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- PDB-7u21: Human Class I MHC HLA-A2 in complex with AVGSYVYSV peptide -

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Basic information

Entry
Database: PDB / ID: 7u21
TitleHuman Class I MHC HLA-A2 in complex with AVGSYVYSV peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen, A-2 alpha chain
  • PGM5 peptide (465-473) (H5Y)
KeywordsIMMUNE SYSTEM / Class I Major Histocompatibility Complex / HLA-A*02 / PGM5
Function / homology
Function and homology information


antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / 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 / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / 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 antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWeiss, L.I. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R35GM118166 United States
CitationJournal: Front Immunol / Year: 2022
Title: Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/MHC Complexes.
Authors: Keller, G.L.J. / Weiss, L.I. / Baker, B.M.
History
DepositionFeb 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: PGM5 peptide (465-473) (H5Y)
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: PGM5 peptide (465-473) (H5Y)


Theoretical massNumber of molelcules
Total (without water)89,3556
Polymers89,3556
Non-polymers00
Water13,367742
1
A: MHC class I antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: PGM5 peptide (465-473) (H5Y)


Theoretical massNumber of molelcules
Total (without water)44,6783
Polymers44,6783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-26 kcal/mol
Surface area19120 Å2
MethodPISA
2
D: MHC class I antigen, A-2 alpha chain
E: Beta-2-microglobulin
F: PGM5 peptide (465-473) (H5Y)


Theoretical massNumber of molelcules
Total (without water)44,6783
Polymers44,6783
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-24 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.481, 84.647, 84.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein MHC class I antigen, A-2 alpha chain


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1Blue / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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): XL1Blue / References: UniProt: P61769
#3: Protein/peptide PGM5 peptide (465-473) (H5Y)


Mass: 944.041 Da / Num. of mol.: 2 / Mutation: H5Y / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 15% PEG 3350, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.05 Å / Num. obs: 61286 / % possible obs: 93.43 % / Redundancy: 2 % / Biso Wilson estimate: 16.05 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.04559 / Rpim(I) all: 0.04559 / Rrim(I) all: 0.06447 / Net I/σ(I): 8.2
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.2133 / Mean I/σ(I) obs: 1.49 / Num. unique obs: 5495 / CC1/2: 0.889 / CC star: 0.97 / Rpim(I) all: 0.2133 / Rrim(I) all: 0.3017 / % possible all: 85.5

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
DIALSdata reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PWL

3pwl


Resolution: 1.9→48.05 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 21.1588
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2143 6097 10.03 %
Rwork0.1926 54684 -
obs0.1948 60781 93.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 0 742 7044
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00586480
X-RAY DIFFRACTIONf_angle_d0.89768792
X-RAY DIFFRACTIONf_chiral_restr0.057894
X-RAY DIFFRACTIONf_plane_restr0.00581148
X-RAY DIFFRACTIONf_dihedral_angle_d15.61622360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.29761770.24791576X-RAY DIFFRACTION81.61
1.92-1.940.26831890.24971730X-RAY DIFFRACTION88.76
1.94-1.960.24191910.23871638X-RAY DIFFRACTION83.06
1.96-1.990.22211710.20321612X-RAY DIFFRACTION84.22
1.99-2.020.26352020.20521859X-RAY DIFFRACTION92.5
2.02-2.040.23372040.20351794X-RAY DIFFRACTION96.1
2.04-2.070.24192080.20821864X-RAY DIFFRACTION96.33
2.07-2.10.27782180.2011924X-RAY DIFFRACTION96.66
2.1-2.140.22682030.20461862X-RAY DIFFRACTION97.18
2.14-2.170.23442170.19671914X-RAY DIFFRACTION96.73
2.17-2.210.21372050.1941843X-RAY DIFFRACTION97.38
2.21-2.250.21492170.20051951X-RAY DIFFRACTION97.88
2.25-2.290.2262110.19731910X-RAY DIFFRACTION97.79
2.29-2.340.24722100.19821913X-RAY DIFFRACTION98.01
2.34-2.390.22832030.20691930X-RAY DIFFRACTION97.58
2.39-2.440.23712160.20841896X-RAY DIFFRACTION98.32
2.44-2.510.22162120.2041899X-RAY DIFFRACTION97.87
2.51-2.570.23522140.20391915X-RAY DIFFRACTION98.02
2.57-2.650.23652070.20781927X-RAY DIFFRACTION98.02
2.65-2.730.23422270.19951868X-RAY DIFFRACTION97.31
2.73-2.830.25251940.21111752X-RAY DIFFRACTION88.49
2.83-2.950.22772090.20391860X-RAY DIFFRACTION95.83
2.95-3.080.21612070.20481911X-RAY DIFFRACTION97.83
3.08-3.240.21742100.18741884X-RAY DIFFRACTION96.06
3.24-3.450.20422170.18581842X-RAY DIFFRACTION94.45
3.45-3.710.18881950.17421826X-RAY DIFFRACTION92.2
3.71-4.080.16331920.16071744X-RAY DIFFRACTION89.67
4.08-4.670.14421940.14671685X-RAY DIFFRACTION85.6
4.68-5.890.20131750.17181623X-RAY DIFFRACTION81.73
5.89-48.050.18662020.19311732X-RAY DIFFRACTION85.61
Refinement TLS params.Method: refined / Origin x: 14.7679611399 Å / Origin y: -20.744828128 Å / Origin z: 21.5311656058 Å
111213212223313233
T0.130483162155 Å2-0.00446909390016 Å2-0.0028126165134 Å2-0.1809075517 Å2-0.0126720487288 Å2--0.128724918013 Å2
L0.215627128324 °2-0.0664263207118 °20.0244920967545 °2-0.199635163549 °2-0.0471511799216 °2--0.0252863333899 °2
S0.0141159833865 Å °-0.0393925750971 Å °0.00358462864443 Å °0.00264245982756 Å °-0.0112463449849 Å °0.00377655986484 Å °0.00366067527521 Å °-0.0209538506118 Å °-0.00319326707078 Å °
Refinement TLS groupSelection details: all

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