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- PDB-8xes: The structure of HLA-A/L1-1 -

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Basic information

Entry
Database: PDB / ID: 8xes
TitleThe structure of HLA-A/L1-1
Components
  • Beta-2-microglobulin
  • HLA class I heavy chain
  • Major capsid protein L1
KeywordsIMMUNE SYSTEM / Complex / Peptide presentation
Function / homology
Function and homology information


T=7 icosahedral viral capsid / antigen processing and presentation / 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 ...T=7 icosahedral viral capsid / antigen processing and presentation / 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 / lumenal side of endoplasmic reticulum membrane / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / 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 / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Modulation by Mtb of host immune system / 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 / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / symbiont entry into host cell / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : ...Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Major capsid protein L1 / Beta-2-microglobulin / HLA class I heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Human papillomavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, J.N. / Yue, C. / Liu, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Immunohorizons / Year: 2024
Title: Uncommon P1 Anchor-featured Viral T Cell Epitope Preference within HLA-A*2601 and HLA-A*0101 Individuals.
Authors: Zhang, J. / Yue, C. / Lin, Y. / Tian, J. / Guo, Y. / Zhang, D. / Guo, Y. / Ye, B. / Chai, Y. / Qi, J. / Zhao, Y. / Gao, G.F. / Sun, Z. / Liu, J.
History
DepositionDec 12, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: HLA class I heavy chain
B: Beta-2-microglobulin
C: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)44,7053
Polymers44,7053
Non-polymers00
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-16 kcal/mol
Surface area18620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.116, 66.534, 49.327
Angle α, β, γ (deg.)90.000, 90.229, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-469-

HOH

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Components

#1: Protein HLA class I heavy chain / HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / A ...HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / A alpha chain / HLA-A26.3 antigen / MHC class I antigen / MHC class I protein


Mass: 31859.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA, HLA-A26 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SPM2
#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 Major capsid protein L1


Mass: 1097.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human papillomavirus / References: UniProt: A0A1U9YFU1
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-Tris, 20%w/v Polyethylene glycol monomethyl ether 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.78→27.58 Å / Num. obs: 52088 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 25.98 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 16.6
Reflection shellResolution: 1.78→1.84 Å / Num. unique obs: 52088 / Rpim(I) all: 0.026

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Processing

Software
NameVersionClassification
PHENIX1.13_2998model building
PHENIX1.13_2998refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→27.58 Å / SU ML: 0.2007 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.5981 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2349 2642 5.1 %
Rwork0.2048 49130 -
obs0.2064 51772 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.93 Å2
Refinement stepCycle: LAST / Resolution: 1.78→27.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3150 0 0 310 3460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663239
X-RAY DIFFRACTIONf_angle_d0.84714396
X-RAY DIFFRACTIONf_chiral_restr0.0502443
X-RAY DIFFRACTIONf_plane_restr0.0049580
X-RAY DIFFRACTIONf_dihedral_angle_d3.17641911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.38271350.33652554X-RAY DIFFRACTION98.32
1.81-1.840.31391330.30632579X-RAY DIFFRACTION98.8
1.84-1.880.35561410.27692561X-RAY DIFFRACTION98.9
1.88-1.920.30581430.272548X-RAY DIFFRACTION98.5
1.92-1.970.28961060.25282625X-RAY DIFFRACTION98.7
1.97-2.010.2891670.25282531X-RAY DIFFRACTION98.9
2.01-2.070.26061430.23552570X-RAY DIFFRACTION99.34
2.07-2.130.24471430.23082577X-RAY DIFFRACTION98.98
2.13-2.20.26121400.23512558X-RAY DIFFRACTION99.08
2.2-2.280.25471450.23522587X-RAY DIFFRACTION99.38
2.28-2.370.31031510.23632593X-RAY DIFFRACTION99.2
2.37-2.480.31711300.23752596X-RAY DIFFRACTION99.2
2.48-2.610.241300.2362591X-RAY DIFFRACTION99.23
2.61-2.770.2631120.22472648X-RAY DIFFRACTION99.17
2.77-2.980.26781410.22292540X-RAY DIFFRACTION98.86
2.98-3.280.24361220.20842631X-RAY DIFFRACTION99.14
3.28-3.760.22751700.18672564X-RAY DIFFRACTION98.24
3.76-4.730.16821460.15292598X-RAY DIFFRACTION98.74
4.73-27.580.17141440.15122679X-RAY DIFFRACTION99.19

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