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Yorodumi- PDB-2ver: Structural model for the complex between the Dr adhesins and carc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ver | ||||||
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Title | Structural model for the complex between the Dr adhesins and carcinoembryonic antigen (CEA) | ||||||
Components |
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Keywords | CELL ADHESION / MEMBRANE / FIMBRIUM / GPI-ANCHOR / LIPOPROTEIN / IMMUNOGLOBULIN DOMAIN / CELL PROJECTION | ||||||
Function / homology | Function and homology information GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / pilus / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall ...GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / pilus / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / negative regulation of apoptotic process / apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / HADDOCK | ||||||
Model type details | MINIMIZED AVERAGE | ||||||
Authors | Korotkova, N. / Yang, Y. / Le Trong, I. / Cota, E. / Demeler, B. / Marchant, J. / Thomas, W.E. / Stenkamp, R.E. / Moseley, S.L. / Matthews, S. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2008 Title: Binding of Dr Adhesins of Escherichia Coli to Carcinoembryonic Antigen Triggers Receptor Dissociation. Authors: Korotkova, N. / Yang, Y. / Le Trong, I. / Cota, E. / Demeler, B. / Marchant, J. / Thomas, W.E. / Stenkamp, R.E. / Moseley, S.L. / Matthews, S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ver.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ver.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ver.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ver_validation.pdf.gz | 497.7 KB | Display | wwPDB validaton report |
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Full document | 2ver_full_validation.pdf.gz | 499.7 KB | Display | |
Data in XML | 2ver_validation.xml.gz | 7 KB | Display | |
Data in CIF | 2ver_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ve/2ver ftp://data.pdbj.org/pub/pdb/validation_reports/ve/2ver | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15456.051 Da / Num. of mol.: 1 / Fragment: RESIDUES 38-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: DR/AFA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q57254 |
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#2: Protein | Mass: 12314.913 Da / Num. of mol.: 1 / Fragment: N DOMAIN, RESIDUES 35-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P06731 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: HSQC |
NMR details | Text: STRUCTURE WAS DETERMINED USING NMR RESTRAINT DRIVEN DOCKING (CHEMICAL SHIFTA AND PARAMAGNETIC RELAXATION ENHANCEMENTS (PRES) |
-Sample preparation
Details | Contents: 10% H20/90% D20 |
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Sample conditions | Ionic strength: 2- mM / pH: 7 / Pressure: 1.0 atm / Temperature: 303.0 K |
-NMR measurement
NMR spectrometer | Type: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: HADDOCK / Software ordinal: 1 / Details: WATER SHELL | |||||||||
NMR ensemble | Conformer selection criteria: REPRESENTATIVE STRUCTURE / Conformers calculated total number: 200 / Conformers submitted total number: 1 |