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- PDB-1kpr: The human non-classical major histocompatibility complex molecule... -

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Basic information

Entry
Database: PDB / ID: 1kpr
TitleThe human non-classical major histocompatibility complex molecule HLA-E
Components
  • BETA-2-MICROGLOBULINBeta-2 microglobulin
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
  • Peptide VMAPRTVLL
KeywordsIMMUNE SYSTEM / HLA-E / MHC / non-classical MHC / HLA / BETA 2 MICROGLOBULIN
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 tumor necrosis factor production / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion
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
HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid-body refinement of 1MHE / Resolution: 2.8 Å
AuthorsHolmes, M.A. / Strong, R.K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: HLA-E allelic variants: Correlating differential expression, peptide affinities, crystal structures and thermal stabilities
Authors: Strong, R.K. / Holmes, M.A. / Li, P. / Braun-Jones, L. / Lee, N. / Geraghty, D.E.
History
DepositionJan 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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, ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
P: Peptide VMAPRTVLL
Q: Peptide VMAPRTVLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8797
Polymers88,7826
Non-polymers961
Water0
1
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
P: Peptide VMAPRTVLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4874
Polymers44,3913
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-37 kcal/mol
Surface area18200 Å2
MethodPISA
2
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
Q: Peptide VMAPRTVLL


Theoretical massNumber of molelcules
Total (without water)44,3913
Polymers44,3913
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-25 kcal/mol
Surface area18070 Å2
MethodPISA
3
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
P: Peptide VMAPRTVLL
Q: Peptide VMAPRTVLL
hetero molecules

A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN
D: BETA-2-MICROGLOBULIN
P: Peptide VMAPRTVLL
Q: Peptide VMAPRTVLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,75714
Polymers177,56512
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area25050 Å2
ΔGint-135 kcal/mol
Surface area65330 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-65 kcal/mol
Surface area34020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.700, 178.700, 88.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN, ALPHA CHAIN / HLA-E heavy chain / major histocompatibility complex / class I / E / HLA-E class I protein / ALPHA ...HLA-E heavy chain / major histocompatibility complex / class I / E / HLA-E class I protein / ALPHA CHAIN OF MHC COMPLEX CLASS I


Mass: 31511.596 Da / Num. of mol.: 2 / Mutation: R107G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E / Production host: Escherichia coli (E. coli) / Strain (production host): UBS / References: UniProt: P13747
#2: Protein BETA-2-MICROGLOBULIN / Beta-2 microglobulin / beta 2-microglobulin / BETA CHAIN OF MHC COMPLEX CLASS I


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide Peptide VMAPRTVLL


Mass: 1000.278 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 4.58 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG 400, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.2 Mammonium sulfate1reservoir
22 %PEG4001reservoir
3100 mMTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 39992 / Num. obs: 38312 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 83.3 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3850 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 299482
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97.3 % / Mean I/σ(I) obs: 3.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
RefinementMethod to determine structure: rigid-body refinement of 1MHE
Starting model: pdb entry 1MHE

1mhe


Resolution: 2.8→20 Å / Isotropic thermal model: isotropic group B's / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.289 3672 10 %random
Rwork0.235 ---
all-36586 --
obs-32914 --
Displacement parametersBiso mean: 63.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.49 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6205 0 5 0 6210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.028
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d1.6
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection
Rfree0.404 319
Rwork0.362 3066
obs-3385
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.6

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