1L6Z - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MURINE CEACAM1A[1,4]: A CORONAVIRUS RECEPTOR AND CELL ADHESION MOLECULE IN THE CEA FAMILY

Authors :   K. Tan, B. D. Zelus, R. Meijers, J. -H. Liu, J. M. Bergelson, N. Duke, R. Zh A. Joachimiak, K. V. Holmes, J. -H. Wang

Date :   14 Mar 02 (Deposition) - 14 Sep 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.32

Chains :   Asym./Biol. Unit : A

Keywords :   Ig-Like Domain, Cea Family, Coronavirus Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, B. D. Zelus, R. Meijers, J. -H. Liu, J. M. Bergelson, N. Duke, R. Zhang, A. Joachimiak, K. V. Holmes, J. -H. Wang
Crystal Structure Of Murine Sceacam1A[1, 4]: A Coronavirus Receptor In The Cea Family
Embo J. V. 21 2076 2002
PubMed-ID: 11980704 | Reference-DOI: 10.1093/EMBOJ/21.9.2076

Molecule 1 - BILIARY GLYCOPROTEIN C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Cell	:	OVARY CELLS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Strain	:	LEC.3.2.8.1
	Expression System Taxid	:	10029
	Expression System Vector Type	:	ADENOVIRUS TYPE 5
	Gene	:	MURINE CEACAM1A
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	BILIARY GLYCOPROTEIN C, CD66A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:37	BINDING SITE FOR RESIDUE NDG A 337
2	AC2	SOFTWARE	ASN A:55 , GLU A:65 , ILE A:66 , ILE A:67 , HOH A:1022	BINDING SITE FOR RESIDUE NAG A 355
3	AC3	SOFTWARE	LEU A:18 , LEU A:20 , ASN A:23 , TYR A:68 , ASN A:70 , NAG A:371	BINDING SITE FOR RESIDUE NAG A 370
4	AC4	SOFTWARE	LEU A:18 , TYR A:68 , NAG A:370 , BMA A:372	BINDING SITE FOR RESIDUE NAG A 371
5	AC5	SOFTWARE	NAG A:371 , HOH A:1020	BINDING SITE FOR RESIDUE BMA A 372
6	AC6	SOFTWARE	ASN A:119 , ILE A:137 , ASN A:161	BINDING SITE FOR RESIDUE NAG A 419

Asymmetric/Biological Unit

No.	Residues
1	A:132	-	A:180

Asymmetric/Biological Unit

No.	Residues
1	Val A:7	-	Pro A:8
2	Asp A:168	-	Pro A:169

(no "SAP(SNP)/Variant" information available for 1L6Z)

(no "PROSITE Motif" information available for 1L6Z)

(no "Exon" information available for 1L6Z)

Asymmetric/Biological Unit

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:203
 aligned with CEAM1_MOUSE | P31809 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:383
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414   
          CEAM1_MOUSE    35 EVTIEAVPPQVAEDNNVLLLVHNLPLALGAFAWYKGNTTAIDKEIARFVPNSNMNFTGQAYSGREIIYSNGSLLFQMITMKDMGVYTLDMTDENYRRTQATVRFHVHPILLKPNITSNNSNPVEGDDSVSLTCDSYTDPDNINYLWSRNGESLSEGDRLKLSEGNRTLTLLNVTRNDTGPYVCETRNPVSVNRSDPFSLNIIYGPDTPIISPSDIYLHPGSNLNLSCHAASNPPAQYFWLINEKPHASSQELFIPNITTNNSGTYTCFVNNSVTGLSRTTVKNITVLEPVTQPFLQVTNTTVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRSNSIKLDIIFDPT 417
               SCOP domains d1l6za1 A:1-107 Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), N-terminal domain                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------d1l6za2 A:108-203 Biliary glycoprotein C (CD66a, CEACAM1A[1,4]), C-terminal domain               SCOP domains
               CATH domains 1l6zA01 A:1-107 Immunoglobulins                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1l6zA02 A:108-203 Immunoglobulins                                                                CATH domains
               Pfam domains V-set-1l6zA01 A:1-106                                                                                     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ig-1l6zA02 A:125-182                                      --------------------- Pfam domains
         Sec.struct. author ..eeeee.........eeeeee.......eeeeee....hhh.eeeee......ee........eee.....eee...hhhhheeeeeeeee..eee....eee...------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------.......ee....ee.....eeeee.......eeeeee..ee......eeee....eeee...hhhhheeeeeeee.....ee....eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l6z A   1 EVTIEAVPPQVAEDNNVLLLVHNLPLALGAFAWYKGNTTAIDKEIARFVPNSNMNFTGQAYSGREIIYSNGSLLFQMITMKDMGVYTLDMTDENYRRTQATVRFHVH------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------QPVTQPFLQVTNTTVKELDSVTLTCLSNDIGANIQWLFNSQSLQLTERMTLSQNNSILRIDPIKREDAGEYQCEISNPVSVRRSNSIKLDIIFDPS 203
                                    10        20        30        40        50        60        70        80        90       100      |  -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       110       120       130       140       150       160       170       180       190       200   
                                                                                                                                    107                                                                                                                                                                                  108

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

House mouse (Mus musculus) (616)

1a	1l6zA01	A:1-107
1b	1l6zA02	A:108-203

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ig (577)

Family: V-set (144)

Mus musculus (Mouse) (63)

V-set-1l6zA01

A:1-106

Family: ig (14)

Mus musculus (Mouse) (3)

ig-1l6zA02

A:125-182

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CEAM1_MOUSE | P31809)

molecular function
	GO:0015125	bile acid transmembrane transporter activity	Enables the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
	GO:0031005	filamin binding	Interacting selectively and non-covalently with a filamin, any member of a family of high molecular mass cytoskeletal proteins that crosslink actin filaments to form networks and stress fibers. Filamins contain an amino-terminal alpha-actinin-like actin binding domain, which is followed by a rod-domain composed of 4 to 24 100-residue repetitive segments including a carboxy-terminal dimerization domain.
	GO:0005130	granulocyte colony-stimulating factor receptor binding	Interacting selectively and non-covalently with the granulocyte colony-stimulating factor receptor.
	GO:0019900	kinase binding	Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0019903	protein phosphatase binding	Interacting selectively and non-covalently with any protein phosphatase.
	GO:1990782	protein tyrosine kinase binding	Interacting selectively and non-covalently with protein tyrosine kinase.
	GO:0046790	virion binding	Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
	GO:0001618	virus receptor activity	Combining with a virus component and mediating entry of the virus into the cell.
biological process
	GO:0048541	Peyer's patch development	The process whose specific outcome is the progression of Peyer's patches over time, from their formation to the mature structure. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes.
	GO:0015721	bile acid and bile salt transport	The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0016339	calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules	The attachment of one cell to another cell via adhesion molecules that require the presence of calcium for the interaction.
	GO:0016338	calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules	The attachment of one cell to another cell via adhesion molecules that do not require the presence of calcium for the interaction.
	GO:0032869	cellular response to insulin stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
	GO:0035726	common myeloid progenitor cell proliferation	The multiplication or reproduction of common myeloid progenitor cells, resulting in the expansion of a cell population. A common myeloid progenitor cell is a progenitor cell committed to the myeloid lineage.
	GO:0038158	granulocyte colony-stimulating factor signaling pathway	A series of molecular signals initiated by the binding of the cytokine granulocyte colony-stimulating factor (G-CSF) to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. G-CSF binds to the receptor (CSF3R).
	GO:0007156	homophilic cell adhesion via plasma membrane adhesion molecules	The attachment of a plasma membrane adhesion molecule in one cell to an identical molecule in an adjacent cell.
	GO:1901143	insulin catabolic process	The chemical reactions and pathways resulting in the breakdown of insulin.
	GO:0038016	insulin receptor internalization	A receptor-mediated endocytosis process that results in the movement of an insulin receptor from the plasma membrane to the inside of the cell.
	GO:0044828	negative regulation by host of viral genome replication	A process in which a host organism stops, prevents or reduces the frequency, rate or extent of viral genome replication.
	GO:0044793	negative regulation by host of viral process	A process in which a host organism stops, prevents or reduces the frequency, rate or extent of a process being mediated by a virus with which it is infected.
	GO:0046329	negative regulation of JNK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0001915	negative regulation of T cell mediated cytotoxicity	Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity.
	GO:0042130	negative regulation of T cell proliferation	Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
	GO:0050860	negative regulation of T cell receptor signaling pathway	Any process that stops, prevents, or reduces the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
	GO:0045779	negative regulation of bone resorption	Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
	GO:0001818	negative regulation of cytokine production	Any process that stops, prevents, or reduces the rate of production of a cytokine.
	GO:0043318	negative regulation of cytotoxic T cell degranulation	Any process that stops, prevents, or reduces the rate of cytotoxic T cell degranulation.
	GO:0045717	negative regulation of fatty acid biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
	GO:0030853	negative regulation of granulocyte differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation.
	GO:2000346	negative regulation of hepatocyte proliferation	Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte proliferation.
	GO:0032703	negative regulation of interleukin-2 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
	GO:0051055	negative regulation of lipid biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids.
	GO:0045671	negative regulation of osteoclast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation.
	GO:0090331	negative regulation of platelet aggregation	Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
	GO:0044794	positive regulation by host of viral process	A process in which a host organism activates or increases the frequency, rate or extent of the release of a process being mediated by a virus with which it is infected.
	GO:2000516	positive regulation of CD4-positive, alpha-beta T cell activation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.
	GO:2000563	positive regulation of CD4-positive, alpha-beta T cell proliferation	Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
	GO:2001187	positive regulation of CD8-positive, alpha-beta T cell activation	Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell activation.
	GO:0046330	positive regulation of JNK cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0051533	positive regulation of NFAT protein import into nucleus	Any process that activates or increases the frequency, rate or extent of the movement of an NFAT protein from the cytoplasm to the nucleus.
	GO:0042102	positive regulation of T cell proliferation	Any process that activates or increases the rate or extent of T cell proliferation.
	GO:0070237	positive regulation of activation-induced cell death of T cells	Any process that activates or increases the frequency, rate or extent of activation-induced cell death of T cells.
	GO:0051024	positive regulation of immunoglobulin secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of immunoglobulins from a cell.
	GO:0070372	regulation of ERK1 and ERK2 cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0060312	regulation of blood vessel remodeling	Any process that modulates the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels.
	GO:0046850	regulation of bone remodeling	Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity.
	GO:0001558	regulation of cell growth	Any process that modulates the frequency, rate, extent or direction of cell growth.
	GO:0045601	regulation of endothelial cell differentiation	Any process that modulates the frequency, rate or extent of endothelial cell differentiation.
	GO:0010594	regulation of endothelial cell migration	Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
	GO:0042058	regulation of epidermal growth factor receptor signaling pathway	Any process that modulates the frequency, rate or extent of epidermal growth factor receptor signaling pathway activity.
	GO:1903385	regulation of homophilic cell adhesion	Any process that modulates the frequency, rate or extent of homophilic cell adhesion.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:1903670	regulation of sprouting angiogenesis	Any process that modulates the frequency, rate or extent of sprouting angiogenesis.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0044319	wound healing, spreading of cells	The migration of a cell along or through a wound gap that contributes to the reestablishment of a continuous surface.
cellular component
	GO:0042101	T cell receptor complex	A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
	GO:0005912	adherens junction	A cell junction at which anchoring proteins (cadherins or integrins) extend through the plasma membrane and are attached to actin filaments.
	GO:0016324	apical plasma membrane	The region of the plasma membrane located at the apical end of the cell.
	GO:0009925	basal plasma membrane	The region of the plasma membrane located at the basal end 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:0031526	brush border membrane	The portion of the plasma membrane surrounding the brush border.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0060170	ciliary membrane	The portion of the plasma membrane surrounding a cilium.
	GO:0009897	external side of plasma membrane	The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016021	integral component of membrane	The component of a 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:0016328	lateral plasma membrane	The portion of the plasma membrane at the lateral side of the cell. In epithelial cells, lateral plasma membranes are on the sides of cells which lie at the interface of adjacent cells.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:168 - Pro A:169	[ RasMol ]
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	1l6z
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	CEAM1_MOUSE \| P31809	:	3r4d

1e4j	CRYSTAL STRUCTURE OF THE SOLUBLE HUMAN FC-GAMMA RECEPTOR III
1hnf	THE N-TERMINAL DOMAINS OF HUMAN CD2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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