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- PDB-2ver: Structural model for the complex between the Dr adhesins and carc... -

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Basic information

Entry
Database: PDB / ID: 2ver
TitleStructural model for the complex between the Dr adhesins and carcinoembryonic antigen (CEA)
Components
  • AFIMBRIAL ADHESIN AFA-III
  • ARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 5
KeywordsCELL ADHESION / MEMBRANE / FIMBRIUM / GPI-ANCHOR / LIPOPROTEIN / IMMUNOGLOBULIN DOMAIN / CELL PROJECTION
Function / homology
Function and homology information


GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / pilus / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall ...GPI anchor binding / homotypic cell-cell adhesion / negative regulation of myotube differentiation / Post-translational modification: synthesis of GPI-anchored proteins / heterophilic cell-cell adhesion / pilus / homophilic cell-cell adhesion / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / apoptotic process / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / : / Adhesion domain superfamily / Immunoglobulin domain / Immunoglobulin domain ...Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / : / Adhesion domain superfamily / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MTN / Cell adhesion molecule CEACAM5 / Afimbrial adhesin AFA-III
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
HOMO SAPIENS (human)
MethodSOLUTION NMR / HADDOCK
Model type detailsMINIMIZED AVERAGE
AuthorsKorotkova, N. / Yang, Y. / Le Trong, I. / Cota, E. / Demeler, B. / Marchant, J. / Thomas, W.E. / Stenkamp, R.E. / Moseley, S.L. / Matthews, S.
CitationJournal: 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
DepositionOct 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 12, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AFIMBRIAL ADHESIN AFA-III
N: ARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5645
Polymers27,7712
Non-polymers7933
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200REPRESENTATIVE STRUCTURE
RepresentativeModel #1

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Components

#1: Protein AFIMBRIAL ADHESIN AFA-III / AFAE


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
#2: Protein ARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 5 / CEA / CARCINOEMBRYONIC ANTIGEN / MECONIUM ANTIGEN 100 / CD66E ANTIGEN


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 ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL


Mass: 264.385 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H18NO3S2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: HSQC
NMR detailsText: STRUCTURE WAS DETERMINED USING NMR RESTRAINT DRIVEN DOCKING (CHEMICAL SHIFTA AND PARAMAGNETIC RELAXATION ENHANCEMENTS (PRES)

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Sample preparation

DetailsContents: 10% H20/90% D20
Sample conditionsIonic strength: 2- mM / pH: 7 / Pressure: 1.0 atm / Temperature: 303.0 K

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NMR measurement

NMR spectrometerType: Bruker OTHER / Manufacturer: Bruker / Model: OTHER / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: HADDOCK / Software ordinal: 1 / Details: WATER SHELL
NMR ensembleConformer selection criteria: REPRESENTATIVE STRUCTURE / Conformers calculated total number: 200 / Conformers submitted total number: 1

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