+Open data
-Basic information
Entry | Database: PDB / ID: 6aw2 | ||||||
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Title | Crystal structure of the HopQ-CEACAM1 complex | ||||||
Components |
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Keywords | CELL ADHESION | ||||||
Function / homology | Function and homology information regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of epidermal growth factor receptor signaling pathway / regulation of sprouting angiogenesis / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / 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 / filamin binding / 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 / microvillus membrane / transport vesicle 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 / protein tyrosine kinase binding / basal plasma membrane / regulation of ERK1 and ERK2 cascade / 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 migration / cell-cell junction / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Helicobacter pylori (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å | ||||||
Authors | Bonsor, D.A. / Sundberg, E.J. | ||||||
Citation | Journal: EMBO J. / Year: 2018 Title: TheHelicobacter pyloriadhesin protein HopQ exploits the dimer interface of human CEACAMs to facilitate translocation of the oncoprotein CagA. Authors: Bonsor, D.A. / Zhao, Q. / Schmidinger, B. / Weiss, E. / Wang, J. / Deredge, D. / Beadenkopf, R. / Dow, B. / Fischer, W. / Beckett, D. / Wintrode, P.L. / Haas, R. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6aw2.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6aw2.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 6aw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/6aw2 ftp://data.pdbj.org/pub/pdb/validation_reports/aw/6aw2 | HTTPS FTP |
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-Related structure data
Related structure data | 6avzC 6aw0C 6aw1C 6aw3C 2gk2S 5lp2S 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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Unit cell |
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-Components
#1: Protein | Mass: 12101.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P13688 |
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#2: Protein | Mass: 47027.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: hopQ / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: H6A3H4 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 6000, 0.1M HEPES , pH 7.5, 0.2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2017 / Details: Rh coated |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.68→103.08 Å / Num. obs: 13386 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.079 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.68→2.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1673 / Rpim(I) all: 0.664 / % possible all: 94.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5lp2 2gk2 Resolution: 2.68→103.08 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.793 / SU ML: 0.374 / Cross valid method: THROUGHOUT / ESU R Free: 0.395 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #Refmac command script from PDB_REDO 6.28 # #Use of riding hydrogens make hydrogen ALL #B-factor model selection refi bref ISOT #Solvent ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #Refmac command script from PDB_REDO 6.28 # #Use of riding hydrogens make hydrogen ALL #B-factor model selection refi bref ISOT #Solvent related settings scal type SIMP lssc function a sigma n solvent YES solvent vdwprobe 1.0 ionprobe 0.9 rshrink 0.9 tlsd waters exclude #Restraint weights weight MATRIX 0.005 temp 1.00
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.376 Å2
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Refinement step | Cycle: 1 / Resolution: 2.68→103.08 Å
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