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- PDB-8e8i: Structures of HLA-B8E76C loaded with long peptides reveal novel f... -

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Basic information

Entry
Database: PDB / ID: 8e8i
TitleStructures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • PHE-VAL-LYS-LYS-LYS-TYR-CYS-LEU
KeywordsIMMUNE SYSTEM / MHC class I / Antigen Processing and Presentation / Long peptides / HLA-B8
Function / homology
Function and homology information


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 / 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 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 / 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 / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / 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
Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsLi, L. / Bouvier, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI114467 United States
CitationJournal: Nat Commun / Year: 2023
Title: Crystal structures of MHC class I complexes reveal the elusive intermediate conformations explored during peptide editing.
Authors: Li, L. / Peng, X. / Batliwala, M. / Bouvier, M.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: PHE-VAL-LYS-LYS-LYS-TYR-CYS-LEU


Theoretical massNumber of molelcules
Total (without water)44,8133
Polymers44,8133
Non-polymers00
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-23 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.645, 81.232, 110.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I antigen


Mass: 31902.004 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: R4ZGR5
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / 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 PHE-VAL-LYS-LYS-LYS-TYR-CYS-LEU


Mass: 1031.333 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 0.2 M ammonium acetate, 15% PEG 1000, 0.1 M sodium citrate

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.49→19.61 Å / Num. obs: 72099 / % possible obs: 96.49 % / Redundancy: 8.2 % / Biso Wilson estimate: 14.37 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.5
Reflection shellResolution: 1.49→1.51 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 10526 / % possible all: 83.93

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6p2s

6p2s


Resolution: 1.49→19.61 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 3619 5.02 %
Rwork0.1795 68480 -
obs0.1811 72099 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.86 Å2 / Biso mean: 20.5807 Å2 / Biso min: 9.61 Å2
Refinement stepCycle: final / Resolution: 1.49→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 546 3696
Biso mean---28.04 -
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.510.3626950.31041738183365
1.51-1.530.28221340.26772567270195
1.53-1.550.28651270.23412589271696
1.55-1.580.2581460.20592621276796
1.58-1.60.25291420.19912583272596
1.6-1.630.25091340.1922612274697
1.63-1.660.24551420.19182583272597
1.66-1.690.22091370.18752648278596
1.69-1.720.23491220.18892631275397
1.72-1.750.22731370.18662630276797
1.75-1.790.24131590.18762587274697
1.79-1.830.2631420.18872665280798
1.83-1.880.25081400.19322637277797
1.88-1.930.21241460.18272649279598
1.93-1.990.19641310.17452681281298
1.99-2.050.18451390.17362637277698
2.05-2.120.18931360.16982681281798
2.12-2.210.21321440.17242684282898
2.21-2.310.20041310.17382683281498
2.31-2.430.23271330.17722712284599
2.43-2.580.20721390.18632726286599
2.58-2.780.20841580.18572701285999
2.78-3.060.19931640.18812711287599
3.06-3.50.24061570.17462762291999
3.5-4.40.17361600.15522787294799
4.4-19.610.16751240.163529753099100
Refinement TLS params.Method: refined / Origin x: -12.0857 Å / Origin y: -8.9393 Å / Origin z: 18.3902 Å
111213212223313233
T0.183 Å20.0024 Å20.0029 Å2-0.0313 Å2-0.0017 Å2--0.1548 Å2
L0.6152 °20.0804 °20.1849 °2-0.169 °20.0561 °2--0.3163 °2
S-0.0217 Å °-0.0199 Å °0.0689 Å °-0.0333 Å °-0.0044 Å °0.0027 Å °-0.0334 Å °-0.0249 Å °0.0133 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 275
2X-RAY DIFFRACTION1allB0 - 99
3X-RAY DIFFRACTION1allC1 - 8
4X-RAY DIFFRACTION1allD1 - 546

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