KIR3DL1*001 with HLA class I molecules is dependent upon molecular microarchitecture within the Bw4 epitope
Authors: Saunders, P.M. / Vivian, J.P. / Baschuk, N. / Beddoe, T. / Widjaja, J. / O'Connor, G.M. / Hitchen, C. / Pymm, P. / Andrews, D.M. / Gras, S. / McVicar, D.W. / Rossjohn, J. / Brooks, A.G.
History
DepositionOct 24, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Nov 8, 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: HLA class I histocompatibility antigen, B-57 alpha chain
B: Beta-2-microglobulin
C: Ig kappa chain C region


Theoretical massNumber of molelcules
Total (without water)44,3953
Polymers44,3953
Non-polymers00
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-19 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.446, 81.097, 108.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31681.012 Da / Num. of mol.: 1
Fragment: HLA-B*57:01 extracellular domain, UNP residues 25-300
Mutation: I80N. L82R. R83G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLA-B*57:01, HLAB / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P18465, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, beta-2-microglobulin, CDABP0092, HDCMA22P / Plasmid: pET-30 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Ig kappa chain C region


Mass: 966.109 Da / Num. of mol.: 1 / Fragment: UNP residues 93-101 / Source method: obtained synthetically / Details: Human peptide synthetically generated / Source: (synth.) Homo sapiens (human) / References: UniProt: P01834
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 12-20% PEG4000, 0.2M ammonium acetate, 0.1M tri-sodium citrate pH 5.4., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9546 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 5, 2012
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9546 Å / Relative weight: 1
ReflectionResolution: 2.14→45.1 Å / Num. obs: 25262 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.6 % / Biso Wilson estimate: 31.89 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.1
Reflection shellResolution: 2.14→2.23 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.1 / Num. unique all: 34827 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RFX

2rfx


Resolution: 2.15→45 Å / Cor.coef. Fo:Fc: 0.9073 / Cor.coef. Fo:Fc free: 0.8791 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1287 5.09 %RANDOM
Rwork0.1881 ---
obs0.1902 25262 --
Displacement parametersBiso mean: 35.41 Å2
Baniso -1Baniso -2Baniso -3
1-10.6601 Å20 Å20 Å2
2--7.7835 Å20 Å2
3----18.4436 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: LAST / Resolution: 2.15→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3107 0 0 236 3343
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013202HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084357HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1087SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes87HARMONIC2
X-RAY DIFFRACTIONt_gen_planes468HARMONIC5
X-RAY DIFFRACTIONt_it3202HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion17.29
X-RAY DIFFRACTIONt_chiral_improper_torsion400SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3717SEMIHARMONIC4
LS refinement shellResolution: 2.15→2.23 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2612 158 5.64 %
Rwork0.2324 2643 -
all0.234 2801 -

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