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- PDB-8f7m: Crystal Structure of HLA-B*57:01-TW10-T242N complex -

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Basic information

Entry
Database: PDB / ID: 8f7m
TitleCrystal Structure of HLA-B*57:01-TW10-T242N complex
Components
  • Beta-2-microglobulin
  • T242N peptide (TW10 mutant)
  • heavy chain HLA-B*57:01
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA-B*57:01 / TW10 / T242N / gag / HIV / HIV controllers
Function / homology
Function and homology information


: / : / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / 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 / 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 / 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 / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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, 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
HIV-1 06TG.HT008 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsChatzileontiadou, D.S.M. / Lobos, C.A. / Gras, S.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Cell Rep / Year: 2024
Title: Public T cell clonotypes are selected in HLA-B ∗ 57:01 + /HIV + patients independently of the viral load.
Authors: Chatzileontiadou, D.S.M. / Lobos, C.A. / Robson, H. / Almedia, C.A. / Szeto, C. / Castley, A. / D'Orsogna, L.J. / Gras, S.
History
DepositionNov 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 18, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: heavy chain HLA-B*57:01
B: Beta-2-microglobulin
C: T242N peptide (TW10 mutant)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0586
Polymers44,8343
Non-polymers2243
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-14 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.942, 82.174, 110.833
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein heavy chain HLA-B*57:01 / MHC class I antigen


Mass: 31910.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: U6BR87
#2: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
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, 1 molecules C

#3: Protein/peptide T242N peptide (TW10 mutant)


Mass: 1175.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HIV-1 06TG.HT008 (virus)

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Non-polymers , 3 types, 416 molecules

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


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 % w/v PEG4000, 0.2 M ammonium acetate, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.88→46.29 Å / Num. obs: 38624 / % possible obs: 99.9 % / Redundancy: 7.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.069 / Rrim(I) all: 0.19 / Χ2: 0.99 / Net I/σ(I): 10.2 / Num. measured all: 293231
Reflection shellResolution: 1.88→1.92 Å / % possible obs: 99.5 % / Redundancy: 7.9 % / Rmerge(I) obs: 1.232 / Num. measured all: 19225 / Num. unique obs: 2428 / CC1/2: 0.712 / Rpim(I) all: 0.468 / Rrim(I) all: 1.319 / Χ2: 0.98 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.3data scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→45.95 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1926 4.99 %
Rwork0.172 --
obs0.1744 38563 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→45.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 15 413 3575
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083375
X-RAY DIFFRACTIONf_angle_d1.0664598
X-RAY DIFFRACTIONf_dihedral_angle_d15.754473
X-RAY DIFFRACTIONf_chiral_restr0.063467
X-RAY DIFFRACTIONf_plane_restr0.006615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.321290.22762566X-RAY DIFFRACTION99
1.93-1.980.27171320.20612568X-RAY DIFFRACTION99
1.98-2.040.26261520.1932572X-RAY DIFFRACTION100
2.04-2.10.25831350.18472584X-RAY DIFFRACTION100
2.1-2.180.23161250.18962578X-RAY DIFFRACTION100
2.18-2.270.21381310.18322583X-RAY DIFFRACTION100
2.27-2.370.24221510.17792583X-RAY DIFFRACTION100
2.37-2.490.25681340.18112605X-RAY DIFFRACTION100
2.49-2.650.25881260.18872621X-RAY DIFFRACTION100
2.65-2.850.24311480.18372608X-RAY DIFFRACTION100
2.85-3.140.22521540.18192614X-RAY DIFFRACTION100
3.14-3.60.22671370.16762649X-RAY DIFFRACTION100
3.6-4.530.15681420.13682675X-RAY DIFFRACTION100
4.53-45.950.16961300.14712831X-RAY DIFFRACTION100

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