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- PDB-8u9g: Human Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoa... -

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Basic information

Entry
Database: PDB / ID: 8u9g
TitleHuman Class I MHC HLA-A2 bound to sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA-A*02:01 alpha chain
  • Sorting nexin 24 (127-135)(P132L) peptide
KeywordsIMMUNE SYSTEM / Complex / MHC-I / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation / 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 processing and presentation / 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 / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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. ...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
DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsArbuiso, A. / Weiss, L.I. / Brambley, C.A. / Ma, J. / Keller, G.L.J. / Ayres, C.M. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: Structure / Year: 2024
Title: Accurate modeling of peptide-MHC structures with AlphaFold.
Authors: Mikhaylov, V. / Brambley, C.A. / Keller, G.L.J. / Arbuiso, A.G. / Weiss, L.I. / Baker, B.M. / Levine, A.J.
History
DepositionSep 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
C: Sorting nexin 24 (127-135)(P132L) peptide
F: Sorting nexin 24 (127-135)(P132L) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,9659
Polymers89,5726
Non-polymers3933
Water88349
1
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135)(P132L) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8924
Polymers44,7863
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-23 kcal/mol
Surface area18880 Å2
MethodPISA
2
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135)(P132L) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0735
Polymers44,7863
Non-polymers2872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-20 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.196, 85.432, 84.075
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ADBE

#1: Protein HLA-A*02:01 alpha chain / HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility ...HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / A alpha chain / MHC class I antigen / MHC class I protein / MHC class I protein (HLA-A)


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Z42
#2: Protein Beta-2-microglobulin / 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 (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Sorting nexin 24 (127-135)(P132L) peptide


Mass: 1052.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 52 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals ...Details: Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.87→59.92 Å / Num. obs: 18717 / % possible obs: 98.56 % / Redundancy: 3.3 % / CC1/2: 0.947 / Rmerge(I) obs: 0.1708 / Rpim(I) all: 0.1116 / Rrim(I) all: 0.2049 / Net I/σ(I): 5.16
Reflection shellResolution: 2.87→2.973 Å / Num. unique obs: 1858 / Rpim(I) all: 0.2445

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
REFMAC5refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.87→59.92 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 --
Rwork0.1999 --
obs-18706 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→59.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 25 49 6390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.888
X-RAY DIFFRACTIONf_dihedral_angle_d8.771879
X-RAY DIFFRACTIONf_chiral_restr0.05900
X-RAY DIFFRACTIONf_plane_restr0.0131147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.050.30951520.24882942X-RAY DIFFRACTION99
3.05-3.290.29721640.23272946X-RAY DIFFRACTION99
3.29-3.620.29321240.22252894X-RAY DIFFRACTION96
3.62-4.140.22331120.18243048X-RAY DIFFRACTION100
4.14-5.210.19441480.15742989X-RAY DIFFRACTION100
5.22-59.92X-RAY DIFFRACTION
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)
10.00320.00340.01690.0041-0.00820.02460.2053-0.14-0.0047-0.02630.1534-0.10010.1695-0.11420-0.05590.01520.0508-0.066-0.0545-0.20423.4621-3.433920.1856
20.01210.01210.0012-0.0006-0.00430.00250.028-0.0983-0.0481-0.07570.01350.0227-0.04190.046800.05160.008-0.00190.04460.00960.0476-7.1505-6.94314.1172
30.0016-0.0004-0.00040.00030.00960.00340.01990.01730.06530.0485-0.028-0.0117-0.0073-0.05060-0.0251-0.0144-0.03270.0914-0.01580.02012.381311.545712.0367
40.0362-0.0189-0.01950.00160.02170.00740.0823-0.10630.0062-0.12030.04030.096-0.0148-0.05-0-0.1793-0.1562-0.0706-0.1365-0.12-0.09655.5087-39.007235.4038
5-0.0001-0.0009-0.0002-0.0028-0.0016-0.00390.00770.0062-0.05570.09990.0811-0.00520.11210.0291-0-0.0520.02960.004-0.31420.1868-0.10526.6591-53.848127.1756
6-0.00170-0.00130.00070.001-0.00010.0025-0.0167-0.0007-0.011-0.0123-0.01230.0043-0.004-00.0455-0.05850.0677-0.04010.0320.064530.8067-4.55623.5001
7-0.00060.0008-0.0003-0.00070.00020.00040.0062-0.01360.0149-0.0007-0.00540.0078-0.01110.0073-00.07210.02530.00890.1131-0.04540.0965-1.66-38.117239.0063
8-0.0057-0.00790.00190.00060.00230.00280.0301-0.05870.0417-0.07630.1049-0.01710.02850.0269-0-0.0493-0.1529-0.0057-0.2756-0.02270.016236.1645-35.337419.3963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 275 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 100 )
4X-RAY DIFFRACTION4chain 'C' and (resid 1 through 180)
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 100 )
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 9)
7X-RAY DIFFRACTION7chain 'F' and (resid 1 through 9 )
8X-RAY DIFFRACTION8chain 'C' and (resid 181 through 275 )

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