+Open data
-Basic information
Entry | Database: PDB / ID: 1fne | ||||||
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Title | HISTOCOMPATIBILITY ANTIGEN | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN / MHC | ||||||
Function / homology | Function and homology information hemoglobin beta binding / positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / erythrocyte development / organic acid binding / cellular oxidant detoxification / hemoglobin binding ...hemoglobin beta binding / positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / erythrocyte development / organic acid binding / cellular oxidant detoxification / hemoglobin binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / regulation of erythrocyte differentiation / oxygen binding / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosomal membrane / heme binding / protein-containing complex binding / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Miley, M.J. / Nelson, C.A. / Fremont, D.H. | ||||||
Citation | Journal: J.Immunol. / Year: 2001 Title: Structural and functional consequences of altering a peptide MHC anchor residue. Authors: Kersh, G.J. / Miley, M.J. / Nelson, C.A. / Grakoui, A. / Horvath, S. / Donermeyer, D.L. / Kappler, J. / Allen, P.M. / Fremont, D.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fne.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fne.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 1fne.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/1fne ftp://data.pdbj.org/pub/pdb/validation_reports/fn/1fne | HTTPS FTP |
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-Related structure data
Related structure data | 1fngC 1ieaS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 22361.051 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTO-DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04224 #2: Protein | Mass: 25362.254 Da / Num. of mol.: 2 Fragment: SOLUBLE ECTO-DOMAIN WITH COVALENTLY ATTACHED HB PEPTIDE Mutation: E(6P)D IN PEPTIDE RESIDUE 6P Source method: isolated from a genetically manipulated source Details: WITH COVALENTLY BOUND HB(D73) PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02089, GenBank: AAA39594 #3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | Compound details | THIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II MOLECULE I- ...THIS ENTRY CONTAINS COORDINATE | Sequence details | RESIDUES (1L - 16L)IN CHAINS B & D FORM A POLYPEPTID | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 15% PEG 4000 15% 2-PROPANOL 300mM-500mM AMMONIUM ACETATE 100mM CITRATE PH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7 | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 364002 / Num. obs: 72521 / % possible obs: 94.4 % / Redundancy: 5.01 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.9→1.96 Å / Rmerge(I) obs: 0.301 / % possible all: 92.6 |
Reflection | *PLUS Num. measured all: 364002 |
Reflection shell | *PLUS % possible obs: 75.6 % / Mean I/σ(I) obs: 2.45 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IEA Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 845534.75 / Data cutoff high rms absF: 845534.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.25 Å2 / ksol: 0.356 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.96 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5.1 % / Rfactor Rfree: 0.27 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 41.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.42 / % reflection Rfree: 5 % / Rfactor Rwork: 0.36 / Rfactor obs: 0.36 |