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- PDB-8ec5: Structures of HLA-B8E76C loaded with long peptides reveal novel f... -

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Basic information

Entry
Database: PDB / ID: 8ec5
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
  • peptide RARARARARARAFVKKKYCL
KeywordsIMMUNE SYSTEM / MHC class I / Antigen Processing and Presentation / Long peptides / HLA-B8
Function / homology
Function and homology information


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 / cellular response to iron(III) ion ...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 / 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 / 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 / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
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: 1.22 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
DepositionSep 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 14, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: peptide RARARARARARAFVKKKYCL


Theoretical massNumber of molelcules
Total (without water)46,0513
Polymers46,0513
Non-polymers00
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-21 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.758, 81.149, 110.580
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: 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
#3: Protein/peptide peptide RARARARARARAFVKKKYCL


Mass: 2400.963 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.: 357 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.26 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.8
Details: 0.2 M ammonium acetate, 15% PEG 10000, 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: Aug 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 133304 / % possible obs: 98.5 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.026 / Rrim(I) all: 0.076 / Χ2: 2.372 / Net I/σ(I): 10.6 / Num. measured all: 1207616
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.22-1.248.10.67266990.8790.2440.7161.06699.9
1.24-1.2690.57667070.9340.1970.6091.12100
1.26-1.299.30.54366540.9440.1840.5741.167100
1.29-1.319.50.46767280.9570.1570.4931.335100
1.31-1.349.60.41366730.9620.1380.4361.294100
1.34-1.379.60.35967230.9690.120.3791.395100
1.37-1.419.60.3167060.9780.1030.3271.515100
1.41-1.459.70.27267210.980.090.2871.678100
1.45-1.499.70.23167190.9850.0770.2441.912100
1.49-1.549.60.19767220.9870.0660.2082.261100
1.54-1.599.60.17267310.990.0580.1822.578100
1.59-1.669.60.14867160.9920.0490.1562.83100
1.66-1.739.60.12767380.9940.0420.1343.026100
1.73-1.829.50.1167770.9950.0370.1163.215100
1.82-1.947.10.09463790.9940.0360.1013.56994.1
1.94-2.099.20.0867840.9970.0280.0853.937100
2.09-2.37.20.07162400.9960.0260.0763.95991.5
2.3-2.639.30.06268330.9980.0210.0663.697100
2.63-3.319.10.05269160.9980.0180.0553.52299.8
3.31-506.80.04861380.9960.020.0533.43785.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6p2s

6p2s


Resolution: 1.22→24 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.603 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 6556 4.9 %RANDOM
Rwork0.1988 ---
obs0.1995 126660 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 18.99 Å2 / Biso min: 9.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---1.13 Å20 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 1.22→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 0 357 3356
Biso mean---28.83 -
Num. residues----366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133080
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172697
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.6584178
X-RAY DIFFRACTIONr_angle_other_deg1.511.5856251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6955362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.67621.32197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33515505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4621529
X-RAY DIFFRACTIONr_chiral_restr0.1080.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023497
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02718
LS refinement shellResolution: 1.221→1.253 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 441 -
Rwork0.262 8925 -
all-9366 -
obs--94.54 %

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