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- PDB-6ghn: HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P9-Phe. -

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Basic information

Entry
Database: PDB / ID: 6ghn
TitleHLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P9-Phe.
Components
  • ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, E alpha chain variant
KeywordsIMMUNE SYSTEM / Complex / Histocompatibility antigen
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 / trans-2-enoyl-CoA reductase (NADH) activity / positive regulation of natural killer cell mediated cytotoxicity / mycolic acid biosynthetic process / positive regulation of interleukin-13 production / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell proliferation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / 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 / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of interleukin-4 production / beta-2-microglobulin binding / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / NAD+ 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 / T cell receptor binding / negative regulation of T cell proliferation / : / : / peptidoglycan-based cell wall / 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 / fatty acid binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / 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 iron ion transport / regulation of erythrocyte differentiation / 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 / positive regulation of T cell activation / peptide antigen binding / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / cellular response to nicotine / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of cellular senescence / positive regulation of protein binding / 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 / MHC class II protein complex binding / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / antibacterial humoral response / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / iron ion transport / negative regulation of neuron projection development / 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
Similarity search - Function
: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 ...: / Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / 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 / 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 / Enoyl-[acyl-carrier-protein] reductase [NADH] / HLA class I histocompatibility antigen, E alpha chain variant
Similarity search - Component
Biological speciesHomo sapiens (human)
Mycobacteriaceae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.542 Å
AuthorsWalters, L.C. / Gillespie, G.M. / McMichael, A.J. / Rozbesky, D. / Jones, E.Y. / Harlos, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationOPP1133649 United States
CitationJournal: Nat Commun / Year: 2018
Title: Pathogen-derived HLA-E bound epitopes reveal broad primary anchor pocket tolerability and conformationally malleable peptide binding.
Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. ...Authors: Walters, L.C. / Harlos, K. / Brackenridge, S. / Rozbesky, D. / Barrett, J.R. / Jain, V. / Walter, T.S. / O'Callaghan, C.A. / Borrow, P. / Toebes, M. / Hansen, S.G. / Sacha, J. / Abdulhaqq, S. / Greene, J.M. / Fruh, K. / Marshall, E. / Picker, L.J. / Jones, E.Y. / McMichael, A.J. / Gillespie, G.M.
History
DepositionMay 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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 1.3Nov 13, 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, E alpha chain variant
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
P: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
Q: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1758
Polymers88,9836
Non-polymers1922
Water4,378243
1
A: HLA class I histocompatibility antigen, E alpha chain variant
B: Beta-2-microglobulin
P: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5874
Polymers44,4913
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-34 kcal/mol
Surface area19400 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, E alpha chain variant
D: Beta-2-microglobulin
Q: ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5874
Polymers44,4913
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-37 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.453, 64.681, 97.308
Angle α, β, γ (deg.)107.03, 93.89, 106.84
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 31597.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: Q59EE1, UniProt: P13747*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): plysS / References: UniProt: P61769
#3: Protein/peptide ARG-LEU-PRO-ALA-LYS-ALA-PRO-LEU-PHE


Mass: 1014.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacteriaceae (bacteria) / References: UniProt: P9WGR1*PLUS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M Ammonium Sulphate, 0.1 M HEPES, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.54→58.5 Å / Num. obs: 26488 / % possible obs: 97.7 % / Redundancy: 4.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.21 / Net I/σ(I): 5.2
Reflection shellResolution: 2.54→2.59 Å / Num. unique obs: 1053 / CC1/2: 0.57 / % possible all: 77.5

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GH1

6gh1


Resolution: 2.542→58.498 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.64
RfactorNum. reflection% reflection
Rfree0.2642 1274 4.84 %
Rwork0.2183 --
obs0.2205 26305 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.542→58.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6231 0 10 245 6486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066424
X-RAY DIFFRACTIONf_angle_d0.8378728
X-RAY DIFFRACTIONf_dihedral_angle_d16.8543800
X-RAY DIFFRACTIONf_chiral_restr0.053893
X-RAY DIFFRACTIONf_plane_restr0.0061142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5418-2.64350.39361240.31722486X-RAY DIFFRACTION87
2.6435-2.76380.32381340.30652738X-RAY DIFFRACTION96
2.7638-2.90950.35481440.27412839X-RAY DIFFRACTION98
2.9095-3.09180.27721470.24692828X-RAY DIFFRACTION98
3.0918-3.33050.28381510.24112795X-RAY DIFFRACTION98
3.3305-3.66560.25051300.20362819X-RAY DIFFRACTION99
3.6656-4.19590.22621490.1742860X-RAY DIFFRACTION99
4.1959-5.28590.2231330.1692844X-RAY DIFFRACTION99
5.2859-58.51330.23321620.21242822X-RAY DIFFRACTION99
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)
11.941-0.9959-0.57541.8327-0.59923.6758-0.02360.2435-0.3670.09460.06240.19720.156-0.497-0.04070.126-0.0216-0.02770.34290.03310.3266-10.46056.0756-5.3734
26.14380.8104-2.1841.4055-1.34733.7309-0.0405-0.2780.695900.31610.19450.00610.072-0.27590.10430.0156-0.02770.2073-0.00230.2281-9.389314.3541-14.4668
32.2978-0.3777-2.69941.1919-0.03055.09950.146-0.22470.30670.0418-0.0118-0.0803-0.34920.3347-0.14110.199-0.0169-0.08140.24920.04410.28314.9614.8111-7.1656
41.20712.0936-2.2523.6313-3.8224.09860.59210.09440.73220.63570.0170.2083-1.08130.043-0.55150.23240.00490.0460.44320.00230.33532.5624.9534-8.9108
52.3773-1.0350.49674.2304-0.77921.3811-0.1636-0.3496-0.3780.45630.21790.11180.08640.002-0.07430.35420.0522-0.01980.37550.00670.22261.331-4.144813.859
63.0798-0.34080.34852.52040.3931.3293-0.572-0.9965-0.27660.44550.5461-0.57740.08470.3097-0.04880.4470.1316-0.02770.48120.08130.39849.8731-10.685616.5224
72.64731.4525-1.59394.7488-0.63353.7714-0.0035-0.0783-0.03040.686-0.1235-0.01920.2680.09040.09520.33620.039-0.02970.2214-0.00190.28791.0105-12.83880.3157
84.56330.9984-1.42025.0113-0.3283.91690.00630.39410.10180.07260.20430.54280.596-0.1504-0.04920.21080.00750.03970.299-0.00340.2473-2.1205-11.6827-5.5862
94.6243-0.2047-0.78144.5059-0.38333.9461-0.25580.8078-0.62870.0377-0.28421.10190.7208-0.76270.18560.3915-0.13940.05010.4311-0.12630.4282-10.1044-18.4754-7.6906
102.7834-0.2021-1.09586.1821-1.88173.77270.3277-0.3372-0.26640.1236-0.5793-0.09920.41250.11270.20350.2424-0.0081-0.06810.25330.03330.161-2.6215-4.7312-3.3014
114.1605-2.2908-0.43573.572-0.68342.46210.1690.1426-0.20170.36760.43820.1038-0.71170.4387-0.64970.95820.25680.14770.5080.01470.4995-3.9206-30.1183.3329
122.4345-0.4908-0.02141.8907-3.62987.5689-0.18260.0642-0.1214-0.0445-0.2939-0.00150.8620.75890.44080.47040.0721-0.02140.2532-0.02830.36373.5965-18.0891-6.0301
132.0084-0.3277-0.1891.7293-0.11322.263-0.1078-0.19940.1876-0.04430.06120.1664-0.071-0.27350.06970.10080.02730.0040.23460.03160.3035-7.7073-30.9572-34.0262
141.5822-1.34322.38981.3731-0.64656.38470.31080.1347-0.2445-0.2298-0.04890.03880.72520.1437-0.23760.2032-0.0191-0.03660.2306-0.00250.30251.752-41.5334-40.3014
153.5832.5324-0.47994.117-1.54331.1036-0.54580.1568-0.2474-0.69420.1737-0.4639-0.15840.19160.34910.46670.01310.06940.3440.04650.24138.2242-11.5062-59.6834
168.1586-4.23273.8665.7163-1.10163.87330.1368-0.82560.1928-0.2860.0475-0.37060.2342-0.3073-0.13740.2676-0.0647-0.03040.2713-0.01510.21876.2437-13.9459-37.3199
170.8742-0.7778-0.90593.22131.13980.97420.20870.77870.5254-1.2159-0.1860.7622-0.4538-0.2494-0.08410.83220.0159-0.22790.30490.11640.5803-7.0871-0.9746-54.6522
182.8065-1.26270.63384.8398-2.18371.5016-0.1641-0.34640.01190.18140.13790.2962-0.6052-0.0295-0.00050.27150.0022-0.0680.2741-0.08180.2584-2.043-10.1301-37.9753
194.57982.7363-0.62794.8405-2.52742.2860.1284-1.18340.94310.7883-0.20451.177-0.3056-0.2836-0.03760.36910.1146-0.00560.4499-0.07730.4791-9.8587-3.4478-35.8013
201.94250.35050.30476.3463-0.64521.04880.28260.0967-0.0607-0.2378-0.27780.3598-0.1611-0.00250.00190.22440.04240.0040.31860.01150.1876-2.5513-17.0776-40.3337
210.0137-0.2080.09893.1123-1.36220.5964-0.1793-0.21891.2891-0.09450.1933-0.6134-0.47830.70080.00840.8865-0.1986-0.41470.3643-0.11731.003-3.98678.4008-46.8197
227.0563-5.12846.17889.01741.98111.9885-0.3903-0.48230.0118-0.2644-0.5115-0.156-1.4282-0.50450.72020.51690.0266-0.10350.2992-0.10930.4207-0.2976-3.3986-35.5389
236.7014-2.1679-3.7055.2726-1.48695.50360.6562-0.64870.76671.12380.3464-0.9526-1.46070.6887-0.72680.5946-0.1319-0.02770.27310.0140.31157.6266-9.0327-27.6077
246.04430.1659-0.90546.39750.46779.46330.31410.3371-0.0668-0.35560.0119-0.4027-0.37150.5077-0.34940.361-0.03580.0360.3333-0.03350.36093.7212-0.6812-44.8535
252.72850.3025-1.42191.5895-0.86893.42570.2035-0.16570.3865-0.07570.46360.0645-0.1856-0.2468-0.5197-0.5604-0.323-0.31490.2486-0.04830.5398-6.067819.12-9.9929
261.6902-0.20690.18493.1033-1.10856.0051-0.14150.0474-0.54820.05690.2380.07720.5648-0.4597-0.08360.1410.03350.05370.32150.05670.2593-6.0728-40.9282-33.4355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 219 )
6X-RAY DIFFRACTION6chain 'A' and (resid 220 through 274 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 20 )
8X-RAY DIFFRACTION8chain 'B' and (resid 21 through 42 )
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 78 )
12X-RAY DIFFRACTION12chain 'B' and (resid 79 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 103 )
14X-RAY DIFFRACTION14chain 'C' and (resid 104 through 174 )
15X-RAY DIFFRACTION15chain 'C' and (resid 175 through 274 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1 through 12 )
17X-RAY DIFFRACTION17chain 'D' and (resid 13 through 20 )
18X-RAY DIFFRACTION18chain 'D' and (resid 21 through 42 )
19X-RAY DIFFRACTION19chain 'D' and (resid 43 through 52 )
20X-RAY DIFFRACTION20chain 'D' and (resid 53 through 72 )
21X-RAY DIFFRACTION21chain 'D' and (resid 73 through 78 )
22X-RAY DIFFRACTION22chain 'D' and (resid 79 through 84 )
23X-RAY DIFFRACTION23chain 'D' and (resid 85 through 91 )
24X-RAY DIFFRACTION24chain 'D' and (resid 92 through 100 )
25X-RAY DIFFRACTION25chain 'P' and (resid 1 through 9 )
26X-RAY DIFFRACTION26chain 'Q' and (resid 1 through 9 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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