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- PDB-8tbw: Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-13... -

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Basic information

Entry
Database: PDB / ID: 8tbw
TitleHuman Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) peptide KLSHQPVLL
Components
  • Beta-2-microglobulin
  • HLA-A*02:01 alpha chain
  • Sorting nexin 24 (127-135) peptide
KeywordsIMMUNE SYSTEM / Complex / MHC-I / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 / 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 peptide antigen via MHC class I / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / 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 / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / 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 / : ...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
NITRATE ION / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.081 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
DepositionJun 29, 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
Revision 1.2Nov 6, 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-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135) peptide
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6648
Polymers89,5406
Non-polymers1242
Water9,710539
1
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8324
Polymers44,7703
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area19280 Å2
MethodPISA
2
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8324
Polymers44,7703
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-18 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.052, 157.570, 185.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

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Components

#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


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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
#3: Protein/peptide Sorting nexin 24 (127-135) peptide


Mass: 1036.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 539 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.47 %
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: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.081→48.71 Å / Num. obs: 58502 / % possible obs: 95.59 % / Redundancy: 13.7 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.995 / Net I/σ(I): 13.57
Reflection shellResolution: 2.081→2.156 Å / Num. unique obs: 4715 / CC1/2: 0.904

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.081→48.71 Å / SU ML: 0.2123 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 20.3002
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2053 5599 10.01 %
Rwork0.1719 50335 -
obs0.1754 55934 95.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.19 Å2
Refinement stepCycle: LAST / Resolution: 2.081→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6314 0 8 539 6861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00756498
X-RAY DIFFRACTIONf_angle_d0.8348812
X-RAY DIFFRACTIONf_chiral_restr0.0532898
X-RAY DIFFRACTIONf_plane_restr0.00821152
X-RAY DIFFRACTIONf_dihedral_angle_d13.63142378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.081-2.10.23891390.20491307X-RAY DIFFRACTION75.91
2.11-2.130.27631640.19821471X-RAY DIFFRACTION83.85
2.13-2.160.24161630.19921464X-RAY DIFFRACTION85.9
2.16-2.180.25931710.19521521X-RAY DIFFRACTION86.55
2.18-2.210.24871680.20131532X-RAY DIFFRACTION88.87
2.21-2.240.23421750.18811595X-RAY DIFFRACTION91.95
2.24-2.270.2041830.19251635X-RAY DIFFRACTION93.71
2.27-2.310.23211860.20231652X-RAY DIFFRACTION95.58
2.31-2.340.26191840.19541650X-RAY DIFFRACTION95.22
2.34-2.380.23741860.19841663X-RAY DIFFRACTION95.16
2.38-2.420.25291870.19861653X-RAY DIFFRACTION96.23
2.42-2.470.23951850.1971679X-RAY DIFFRACTION96.28
2.47-2.520.24051880.18781704X-RAY DIFFRACTION97.63
2.52-2.570.21831910.18651701X-RAY DIFFRACTION97.43
2.57-2.620.22691950.18951707X-RAY DIFFRACTION97.89
2.62-2.680.2591880.20421713X-RAY DIFFRACTION98.34
2.68-2.750.22291960.2051729X-RAY DIFFRACTION98.06
2.75-2.820.23441890.20371697X-RAY DIFFRACTION98.43
2.82-2.910.24641940.19271737X-RAY DIFFRACTION99.03
2.91-30.21271910.18991739X-RAY DIFFRACTION98.72
3-3.110.20971940.17181721X-RAY DIFFRACTION99.02
3.11-3.230.19971930.17911743X-RAY DIFFRACTION99.33
3.23-3.380.1941920.17911748X-RAY DIFFRACTION99.28
3.38-3.560.20191940.17631763X-RAY DIFFRACTION99.49
3.56-3.780.18491960.15161758X-RAY DIFFRACTION99.85
3.78-4.070.17551980.14391786X-RAY DIFFRACTION99.75
4.07-4.480.17111980.13361778X-RAY DIFFRACTION99.95
4.48-5.130.16391990.12861790X-RAY DIFFRACTION100
5.13-6.460.18642000.16211802X-RAY DIFFRACTION99.8
6.46-48.710.18582120.16661897X-RAY DIFFRACTION99.62
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)
11.974280301980.136619768909-1.321868533422.14641167405-0.1636536590763.023551364130.0803860714746-0.07883219812820.12175916449-0.076134898042-0.00403913170374-0.148834431607-0.2268128652780.112494677722-0.05028025075010.173322885901-0.05572607629730.008510677216030.182804755228-0.03106774354940.230628202228-9.72014272483-8.2680944938530.3475511141
21.725518565330.8761359769410.2001165794887.241850514470.7428448426443.156858555820.12219002282-0.027235719889-0.144760007215-0.106365500881-0.1768299226250.1262890030710.485538121105-0.09550542685050.08872050518430.212162436223-0.04384200282450.03132359802210.22853031629-0.02201934959130.20932575712-30.0665699255-36.934068695134.9877636078
36.004179825610.847307169175-0.5945414881652.044557619010.3363651548252.98625434255-0.07812208524560.1105733332750.0694164951211-0.266723811607-0.03615744330380.333486935688-0.151429725572-0.3829599442210.1768148291740.247192993950.0177432339642-0.05586493204230.182120488511-0.02668445474450.232945841539-33.6435956522-18.228903885222.7001960161
48.05071951656-1.3570742536-7.782125059453.39219238251.59287340637.60431836960.151421785298-0.7230506231740.445566481112-0.1189859624190.122955794571-0.35952921848-0.05716632214531.05874924744-0.2809060825950.438519989758-0.068661817430.01610730098020.286827000966-0.03599556210030.354588762107-3.64507220183-2.9381805090131.0564310809
53.796261984010.0546390035438-1.396944867022.026135384960.1514789063412.123157274080.0564267541467-0.188725940866-0.2536619994910.110643098664-0.113517842816-0.1578887504270.1443992279840.1567476870320.05844914932760.271874690246-0.0420131318507-0.03175951957430.1499889205940.04317564295750.260711493351-21.6599886756-69.285499832122.0110687491
61.944929246762.125314361650.1687367853177.831624749450.7042128226043.178926212370.133386973673-0.09766277455690.08742180321960.237866399976-0.108494605876-0.0106073084696-0.1316512145280.0272394042236-0.04168751277470.154809874374-0.0154215910518-0.003235879848440.213519168869-0.01204069829640.18644717373-4.01575940505-39.505123951413.9979388987
73.232610751190.90418602558-1.935569252512.5075253893-1.167568292524.779500959490.06397495203820.359335497266-0.053057326079-0.1361673433050.02755745936070.00431857805051-0.247798798905-0.066597831985-0.116605885230.238322804824-0.0208356438518-0.03543239606780.188340610673-0.02858743559730.185336680741-19.2741185781-51.23033253762.10166751054
87.98547404276-5.78520447072-5.121557502185.598820202163.982767472246.124546766150.147856524907-1.43052484153-0.4477730443580.151954764232-0.1757786620180.1024822377730.1306513086610.06063444112420.2671593087360.420002057727-0.098391226792-0.09191557359970.2883559560540.06414596267460.412329444163-24.5753713653-75.90438022225.7339011267
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 180 )AA1 - 1801 - 180
22chain 'A' and (resid 181 through 275 )AA181 - 275181 - 275
33chain 'B' and (resid 1 through 100 )BB1 - 1001 - 100
44chain 'C' and (resid 1 through 9 )CC1 - 91 - 9
55chain 'D' and (resid 1 through 180 )DD1 - 1801 - 180
66chain 'D' and (resid 181 through 275 )DD181 - 275181 - 275
77chain 'E' and (resid 1 through 100 )EE1 - 1001 - 100
88chain 'F' and (resid 1 through 9 )FF1 - 91 - 9

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