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

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Basic information

Entry
Database: PDB / ID: 8tbv
TitleHuman Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Components
  • Beta-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 of peptide antigen via MHC class I / : / : / 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 / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane ...antigen processing and presentation of peptide antigen via MHC class I / : / : / 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 / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / 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 erythrocyte differentiation / regulation of iron ion transport / 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 / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal 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
DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 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.
#1: Journal: bioRxiv / Year: 2023
Title: Accurate modeling of peptide-MHC structures with AlphaFold.
Authors: Mikhaylov, V. / Brambley, C.A. / Arbuiso, A. / Weiss, L. / Ma, J. / Keller, G.L.J. / Ayres, C.M. / Baker, B.M. / Levine, A.J.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135)(P132L) peptide
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)89,8629
Polymers89,5726
Non-polymers2903
Water2,954164
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)45,0766
Polymers44,7863
Non-polymers2903
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-15 kcal/mol
Surface area18740 Å2
MethodPISA
2
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135)(P132L) peptide


Theoretical massNumber of molelcules
Total (without water)44,7863
Polymers44,7863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-20 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.226, 86.726, 79.268
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 275)
d_2ens_1chain "D"
d_1ens_2(chain "B" and resid 1 through 100)
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3chain "F"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYGLUGLUAA1 - 2751 - 275
d_2ens_1GLYGLYGLUGLUDD1 - 2751 - 275
d_1ens_2METMETMETMETBB1 - 1001 - 100
d_2ens_2METMETMETMETEE1 - 1001 - 100
d_1ens_3LYSLYSLEULEUCC1 - 91 - 9
d_2ens_3LYSLYSLEULEUFF1 - 91 - 9

NCS ensembles :
ID
ens_1
ens_2
ens_3

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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


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

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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 , 3 types, 167 molecules

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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
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: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→62.23 Å / Num. obs: 23797 / % possible obs: 92.02 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.944 / Net I/σ(I): 4.32
Reflection shellResolution: 2.64→2.734 Å / Num. unique obs: 2209 / CC1/2: 0.649 / % possible all: 88.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS2.2.10data reduction
DIALS2.2.10data scaling
PHENIX1.20rc3_4406phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→62.23 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.0484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2744 2268 9.9 %
Rwork0.2292 20652 -
obs0.2337 22920 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 2.64→62.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 19 164 6499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156508
X-RAY DIFFRACTIONf_angle_d0.42128819
X-RAY DIFFRACTIONf_chiral_restr0.0385900
X-RAY DIFFRACTIONf_plane_restr0.00271148
X-RAY DIFFRACTIONf_dihedral_angle_d12.33892383
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.822506075325
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.805420578925
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.553056676168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.70.34361380.29451230X-RAY DIFFRACTION88.83
2.7-2.760.41591320.31141242X-RAY DIFFRACTION89.69
2.76-2.830.41431460.29941279X-RAY DIFFRACTION89.85
2.83-2.910.32511350.28281278X-RAY DIFFRACTION92.96
2.91-2.990.31861410.2691305X-RAY DIFFRACTION92.22
2.99-3.090.29721410.25651291X-RAY DIFFRACTION93.05
3.09-3.20.29521390.24541307X-RAY DIFFRACTION93.71
3.2-3.330.28971470.24361319X-RAY DIFFRACTION94.28
3.33-3.480.30171500.24681321X-RAY DIFFRACTION94.05
3.48-3.660.25431360.22361221X-RAY DIFFRACTION87.72
3.66-3.890.25261340.20651221X-RAY DIFFRACTION86.86
3.89-4.190.24481470.20911330X-RAY DIFFRACTION95.05
4.19-4.610.22191480.18481348X-RAY DIFFRACTION95.9
4.61-5.280.22641480.17691335X-RAY DIFFRACTION95.25
5.28-6.650.26881420.22431308X-RAY DIFFRACTION91.77
6.65-62.230.22581440.20971317X-RAY DIFFRACTION91.43
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)
12.244201110560.191409750603-0.2126307395551.422249392250.2252412792140.9780763129950.01333378163920.314450538059-0.01904195581340.0905303256415-0.033337904538-0.2911338147590.07568718895580.2471864338110.01151208683960.1495498202980.0119939448386-0.1043326828260.3455511361650.05782555574010.22587275271525.8338846432-3.4514600482919.8337705883
22.094619738650.3452061851171.480158514891.116528296150.5377149326712.311068052160.01046981795210.2657752717310.0604731277702-0.103094676430.06759540461690.0966169353950.1333811675970.0313177484315-0.1076961667460.15147050867-0.0147899441368-0.08450528638610.475098644048-0.08100220248650.308805740067-5.48288221528-7.787595026133.98570145843
33.80455784798-0.235990374732-0.009228720792490.787085426893-0.4703126575290.700329228861-0.02994280688080.1655952756020.593428894909-0.1048348323470.01336025992770.203213161926-0.0179483563146-0.1071105875340.04268158829350.1815793514230.0308199615211-0.09407648320390.483965123807-0.07807265177870.2973703834354.6857804265810.684817384411.5518639179
46.829412490842.38078780578-5.501036394940.939397404642-2.375444044718.48762435041-0.0699442979183-0.507769801387-0.103261996729-0.00610747895106-0.513220568415-0.69016934972-0.102929698241.248231592430.5567397379110.204786477543-0.0279851105349-0.04770627393420.3052974342710.1091222296560.46668932646733.0281981639-4.5225269998223.5223345446
51.8088969930.07057226971351.087493355531.026482432950.1936842945670.97020738172-0.0315312493421-0.04465807714840.0742291566481-0.08545856434450.04774895863460.2432490007140.0113080550954-0.006318552787630.006894865807350.162394171826-0.0280260862392-0.05297040067270.5990059671010.05598879600670.2332591620375.2323986003-39.794662210134.791031207
61.849877043070.593746218855-1.225301097620.7148599970250.04433675843411.708135940410.131027260390.495027930923-0.0964053886547-0.1445890703450.17085687874-0.180600578996-0.02124134272460.0990958902278-0.2301290468970.1550285079650.0213376193558-0.01990105510510.596557141292-0.02938461884270.25890141962536.7452067529-35.295867469918.6933947389
71.26893424433-0.09601264979010.7469038426680.445530857608-0.06534484297340.4609101433440.1191762744490.155872937504-0.217645536593-0.039864262755-0.0182631263579-0.01280182577570.07230096547080.0649495508259-0.1192437915630.193057324555-0.00948969849321-0.1028175591190.5719133361160.01938462644710.25820374393326.4161960943-53.809732207826.1642063485
87.505169404736.737964042337.613454062336.053761003876.839610591387.72760602404-0.305290765804-0.7668544881440.878272875632-0.172691528731-0.4276132503181.10454997617-0.564930603981-1.005391247050.7229390165390.3761664648360.0327200791865-0.0006117780943080.4072997781310.09141034146820.511509407568-1.9301936521-39.00490398638.3925935804
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 )BD1 - 1001 - 100
44chain 'C' and (resid 1 through 9 )CF1 - 91 - 9
55chain 'D' and (resid 1 through 180)DG1 - 1801 - 180
66chain 'D' and (resid 181 through 275 )DG181 - 275181 - 275
77chain 'E' and (resid 1 through 100 )EH1 - 1001 - 100
88chain 'F' and (resid 1 through 9 )FI1 - 91 - 9

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