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Yorodumi- PDB-5knm: Human leukocyte antigen F (HLA-F) presents peptides and regulates... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5knm | ||||||
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| Title | Human leukocyte antigen F (HLA-F) presents peptides and regulates immunity through interactions with NK-cell receptors | ||||||
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Keywords | PROTEIN BINDING / MHC-Ib / IMMUNE SYSTEM / PEPTIDE BINDING PROTEIN | ||||||
| Function / homology | Function and homology informationnegative regulation of natural killer cell cytokine production / negative regulation of natural killer cell degranulation / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / MHC class Ib protein complex binding / positive regulation of natural killer cell degranulation / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity ...negative regulation of natural killer cell cytokine production / negative regulation of natural killer cell degranulation / HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / MHC class Ib protein complex binding / positive regulation of natural killer cell degranulation / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / MHC class Ib receptor activity / negative regulation of T cell cytokine production / positive regulation of natural killer cell cytokine production / TAP2 binding / TAP1 binding / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of osteoclast development / protein phosphatase 1 binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / T cell proliferation involved in immune response / positive regulation of macrophage cytokine production / negative regulation of interleukin-10 production / beta-2-microglobulin binding / negative regulation of calcium ion transport / negative regulation of cell cycle / MHC class I protein binding / negative regulation of type II interferon production / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / 14-3-3 protein binding / SH2 domain binding / 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 / lumenal side of endoplasmic reticulum membrane / 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 / receptor internalization / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to virus / specific granule lumen / positive regulation of type II interferon production / 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 / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane Similarity search - Function | ||||||
| Biological species | Homo sapiens (human) Trichoplusia ni (cabbage looper) | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Dulberger, C.L. / Adams, E.J. | ||||||
| Funding support | United States, 1items
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Citation | Journal: Immunity / Year: 2017Title: Human Leukocyte Antigen F Presents Peptides and Regulates Immunity through Interactions with NK Cell Receptors. Authors: Dulberger, C.L. / McMurtrey, C.P. / Holzemer, A. / Neu, K.E. / Liu, V. / Steinbach, A.M. / Garcia-Beltran, W.F. / Sulak, M. / Jabri, B. / Lynch, V.J. / Altfeld, M. / Hildebrand, W.H. / Adams, E.J. | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5knm.cif.gz | 258.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5knm.ent.gz | 210.2 KB | Display | PDB format |
| PDBx/mmJSON format | 5knm.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5knm_validation.pdf.gz | 501.5 KB | Display | wwPDB validaton report |
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| Full document | 5knm_full_validation.pdf.gz | 515.3 KB | Display | |
| Data in XML | 5knm_validation.xml.gz | 22.8 KB | Display | |
| Data in CIF | 5knm_validation.cif.gz | 30.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/5knm ftp://data.pdbj.org/pub/pdb/validation_reports/kn/5knm | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5iueC ![]() 1psaS C: citing same article ( S: Starting model for refinement |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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Components
| #1: Protein | Mass: 32769.074 Da / Num. of mol.: 1 / Fragment: UNP residues 22-305 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACgp67a / Cell (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3KUD8, UniProt: P30511*PLUS |
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| #2: Protein | Mass: 20060.281 Da / Num. of mol.: 1 / Fragment: UNP rrsidues 21-119 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pACgp67a / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61769 |
| #3: Protein | Mass: 29467.047 Da / Num. of mol.: 1 / Fragment: UNP residues 24-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LILRB1, ILT2, LIR1, MIR7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NHL6 |
| #4: Protein/peptide | Mass: 844.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Production host: Trichoplusia ni (cabbage looper) |
| #5: Sugar | ChemComp-NAG / |
| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 67.59 % / Description: hexagonal plates |
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| Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 27% PEG 550 MME .1 M Tris-HCl 300 mM NaCl |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å |
| Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 20, 2014 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.03318 Å / Relative weight: 1 |
| Reflection | Resolution: 3.304→49.406 Å / Num. obs: 17859 / % possible obs: 99 % / Redundancy: 9.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1413 / Net I/σ(I): 1.57 |
| Reflection shell | Resolution: 3.304→3.422 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.136 / Mean I/σ(I) obs: 1.57 / CC1/2: 0.801 / % possible all: 99 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1PSA Resolution: 3.3→49.41 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.49 / Stereochemistry target values: ML
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| Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 3.3→49.41 Å
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| Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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About Yorodumi



Homo sapiens (human)
Trichoplusia ni (cabbage looper)
X-RAY DIFFRACTION
United States, 1items
Citation











PDBj






