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- PDB-7p49: HLA-E*01:03 in complex with Mtb14 -

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Basic information

Entry
Database: PDB / ID: 7p49
TitleHLA-E*01:03 in complex with Mtb14
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, alpha chain E
  • Phenolphthiocerol/phthiocerol polyketide synthase subunit B
KeywordsIMMUNE SYSTEM / HLA-E MHC
Function / homology
Function and homology information


(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / 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 ...(phenol)carboxyphthiodiolenone synthase / phthiocerol biosynthetic process / phenolic phthiocerol biosynthetic process / polyketide synthase complex / 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 / DIM/DIP cell wall layer assembly / positive regulation of interleukin-13 production / negative regulation of natural killer cell mediated cytotoxicity / 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 / fatty acid synthase activity / positive regulation of interleukin-4 production / beta-2-microglobulin binding / positive regulation of natural killer cell proliferation / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / phosphopantetheine binding / 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 / 3-oxoacyl-[acyl-carrier-protein] synthase activity / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / 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 / 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 / fatty acid biosynthetic process / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / oxidoreductase activity / defense response to Gram-positive bacterium / immune response / receptor ligand activity
Similarity search - Function
PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. ...PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / PKS_KR / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / MHC class I, alpha chain, C-terminal / Thiolase-like / 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 / Phosphopantetheine attachment site / Class I Histocompatibility antigen, domains alpha 1 and 2 / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / 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 / NAD(P)-binding 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 / Beta-2-microglobulin / Phenolphthiocerol/phthiocerol polyketide synthase subunit B
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.0Jun 22, 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
Q: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
R: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
Z: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,39652
Polymers178,65812
Non-polymers3,73840
Water11,710650
1
A: HLA class I histocompatibility antigen, alpha chain E
B: Beta-2-microglobulin
P: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,80115
Polymers44,6653
Non-polymers1,13712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-105 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, alpha chain E
D: Beta-2-microglobulin
Q: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,79715
Polymers44,6653
Non-polymers1,13312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-107 kcal/mol
Surface area18480 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, alpha chain E
F: Beta-2-microglobulin
R: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39811
Polymers44,6653
Non-polymers7348
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-94 kcal/mol
Surface area18510 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, alpha chain E
H: Beta-2-microglobulin
Z: Phenolphthiocerol/phthiocerol polyketide synthase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,39811
Polymers44,6653
Non-polymers7348
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-105 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)245.150, 47.926, 152.445
Angle α, β, γ (deg.)90.000, 117.452, 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-302-

ZN

21G-302-

ZN

31G-406-

HOH

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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: 31824.008 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


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
Phenolphthiocerol/phthiocerol polyketide synthase subunit B / (Phenol)carboxyphthiodiolenone synthase subunit B / Beta-ketoacyl-acyl-carrier-protein synthase I / ...(Phenol)carboxyphthiodiolenone synthase subunit B / Beta-ketoacyl-acyl-carrier-protein synthase I / Phthiocerol synthesis polyketide synthase type I PpsB


Mass: 961.159 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: ppsB, Rv2932, MTCY338.21, MTV011.01 / Production host: Escherichia (bacteria)
References: UniProt: P9WQE5, (phenol)carboxyphthiodiolenone synthase

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Non-polymers , 4 types, 690 molecules

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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 27 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3 M AS, 0.1 M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.05→57.16 Å / Num. obs: 99611 / % possible obs: 98.95 % / Redundancy: 12.7 % / Biso Wilson estimate: 32.14 Å2 / CC1/2: 0.99 / Net I/σ(I): 9.7
Reflection shellResolution: 2.05→2.124 Å / Num. unique obs: 9754 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
REFMAC1.18.2_3874refinement
PHENIX1.18.2_3874refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GL1

6gl1


Resolution: 2.05→57.16 Å / SU ML: 0.331 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.7647
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2791 4961 5.03 %
Rwork0.2373 93702 -
obs0.2394 98663 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.02 Å2
Refinement stepCycle: LAST / Resolution: 2.05→57.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12514 0 208 650 13372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003113037
X-RAY DIFFRACTIONf_angle_d0.559617701
X-RAY DIFFRACTIONf_chiral_restr0.04111800
X-RAY DIFFRACTIONf_plane_restr0.00352296
X-RAY DIFFRACTIONf_dihedral_angle_d20.45114738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.43011660.42242940X-RAY DIFFRACTION93.39
2.07-2.10.42431550.37783025X-RAY DIFFRACTION97.37
2.1-2.120.43511530.37243035X-RAY DIFFRACTION97.88
2.12-2.150.39431620.37253072X-RAY DIFFRACTION97.67
2.15-2.180.3591770.35083070X-RAY DIFFRACTION98.39
2.18-2.210.41921580.34483054X-RAY DIFFRACTION98.56
2.21-2.240.36051630.33013105X-RAY DIFFRACTION98.88
2.24-2.270.35381630.32433126X-RAY DIFFRACTION98.74
2.27-2.310.38581800.32443064X-RAY DIFFRACTION98.42
2.31-2.350.39441450.32093100X-RAY DIFFRACTION99.14
2.35-2.390.37891590.32253142X-RAY DIFFRACTION98.86
2.39-2.430.36811570.30993064X-RAY DIFFRACTION98.89
2.43-2.480.33061600.28623077X-RAY DIFFRACTION98.96
2.48-2.530.30981730.27993194X-RAY DIFFRACTION99.35
2.53-2.580.37721530.28973075X-RAY DIFFRACTION99.32
2.58-2.640.35411630.29083137X-RAY DIFFRACTION99.16
2.64-2.710.2881570.2783121X-RAY DIFFRACTION99.54
2.71-2.780.32481910.26093119X-RAY DIFFRACTION99.22
2.78-2.860.33411560.26193125X-RAY DIFFRACTION99.54
2.86-2.960.30511680.25373167X-RAY DIFFRACTION99.73
2.96-3.060.2851540.24073148X-RAY DIFFRACTION99.58
3.06-3.180.33151460.22973200X-RAY DIFFRACTION99.82
3.18-3.330.29861600.22463109X-RAY DIFFRACTION99.97
3.33-3.510.29781670.21353170X-RAY DIFFRACTION99.88
3.51-3.720.23511880.19323170X-RAY DIFFRACTION99.85
3.72-4.010.21291790.17843179X-RAY DIFFRACTION99.94
4.01-4.420.21621610.17473182X-RAY DIFFRACTION100
4.42-5.050.20721880.16223182X-RAY DIFFRACTION99.85
5.06-6.370.21421820.19643230X-RAY DIFFRACTION99.85
6.37-57.160.21031770.21423320X-RAY DIFFRACTION98.7

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