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- PDB-3bzf: The human non-classical major histocompatibility complex molecule... -

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Basic information

Entry
Database: PDB / ID: 3bzf
TitleThe human non-classical major histocompatibility complex molecule HLA-E
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain
KeywordsIMMUNE SYSTEM / MHC fold / Glycoprotein / Immune response / Membrane / MHC I / Polymorphism / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Host-virus interaction / Ubl conjugation
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 lectin-like receptor binding / natural killer cell tolerance induction / 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 lectin-like receptor binding / natural killer cell tolerance induction / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / 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 CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein binding / 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 / T cell receptor binding / negative regulation of T cell proliferation / : / : / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of tumor necrosis factor production / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / receptor ligand activity / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane
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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, C alpha chain / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHoare, H.L. / Sullivan, L.C. / Ely, L.K. / Beddoe, T. / Henderson, K.N. / Lin, J. / Clements, C.S. / Reid, H.H. / Brooks, A.G. / Rossjohn, J.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Subtle changes in peptide conformation profoundly affect recognition of the non-classical MHC class I molecule HLA-E by the CD94-NKG2 natural killer cell receptors
Authors: Hoare, H.L. / Sullivan, L.C. / Clements, C.S. / Ely, L.K. / Beddoe, T. / Henderson, K.N. / Lin, J. / Reid, H.H. / Brooks, A.G. / Rossjohn, J.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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, alpha chain E
B: Beta-2-microglobulin
P: leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
Q: leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain


Theoretical massNumber of molelcules
Total (without water)88,8316
Polymers88,8316
Non-polymers00
Water4,504250
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
P: leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,4153
Polymers44,4153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-24 kcal/mol
Surface area18740 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
Q: leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,4153
Polymers44,4153
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-23 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.520, 62.301, 98.769
Angle α, β, γ (deg.)90.00, 106.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E


Mass: 31924.148 Da / Num. of mol.: 2 / Fragment: residues 1-276
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein Beta-2-microglobulin


Mass: 11506.874 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide leader peptide of HLA class I histocompatibility antigen, Cw-7 alpha chain / MHC class I antigen Cw*7


Mass: 984.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P10321
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 19% PEG 3350, 0.3M NaCl, 0.1M Tris, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32033 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.565 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2065

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHE

1mhe


Resolution: 2.5→29.6 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.888 / SU B: 11.12 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26936 1620 5.1 %RANDOM
Rwork0.20018 ---
obs0.20374 30365 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.031 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-2.55 Å2
2---1.94 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6266 0 0 250 6516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0340.0216460
X-RAY DIFFRACTIONr_bond_other_d0.0080.024424
X-RAY DIFFRACTIONr_angle_refined_deg2.3541.9318782
X-RAY DIFFRACTIONr_angle_other_deg1.2643.00210650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9175761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08123.353346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.711554
X-RAY DIFFRACTIONr_chiral_restr0.1530.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.027259
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021401
X-RAY DIFFRACTIONr_nbd_refined0.2530.21572
X-RAY DIFFRACTIONr_nbd_other0.2540.24966
X-RAY DIFFRACTIONr_nbtor_refined0.2090.23094
X-RAY DIFFRACTIONr_nbtor_other0.1080.23585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2307
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0530.24
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.25234694
X-RAY DIFFRACTIONr_mcbond_other1.06531530
X-RAY DIFFRACTIONr_mcangle_it4.76556190
X-RAY DIFFRACTIONr_scbond_it6.82473110
X-RAY DIFFRACTIONr_scangle_it6.884102592
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
Rfree0.368 132 -
Rwork0.291 2065 -
obs--92.74 %

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