+Open data
-Basic information
Entry | Database: PDB / ID: 6xnt | ||||||
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Title | Crystal structure of I91A mutant of human CEACAM1 | ||||||
Components | Carcinoembryonic antigen-related cell adhesion molecule 1 | ||||||
Keywords | IMMUNE SYSTEM / CEACAM1 | ||||||
Function / homology | Function and homology information regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / Regulation of MITF-M dependent genes involved in invasion / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / filamin binding / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / bile acid transmembrane transporter activity / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / Fibronectin matrix formation / insulin catabolic process / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / regulation of immune system process / negative regulation of platelet aggregation / bile acid and bile salt transport / negative regulation of vascular permeability / wound healing, spreading of cells / transport vesicle membrane / microvillus membrane / negative regulation of T cell receptor signaling pathway / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / blood vessel development / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / specific granule membrane / regulation of cell migration / regulation of ERK1 and ERK2 cascade / protein tyrosine kinase binding / basal plasma membrane / integrin-mediated signaling pathway / regulation of cell growth / Cell surface interactions at the vascular wall / adherens junction / negative regulation of protein kinase activity / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell migration / cell junction / actin binding / protein phosphatase binding / angiogenesis / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Gandhi, A.K. / Kim, W.M. / Sun, Z.-Y. / Huang, Y.H. / Bonsor, D. / Petsko, G.A. / Kuchroo, V. / Blumberg, R.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Structural basis of the dynamic human CEACAM1 monomer-dimer equilibrium. Authors: Gandhi, A.K. / Sun, Z.J. / Kim, W.M. / Huang, Y.H. / Kondo, Y. / Bonsor, D.A. / Sundberg, E.J. / Wagner, G. / Kuchroo, V.K. / Petsko, G.A. / Blumberg, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xnt.cif.gz | 56.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xnt.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/6xnt ftp://data.pdbj.org/pub/pdb/validation_reports/xn/6xnt | HTTPS FTP |
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-Related structure data
Related structure data | 6xnoC 6xnwC 6xo1C 4qxwS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11857.090 Da / Num. of mol.: 2 / Mutation: I91A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13688 #2: Sugar | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 54% Tascimate with 0.5 % n-Octyl-D-glucoside pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | ||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 7, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→72.2 Å / Num. obs: 6265 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.963 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.077 / Rrim(I) all: 0.263 / Net I/σ(I): 9.4 / Num. measured all: 73320 / Scaling rejects: 95 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QXW Resolution: 3.1→72.2 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.848 / SU B: 16.549 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.99 Å2 / Biso mean: 42.332 Å2 / Biso min: 25.37 Å2
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Refinement step | Cycle: final / Resolution: 3.1→72.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 /
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