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- PDB-1e07: Model of human carcinoembryonic antigen by homology modelling and... -

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Basic information

Entry
Database: PDB / ID: 10000000
TitleModel of human carcinoembryonic antigen by homology modelling and curve-fitting to experimental solution scattering data
ComponentsCARCINOEMBRYONIC ANTIGEN
KeywordsGLYCOPROTEIN / CEA / TUMOUR MARKER / IMMUNOGLOBULIN-FOLD
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 / 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 ...GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / 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
: / 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 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
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION SCATTERING
Model type detailsCA ATOMS ONLY, CHAIN A
AuthorsBoehm, M.K. / Perkins, S.J.
Citation
Journal: Febs Lett. / Year: 2000
Title: Structural models for carcinoembryonic antigen and its complex with the single-chain Fv antibody molecule MFE23.
Authors: Boehm, M.K. / Perkins, S.J.
#1: Journal: Biochem.J. / Year: 2000
Title: Crystal Structure of the Anti-(Carcinoembryonic Antigen) Single-Chain Fv Antibody Mfe-23 and a Model for Antigen Binding Based on Intermolecular Contacts.
Authors: Boehm, M.K. / Corper, A.L. / Wan, T. / Sohi, M.K. / Sutton, B.J. / Thornton, J.D. / Keep, P.A. / Chester, K.A. / Begent, R.H. / Perkins, S.J.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Extended Glycoprotein Structure of the Seven Domains in Human Carcinoembryonic Antigen by X-Ray and Neutron Solution Scattering and an Automated Curve Fitting Procedure: Implications for Cellular Adhesion.
Authors: Boehm, M.K. / Mayans, M.O. / Thornton, J.D. / Begent, R.H. / Keep, P.A. / Perkins, S.J.
History
DepositionMar 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2000Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Version format compliance
Revision 1.2Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARCINOEMBRYONIC ANTIGEN


Theoretical massNumber of molelcules
Total (without water)70,6211
Polymers70,6211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein CARCINOEMBRYONIC ANTIGEN / Coordinate model: Cα atoms only


Mass: 70620.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P06731
Sequence detailsTHE CARCINOEMBRYONIC ANTIGEN PRECURSOR CONTAINS A 34-RESIDUE N-TERMINAL SIGNAL PEPTIDE AND A 26- ...THE CARCINOEMBRYONIC ANTIGEN PRECURSOR CONTAINS A 34-RESIDUE N-TERMINAL SIGNAL PEPTIDE AND A 26-RESIDUE C-TERMINAL HYDROPHOBIC PEPTIDE, BOTH OF WHICH ARE POST-TRANSLATIONALLY CLEAVED.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION SCATTERING

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: solution scattering

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Data collection

Soln scatter
TypeIDBuffer nameConc. range (mg/ml)Data reduction software listDetector typeMean guiner radius (nm)Mean guiner radius esd (nm)Min mean cross sectional radii gyration (nm)Min mean cross sectional radii gyration esd (nm)Num. of time framesProtein lengthSource classSource typeTemperature (K)
x-ray112 MM NA, K PHOSPHATE, 140 MM NACL1.2-7.0OTOKOQUADRANT DETECTOR80.62.10.21033YESRF BEAMLINE ID02288
neutron212 MM NA, K PHOSPHATE, 140 MM NACL 99.9% D2O3.6-7.3COLETTEHE-3 ORDELA DETECTOR8.80.52.30.3129NISIS RUTHERFORD LOQ288
modelling3

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Processing

SoftwareName: DISCOVERY / Classification: refinement
RefinementDetails: ENERGY MINIMIZATION. DETAILS ARE GIVEN IN THE PRIMARY REFERENCE.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms642 0 0 0 642
Soln scatter modelMethod: CONSTRAINED SCATTERING FITTING OF HOMOLOGY MODELS
Details: HUMAN CARCINOEMBRYONIC ANTIGEN (CEA) CONTAINS SEVEN EXTRACELLULAR IMMUNOGLOBULIN (IG) FOLD DOMAINS. THE N- TERMINAL DOMAIN IS PREDICTED TO HAVE A V-TYPE IG FOLD, AND WAS MODELLED USING THE V- ...Details: HUMAN CARCINOEMBRYONIC ANTIGEN (CEA) CONTAINS SEVEN EXTRACELLULAR IMMUNOGLOBULIN (IG) FOLD DOMAINS. THE N- TERMINAL DOMAIN IS PREDICTED TO HAVE A V-TYPE IG FOLD, AND WAS MODELLED USING THE V-TYPE DOMAIN STRUCTURES FROM HUMAN CD2 (CODE: 1HNF), HUMAN CD4 (CODE: 3CD4) AND HUMAN CD8 (CODE: 1CD8) . THE SECOND, FOURTH AND SIXTH DOMAINS (COMMONLY REFERRED TO AS IA, IIA AND IIIA) ARE PREDICTED TO HAVE I-TYPE IG FOLDS, AND WERE MODELLED USING THE I-TYPE DOMAIN STRUCTURE FROM HUMAN VCAM-1 (CODE: 1VCA). THE THIRD, FIFTH AND SEVENTH DOMAINS (COMMONLY REFERRED TO AS IB, IIB AND IIIB) ARE PREDICTED TO HAVE C2-TYPE IG FOLDS, AND WERE MODELLED USING THE C2-TYPE DOMAIN STRUCTURE FROM HUMAN CD2 (CODE: 1HNF). FURTHER DETAILS OF THE HOMOLOGY MODELLING ARE GIVEN IN THE PRIMARY REFERENCE. IN THE COMPLETE CEA MODEL, ALL INTER-DOMAIN ORIENTATIONS BETWEEN NEIGHBOURING DOMAINS ARE BASED ON THAT BETWEEN THE TWO DOMAINS IN HUMAN CD2. SUCH AN ARRANGEMENT OF THE DOMAINS WAS SHOWN TO BE COMPATIBLE WITH THE SOLUTION STRUCTURE OF CEA BY X- RAY AND NEUTRON SCATTERING (SEE REFERENCE TWO).
Entry fitting list: PDB CODE 3CD4, 1CD8 / Num. of conformers submitted: 1 / Software author list: BIOSYM/MSI / Software list: INSIGHT II, HOMOLOGY, SCTPL4, GNOM

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