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

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Basic information

Entry
Database: PDB / ID: 3bze
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, alpha chain G
KeywordsIMMUNE SYSTEM / MHC fold / Transmembrane / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / 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 ...peripheral B cell tolerance induction / positive regulation of tolerance induction / immune response-inhibiting cell surface receptor signaling pathway / negative regulation of dendritic cell differentiation / 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 / negative regulation of T cell mediated cytotoxicity / cis-Golgi network membrane / negative regulation of immune response / positive regulation of T cell tolerance induction / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / negative regulation of G0 to G1 transition / negative regulation of natural killer cell mediated cytotoxicity / filopodium membrane / positive regulation of macrophage cytokine production / positive regulation of regulatory T cell differentiation / 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 immunoglobulin production / CD8 receptor binding / positive regulation of interleukin-4 production / protein homotrimerization / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein 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 / positive regulation of endothelial cell apoptotic process / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of interleukin-12 production / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of receptor binding / early endosome lumen / negative regulation of angiogenesis / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / 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 / 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 / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / 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 / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding
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, alpha chain E / HLA class I histocompatibility antigen, alpha chain G / 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: Advisory / 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 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, alpha chain E
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen, alpha chain E
F: Beta-2-microglobulin
G: HLA class I histocompatibility antigen, alpha chain E
H: Beta-2-microglobulin
P: leader peptide of HLA class I histocompatibility antigen, alpha chain G
Q: leader peptide of HLA class I histocompatibility antigen, alpha chain G
R: leader peptide of HLA class I histocompatibility antigen, alpha chain G
S: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)178,27412
Polymers178,27412
Non-polymers00
Water3,873215
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
P: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)44,5683
Polymers44,5683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-27 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, alpha chain G


Theoretical massNumber of molelcules
Total (without water)44,5683
Polymers44,5683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-30 kcal/mol
Surface area18700 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, alpha chain E
F: Beta-2-microglobulin
R: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)44,5683
Polymers44,5683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-28 kcal/mol
Surface area18620 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, alpha chain E
H: Beta-2-microglobulin
S: leader peptide of HLA class I histocompatibility antigen, alpha chain G


Theoretical massNumber of molelcules
Total (without water)44,5683
Polymers44,5683
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.778, 73.354, 131.535
Angle α, β, γ (deg.)90.00, 112.70, 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: 31640.803 Da / Num. of mol.: 4 / Fragment: residues 2-274
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: 11879.356 Da / Num. of mol.: 4
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, alpha chain G / HLA G antigen


Mass: 1048.321 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / References: UniProt: P17693
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 14-19% PEG 3350, 2% MPD, 0.2M MgCl2, 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: 63040 / Rmerge(I) obs: 0.052 / Net I/σ(I): 21.6

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Processing

SoftwareName: REFMAC / Version: 5.2.0005 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MHE

1mhe


Resolution: 2.5→15 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.882 / SU B: 29.343 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.743 / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29625 3180 5.1 %RANDOM
Rwork0.24216 ---
obs0.2449 59588 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.048 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20.35 Å2
2--0.69 Å20 Å2
3----3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12529 0 0 215 12744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.02112843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9041.93117452
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.78451505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.123.29687
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.737152078
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.24115108
X-RAY DIFFRACTIONr_chiral_restr0.1030.21798
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0210114
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3380.26529
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3420.28714
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3250.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5170.2137
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.630.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6451.57752
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.029212272
X-RAY DIFFRACTIONr_scbond_it6.42935846
X-RAY DIFFRACTIONr_scangle_it9.1154.55180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.501→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 235 -
Rwork0.369 4156 -
obs--96 %
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)
11.75360.1344-0.71690.9557-0.38873.0807-0.101-0.0588-0.10950.17550.0290.0722-0.0183-0.41690.072-0.1634-0.0069-0.0267-0.0850.0005-0.13645.61952.526617.814
23.22120.8835-0.47262.6718-2.13296.72190.0826-0.2547-0.43760.262-0.1317-0.11210.36950.03170.0491-0.1078-0.0298-0.0385-0.08370.0151-0.11514.2119-5.876532.8802
30.9112-0.3132-2.41340.97390.494610.05540.02310.1474-0.03630.3317-0.07720.1419-0.4155-0.56780.05410.0094-0.0871-0.0419-0.1912-0.06010.088327.856726.829424.6947
46.85853.1342-1.84844.6078-2.47658.37680.0891-0.39270.55460.2384-0.1661-0.0445-0.32010.36440.0769-0.1446-0.07810.0139-0.1357-0.1234-0.069845.269533.100220.0839
52.89180.3003-1.40421.1920.09615.2086-0.06760.3489-0.1066-0.1416-0.0672-0.00430.4153-0.42540.1348-0.08970.08390.00490.01950.0284-0.0898-27.640965.590391.5365
65.89211.7275-1.54674.2121-1.774810.6618-0.05091.09660.8864-0.48680.0589-0.0624-0.91370.0082-0.008-0.0170.0950.02890.14940.15330.016-16.529378.083481.9935
72.1975-0.1271-0.75781.48390.30242.52080.1092-0.0869-0.01090.0855-0.02460.4497-0.0277-0.5337-0.0846-0.0834-0.0427-0.0376-0.190.00860.0398.970439.133172.4654
89.22581.1859-3.70892.8315-0.89915.3003-0.0149-1.1267-1.03450.46350.12450.86860.6667-0.4346-0.10960.1301-0.10080.05390.06260.22190.27838.086425.644685.859
912.26132.5613-2.2062.08690.09412.0644-0.46990.38720.356-0.3890.1550.20310.0055-0.30930.3149-0.2621-0.0093-0.034-0.1204-0.0219-0.237613.22052.1032-0.0176
101.6961-0.1324-3.75955.58878.439320.2281-1.20180.04890.00560.47120.25440.7629-1.1298-2.59990.94740.0083-0.0230.00850.023-0.08130.030420.569727.823443.0908
114.5155-1.36524.32760.466-2.250520.80720.8522-0.8309-0.6068-0.1433-0.06070.61781.2409-1.1362-0.7915-0.0143-0.0627-0.033-0.01580.0497-0.0699-31.897767.3896110.091
120.3965-1.4916-0.11085.61180.4170.0311.1152-0.0117-0.6926-0.4448-0.5444-0.0814-0.2173-0.5723-0.57080.0403-0.2174-0.1344-0.01690.1443-0.038518.2636.271155.1783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1801 - 179
2X-RAY DIFFRACTION1AA181 - 274180 - 273
3X-RAY DIFFRACTION2BB1 - 992 - 100
4X-RAY DIFFRACTION3CC2 - 1801 - 179
5X-RAY DIFFRACTION3CC181 - 274180 - 273
6X-RAY DIFFRACTION4DD1 - 992 - 100
7X-RAY DIFFRACTION5EE2 - 1801 - 179
8X-RAY DIFFRACTION5EE181 - 274180 - 273
9X-RAY DIFFRACTION6FF1 - 992 - 100
10X-RAY DIFFRACTION7GG2 - 1801 - 179
11X-RAY DIFFRACTION7GG181 - 274180 - 273
12X-RAY DIFFRACTION8HH1 - 992 - 100
13X-RAY DIFFRACTION9PI1 - 91 - 9
14X-RAY DIFFRACTION10QJ1 - 91 - 9
15X-RAY DIFFRACTION11RK1 - 91 - 9
16X-RAY DIFFRACTION12SL1 - 91 - 9

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