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- PDB-8e2z: Structures of HLA-B8E76C loaded with long peptides reveal novel f... -

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Basic information

Entry
Database: PDB / ID: 8e2z
TitleStructures of HLA-B8E76C loaded with long peptides reveal novel features at the N-terminus of the groove
Components
  • ALA-PHE-ALA-LYS-LYS-LYS-TYR-CYS-LEU
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I protein (Fragment)
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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / 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 / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / 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 / 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 / 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, 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 ...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
MHC class I protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 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 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 2.0Aug 23, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.details
Revision 2.1Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: MHC class I protein (Fragment)
B: Beta-2-microglobulin
C: ALA-PHE-ALA-LYS-LYS-LYS-TYR-CYS-LEU


Theoretical massNumber of molelcules
Total (without water)46,1543
Polymers46,1543
Non-polymers00
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-28 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.742, 81.388, 110.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I protein (Fragment)


Mass: 31902.004 Da / Num. of mol.: 1 / Mutation: E76C
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: A0A3G6II09
#2: Protein Beta-2-microglobulin / 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 ALA-PHE-ALA-LYS-LYS-LYS-TYR-CYS-LEU


Mass: 2372.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.2 M ammonium acetate, 15% PEG 4000, 0.1 M sodium citrate, pH5.6,

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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: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.07→99 Å / Num. obs: 196900 / % possible obs: 98.3 % / Redundancy: 1.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.025 / Rrim(I) all: 0.036 / Χ2: 0.509 / Net I/σ(I): 20 / Num. measured all: 328562
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.13-1.1610.00599400.9490.9870.0050.0050100
1.16-1.1810.00599250.9490.9870.0050.0050100
1.18-1.2110.00599100.9490.9870.0050.0050100
1.21-1.241.60.11999540.9490.9870.1190.1681.068100
1.24-1.2720.09299460.9650.9910.0920.130.951100
1.27-1.3120.07299380.9770.9940.0720.1020.832100
1.31-1.3520.05699540.980.9950.0560.080.691100
1.35-1.420.04299500.9860.9970.0420.0590.541100
1.4-1.4620.03299960.9870.9970.0320.0460.443100
1.46-1.5220.02799590.9860.9970.0270.0380.373100
1.52-1.620.026100210.9840.9960.0260.0360.35399.9
1.6-1.720.024100030.9820.9950.0240.0340.30999.8
1.7-1.8420.021100160.9870.9970.0210.0290.26999.6
1.84-2.021.90.0297730.9910.9980.020.0290.29297.1
2.02-2.311.90.0296570.990.9970.020.0290.30495.2
2.31-2.9120.022100050.990.9970.0220.0310.34398.1
2.91-991.90.02791210.9810.9950.0270.0380.53986.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6p2s

6p2s


Resolution: 1.13→32.84 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.784 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21701 7053 4.9 %RANDOM
Rwork0.18928 ---
obs0.19061 137770 85.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.776 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2--1.35 Å2-0 Å2
3----1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.13→32.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 0 379 3482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0133189
X-RAY DIFFRACTIONr_bond_other_d0.0180.0172792
X-RAY DIFFRACTIONr_angle_refined_deg1.4031.664327
X-RAY DIFFRACTIONr_angle_other_deg1.631.5846475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8625374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32621.22205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7441531
X-RAY DIFFRACTIONr_chiral_restr0.0690.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023618
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02743
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.313.2241508
X-RAY DIFFRACTIONr_mcbond_other8.3123.2241507
X-RAY DIFFRACTIONr_mcangle_it10.4314.8161878
X-RAY DIFFRACTIONr_mcangle_other10.4284.8161879
X-RAY DIFFRACTIONr_scbond_it4.7383.6031681
X-RAY DIFFRACTIONr_scbond_other4.7383.6031681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2135.2892449
X-RAY DIFFRACTIONr_long_range_B_refined7.92136.9123547
X-RAY DIFFRACTIONr_long_range_B_other7.92336.3883476
X-RAY DIFFRACTIONr_rigid_bond_restr13.60635981
X-RAY DIFFRACTIONr_sphericity_free19.8445257
X-RAY DIFFRACTIONr_sphericity_bonded18.10456017
LS refinement shellResolution: 1.134→1.164 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.487 115 -
Rwork0.41 2330 -
obs--19.58 %

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