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NMR Structure - model 1

NMR Structure - model 1, sites

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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Description

Title :   STRUCTURAL MODEL FOR THE COMPLEX BETWEEN THE DR ADHESINS AND CARCINOEMBRYONIC ANTIGEN (CEA)

Authors :   N. Korotkova, Y. Yang, I. Le Trong, E. Cota, B. Demeler, J. Marchant, W. R. E. Stenkamp, S. L. Moseley, S. Matthews

Date :   26 Oct 07 (Deposition) - 08 Jan 08 (Release) - 18 May 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,N
NMR Structure *: A,N  (1x)

Keywords :   Membrane, Fimbrium, Gpi-Anchor, Lipoprotein, Immunoglobulin Domain, Cell Adhesion, Cell Projection (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Korotkova, Y. Yang, I. Le Trong, E. Cota, B. Demeler, J. Marchant, W. E. Thomas, R. E. Stenkamp, S. L. Moseley, S. Matthews
Binding Of Dr Adhesins Of Escherichia Coli To Carcinoembryonic Antigen Triggers Receptor Dissociation.
Mol. Microbiol. V. 67 420 2008
PubMed-ID: 18086185 | Reference-DOI: 10.1111/J.1365-2958.2007.06054.X

Compounds

Molecule 1 - AFIMBRIAL ADHESIN AFA-III
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 38-160
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	DR/AFA
	Synonym	:	AFAE

Molecule 2 - ARCINOEMBRYONIC ANTIGEN-RELATED CELL ADHESION MOLECULE 5
	Chains	:	N
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	N DOMAIN, RESIDUES 35-144
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CEA, CARCINOEMBRYONIC ANTIGEN, MECONIUM ANTIGEN 100, CD66E ANTIGEN

Structural Features

Chains, Units

		1	2
NMR Structure	:	A	N
NMR Structure * (1x)	:	A	N

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 3)

NMR Structure (1, 3)

No.	Name	Count	Type	Full Name
1	MTN	3	Ligand/Ion	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE

NMR Structure * (1, 3)

No.	Name	Count	Type	Full Name
1	MTN	3	Ligand/Ion	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE

Sites (3, 3)

NMR Structure (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:72 , CYS N:39 , HIS N:89 , LEU N:95 , ASN N:97 , GLU N:99	BINDING SITE FOR RESIDUE MTN N1111
2	AC2	SOFTWARE	CYS N:43 , PRO N:59	BINDING SITE FOR RESIDUE MTN N1112
3	AC3	SOFTWARE	THR N:52 , CYS N:54	BINDING SITE FOR RESIDUE MTN N1113

SS Bonds (1, 1)

NMR Structure

No.	Residues
1	A:3	-	A:35

Cis Peptide Bonds (1, 1)

NMR Structure

No.	Residues
1	Thr N:7	-	Pro N:8

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

NMR Structure (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AFAE3_ECOLX_001 *	A	59	T	AFAE3_ECOLX	---	---	A	A	22	T
2	UniProt	VAR_AFAE3_ECOLX_002 *	N	73	D	AFAE3_ECOLX	---	---	A	N	36	D
3	UniProt	VAR_061310	I	80	V	CEAM5_HUMAN	Polymorphism	12971352	N	I	46	V
4	UniProt	VAR_061311	V	83	A	CEAM5_HUMAN	Polymorphism	28683503	N	V	49	A
5	UniProt	VAR_056028	Q	137	P	CEAM5_HUMAN	Polymorphism	3815780	N	Q	103	P
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

NMR Structure * (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_AFAE3_ECOLX_001 *	A	59	T	AFAE3_ECOLX	---	---	A	A	22	T
2	UniProt	VAR_AFAE3_ECOLX_002 *	N	73	D	AFAE3_ECOLX	---	---	A	N	36	D
3	UniProt	VAR_061310	I	80	V	CEAM5_HUMAN	Polymorphism	12971352	N	I	46	V
4	UniProt	VAR_061311	V	83	A	CEAM5_HUMAN	Polymorphism	28683503	N	V	49	A
5	UniProt	VAR_056028	Q	137	P	CEAM5_HUMAN	Polymorphism	3815780	N	Q	103	P
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 2VER)

Exons (2, 2)

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000221992	1a	ENSE00001824227	chr19:42212504-42212714	211	CEAM5_HUMAN	1-22	22	0	-	-
1.2b	ENST00000221992	2b	ENSE00001673438	chr19:42213599-42213958	360	CEAM5_HUMAN	22-142	121	1	N:1-108	108
1.3	ENST00000221992	3	ENSE00001745070	chr19:42218890-42219168	279	CEAM5_HUMAN	142-235	94	1	N:108-110	3
1.4	ENST00000221992	4	ENSE00001616278	chr19:42219569-42219823	255	CEAM5_HUMAN	235-320	86	0	-	-
1.5a	ENST00000221992	5a	ENSE00001769209	chr19:42221374-42221652	279	CEAM5_HUMAN	320-413	94	0	-	-
1.6	ENST00000221992	6	ENSE00001779224	chr19:42222047-42222301	255	CEAM5_HUMAN	413-498	86	0	-	-
1.7	ENST00000221992	7	ENSE00001731243	chr19:42223849-42224127	279	CEAM5_HUMAN	498-591	94	0	-	-
1.8	ENST00000221992	8	ENSE00000842483	chr19:42224842-42225096	255	CEAM5_HUMAN	591-676	86	0	-	-
1.9b	ENST00000221992	9b	ENSE00001053043	chr19:42231154-42231272	119	CEAM5_HUMAN	676-702	27	0	-	-
1.10a	ENST00000221992	10a	ENSE00001942723	chr19:42233104-42233718	615	CEAM5_HUMAN	-	0	0	-	-

Sequences/Alignments

NMR Structure

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:143
 aligned with AFAE3_ECOLX | Q57254 from UniProtKB/Swiss-Prot  Length:160

    Alignment length:143
                                                                                                                                                    160                    
                                    47        57        67        77        87        97       107       117       127       137       147       157  |      -         -   
          AFAE3_ECOLX    38 EECQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCNARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPMDNSAWTTDNGVFYKNDVGSWGGTIGIYVDGQQTNTPPGNYTLTLTGGYWAK--------------------   -
               SCOP domains d2vera1 A:1-133 DraA/Afimbrial adhesin Afa-III                                                                                       ---------- SCOP domains
               CATH domains 2verA00 A:1-143 Afimbrial adhesin afa-iii.                                                                                                      CATH domains
               Pfam domains Adhesin_Dr-2verA01 A:1-123                                                                                                 -------------------- Pfam domains
         Sec.struct. author ...eee...eeee..............eeeeee...................eeeee......eeeeeeee.....................eeeeeeee..........eeeeeeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------T-------------D----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ver A   1 EECQVRVGDLTVAKTRGQLTDAAPIGPVTVQALGCNARQVALKADTDNFEQGKFFLISDNNRDKLYVNIRPMDNSAWTTDNGVFYKNDVGSWGGTIGIYVDGQQTNTPPGNYTLTLTGGYWAKDNKQGFTPSGTTGTTKLTVT 143
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140

Chain N from PDB  Type:PROTEIN  Length:110
 aligned with CEAM5_HUMAN | P06731 from UniProtKB/Swiss-Prot  Length:702

    Alignment length:110
                                    44        54        64        74        84        94       104       114       124       134       144
          CEAM5_HUMAN    35 KLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERVDGNRQIIGYVIGTQQATPGPAYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPEL 144
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2verN00 N:1-110 Immunoglobulins                                                                                CATH domains
               Pfam domains V-set-2verN01 N:1-106                                                                                     ---- Pfam domains
         Sec.struct. author ..eeeee..eee....eeeeee.....eeeeeee.........eeeeee....eeee.......eee.....eee...hhhhheeeeeeeee......eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------V--A-----------------------------------------------------P------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: N:1-108 UniProt: 22-142 [INCOMPLETE]                                                        -- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------1.3 Transcript 1 (2)
                 2ver N   1 KLTIESTPFNVAEGKEVLLLVHNLPQHLFGYSWYKGERCDGNCQIIGYVIGTQCATPGPAYSGREIIYPNASLLIQNIIQNDTGFYTLHVIKSDLVNEEATGQFRVYPEL 110
                                    10        20        30        40        50        60        70        80        90       100       110

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

NMR Structure

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Bacterial adhesins (93)

Family: Dr-family adhesin (11)

Protein domain: DraA/Afimbrial adhesin Afa-III (11)

Escherichia coli [TaxId: 562] (11)

d2vera1

A:1-133

CATH Domains (2, 2)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Afimbrial adhesin afa-iii. (12)

Escherichia coli. Organism_taxid: 562. Strain: dr/afa. (1)

2verA00

A:1-143

Homologous Superfamily: Immunoglobulins (2282)

Escherichia coli. Organism_taxid: 562. Strain: dr/afa. (1)

2verN00

N:1-110

Pfam Domains (2, 2)

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: Adhesin_Dr (9)

Escherichia coli (9)

Adhesin_Dr-2verA01

A:1-123

Clan: Ig (577)

Family: V-set (144)

Homo sapiens (Human) (61)

V-set-2verN01

N:1-106

Gene Ontology (15, 15)

NMR Structure(hide GO term definitions)

Chain A (AFAE3_ECOLX | Q57254)

cellular component
	GO:0009289		pilus		A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Chain N (CEAM5_HUMAN | P06731)

molecular function
	GO:0034235	GPI anchor binding	Interacting selectively and non-covalently with any glycosylphosphatidylinositol anchor. GPI anchors serve to attach membrane proteins to the lipid bilayer of cell membranes.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0034109	homotypic cell-cell adhesion	The attachment of a cell to a second cell of the identical type via adhesion molecules.
	GO:2000811	negative regulation of anoikis	Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0010832	negative regulation of myotube differentiation	Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0016323	basolateral plasma membrane	The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0071575	integral component of external side of plasma membrane	The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	AFAE3_ECOLX \| Q57254	:	1rxl 1usz 1ut2 2ixq
	CEAM5_HUMAN \| P06731	:	1e07 2qsq 2qst

Related Entries Specified in the PDB File

1e07	THEORETICAL MODEL OF HUMAN CARCINOEMBRYONIC ANTIGEN BY HOMOLOGY MODELLING AND CURVE- FITTING TO EXPERIMENTAL SOLUTION SCATTERING DATA
1rxl	SOLUTION STRUCTURE OF THE ENGINEERED PROTEIN AFAE-DSC
1usz	SEMET AFAE-3 ADHESIN FROM ESCHERICHIA COLI
1ut2	AFAE-3 ADHESIN FROM ESCHERICHIA COLI
2ixq	THE SOLUTION STRUCTURE OF THE INVASIVE TIP COMPLEX FROM AFA-DR FIBRILS