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- PDB-9mda: Conformational flexibility in HLA-B8: peptide tuning structural a... -

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Basic information

Entry
Database: PDB / ID: 9mda
TitleConformational flexibility in HLA-B8: peptide tuning structural and dynamical changes
Components
  • ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-PHE-ALA-GLY-LYS-LYS-TYR-CYS-LEU
  • Beta-2-microglobulin
  • MHC class I protein
KeywordsIMMUNE SYSTEM / HLA-B8 Long MHC I peptides MHC I intermediate forms
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / 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 ...antigen processing and presentation of peptide antigen via MHC class I / 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 / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen binding / positive regulation of T cell activation / 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 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
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: 1.6 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: To Be Published
Title: Conformational flexibility in HLA-B8: peptide tuning structural and dynamical changes
Authors: Li, L. / Peng, X. / Vinjamuri, S. / Bouvier, M.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,8543
Polymers45,8543
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: refolding
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-24 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.740, 81.550, 110.600
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


Mass: 31804.891 Da / Num. of mol.: 1 / Mutation: E76C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: PLM1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: A0A3G6II09
#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 / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: P61769
#3: Protein/peptide ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-ARG-ALA-PHE-ALA-GLY-LYS-LYS-TYR-CYS-LEU


Mass: 2300.782 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.: 188 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12.5-16% PEG 4000,100mM citrate acid pH5.5 ,100mM ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.87313 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Dec 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.6→45.79 Å / Num. obs: 65307 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 7.2
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 3.5 % / Num. unique obs: 3265 / CC1/2: 0.862 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.705 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23947 3051 5 %RANDOM
Rwork0.20161 ---
obs0.20348 57580 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.074 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-0 Å2
2---0.19 Å20 Å2
3---1.28 Å2
Refinement stepCycle: 1 / Resolution: 1.6→45.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3140 0 0 188 3328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142869
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.6614385
X-RAY DIFFRACTIONr_angle_other_deg1.4541.5876607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.67521.34209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3341531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023712
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
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_it2.4482.5441529
X-RAY DIFFRACTIONr_mcbond_other2.4482.5441528
X-RAY DIFFRACTIONr_mcangle_it3.3983.8061906
X-RAY DIFFRACTIONr_mcangle_other3.3973.8061907
X-RAY DIFFRACTIONr_scbond_it3.9483.0381700
X-RAY DIFFRACTIONr_scbond_other3.9483.0381700
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9944.372479
X-RAY DIFFRACTIONr_long_range_B_refined7.47849.20612836
X-RAY DIFFRACTIONr_long_range_B_other7.48349.12412737
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 204 -
Rwork0.272 3871 -
obs--91.04 %

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