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- PDB-7p4b: HLA-E*01:03 in complex with IL9 -

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Basic information

Entry
Database: PDB / ID: 7p4b
TitleHLA-E*01:03 in complex with IL9
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • ESAT-6-like protein EsxH
  • HLA class I histocompatibility antigen, alpha chain E
KeywordsIMMUNE SYSTEM / HLA-E MHC
Function / homology
Function and homology information


Inhibition of membrane repair / phagocytic vesicle lumen / 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 ...Inhibition of membrane repair / phagocytic vesicle lumen / 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 CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding / beta-2-microglobulin binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / Prevention of phagosomal-lysosomal fusion / 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 / positive regulation of receptor binding / early endosome lumen / 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 / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of tumor necrosis factor production / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / 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 / external side of plasma membrane / endoplasmic reticulum lumen
Similarity search - Function
ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...ESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
PHOSPHATE ION / HLA class I histocompatibility antigen, alpha chain E / Beta-2-microglobulin / ESAT-6-like protein EsxH
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsWalters, L.C. / Gillespie, G.M.
Funding support1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation
CitationJournal: Cell Rep / Year: 2022
Title: Primary and secondary functions of HLA-E are determined by stability and conformation of the peptide-bound complexes.
Authors: Walters, L.C. / Rozbesky, D. / Harlos, K. / Quastel, M. / Sun, H. / Springer, S. / Rambo, R.P. / Mohammed, F. / Jones, E.Y. / McMichael, A.J. / Gillespie, G.M.
History
DepositionJul 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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 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: ESAT-6-like protein EsxH
Q: ESAT-6-like protein EsxH
R: ESAT-6-like protein EsxH
Z: ESAT-6-like protein EsxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,34741
Polymers179,66312
Non-polymers2,68429
Water19,9791109
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
P: ESAT-6-like protein EsxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2967
Polymers44,9163
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-57 kcal/mol
Surface area19080 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
Q: ESAT-6-like protein EsxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,94514
Polymers44,9163
Non-polymers1,02911
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-68 kcal/mol
Surface area18710 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, alpha chain E
F: Beta-2-microglobulin
R: ESAT-6-like protein EsxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2687
Polymers44,9163
Non-polymers3534
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-61 kcal/mol
Surface area18630 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, alpha chain E
H: Beta-2-microglobulin
Z: ESAT-6-like protein EsxH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,83813
Polymers44,9163
Non-polymers92210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-102 kcal/mol
Surface area19090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)244.562, 48.529, 153.161
Angle α, β, γ (deg.)90.000, 116.948, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11E-301-

ZN

21G-302-

ZN

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 31921.121 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia (bacteria) / References: UniProt: P13747
#2: Protein
Beta-2-microglobulin / 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) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia (bacteria) / References: UniProt: P61769

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Protein/peptide , 1 types, 4 molecules PQRZ

#3: Protein/peptide
ESAT-6-like protein EsxH / 10 kDa antigen CFP7 / CFP-7 / Low molecular weight protein antigen 7 / Protein TB10.4


Mass: 1115.365 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: esxH, cfp7, Rv0288, MTV035.16 / Production host: Escherichia (bacteria) / References: UniProt: P9WNK3

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Non-polymers , 5 types, 1138 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1109 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / Details: 2.2 M AS 0.1 M MES pH 5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.72→114.03 Å / Num. obs: 171397 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 22.93 Å2 / CC1/2: 1 / Net I/σ(I): 8.1
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 8228 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH1

6gh1


Resolution: 1.72→75.18 Å / SU ML: 0.2346 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5796
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2371 8627 5.04 %
Rwork0.2007 162635 -
obs0.2026 171262 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.57 Å2
Refinement stepCycle: LAST / Resolution: 1.72→75.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12510 0 159 1109 13778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313066
X-RAY DIFFRACTIONf_angle_d0.615817744
X-RAY DIFFRACTIONf_chiral_restr0.04381798
X-RAY DIFFRACTIONf_plane_restr0.00352309
X-RAY DIFFRACTIONf_dihedral_angle_d19.93624774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.740.3642520.34355171X-RAY DIFFRACTION94.74
1.74-1.760.34262690.32525351X-RAY DIFFRACTION99.84
1.76-1.780.35422820.30945405X-RAY DIFFRACTION99.54
1.78-1.80.33852850.29625385X-RAY DIFFRACTION99.82
1.8-1.830.35312740.28375349X-RAY DIFFRACTION99.88
1.83-1.850.28153030.2615396X-RAY DIFFRACTION99.93
1.85-1.880.28873040.24595364X-RAY DIFFRACTION99.93
1.88-1.910.28362830.23525365X-RAY DIFFRACTION99.88
1.91-1.940.29032670.2345478X-RAY DIFFRACTION99.88
1.94-1.970.26782970.23015310X-RAY DIFFRACTION99.93
1.97-20.2712840.22325442X-RAY DIFFRACTION99.95
2-2.040.26412900.22745401X-RAY DIFFRACTION99.93
2.04-2.080.2422640.21215403X-RAY DIFFRACTION99.95
2.08-2.120.24742770.20745457X-RAY DIFFRACTION99.95
2.12-2.160.25333250.20865297X-RAY DIFFRACTION99.95
2.16-2.220.27312910.20825465X-RAY DIFFRACTION99.97
2.22-2.270.28162870.20495404X-RAY DIFFRACTION99.98
2.27-2.330.25452840.20955433X-RAY DIFFRACTION99.95
2.33-2.40.27042790.20985428X-RAY DIFFRACTION99.95
2.4-2.480.26812690.20685397X-RAY DIFFRACTION99.98
2.48-2.570.2782870.21055476X-RAY DIFFRACTION100
2.57-2.670.2763030.21465399X-RAY DIFFRACTION100
2.67-2.790.24332780.20695459X-RAY DIFFRACTION99.98
2.79-2.940.2512870.20185425X-RAY DIFFRACTION99.98
2.94-3.120.23353040.19815497X-RAY DIFFRACTION100
3.12-3.360.21662970.18665430X-RAY DIFFRACTION100
3.36-3.70.19352810.17215509X-RAY DIFFRACTION100
3.7-4.240.19263100.16135483X-RAY DIFFRACTION100
4.24-5.340.16652960.15385565X-RAY DIFFRACTION99.95
5.34-75.180.22063180.20655691X-RAY DIFFRACTION99.72

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