2A62 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF MOUSE CADHERIN-8 EC1-3

Authors :   S. D. Patel, C. Ciatto, C. P. Chen, F. Bahna, N. Arkus, I. Schieren, T. M. J B. Honig, S. R. Price, L. Shapiro

Date :   01 Jul 05 (Deposition) - 25 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Cadherin, Extracellular Domain, Homodimer, Calcium Binding, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Patel, C. Ciatto, C. P. Chen, F. Bahna, M. Rajebhosale, N. Arkus, I. Schieren, T. M. Jessell, B. Honig, S. R. Price, L. Shapiro
Type Ii Cadherin Ectodomain Structures: Implications For Classical Cadherin Specificity.
Cell(Cambridge, Mass. ) V. 124 1255 2006
PubMed-ID: 16564015 | Reference-DOI: 10.1016/J.CELL.2005.12.046

Molecule 1 - CADHERIN-8
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CDH8
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:100 , ASN A:102 , ASP A:132 , ASP A:134 , SER A:141 , ASP A:187	BINDING SITE FOR RESIDUE CA A 323
2	AC2	SOFTWARE	GLU A:11 , GLU A:66 , ASP A:98 , ILE A:99 , ASP A:101 , ASN A:102 , ASP A:134 , CA A:325	BINDING SITE FOR RESIDUE CA A 324
3	AC3	SOFTWARE	GLU A:11 , GLU A:12 , ASP A:64 , GLU A:66 , ASP A:101 , CA A:324	BINDING SITE FOR RESIDUE CA A 325
4	AC4	SOFTWARE	ASN A:209 , ASN A:211 , ASP A:241 , ASP A:243 , ASN A:247 , ASN A:298	BINDING SITE FOR RESIDUE CA A 326
5	AC5	SOFTWARE	GLU A:117 , ASP A:207 , VAL A:208 , ASP A:210 , ASP A:243 , CA A:328	BINDING SITE FOR RESIDUE CA A 327
6	AC6	SOFTWARE	GLU A:117 , ARG A:173 , GLU A:174 , ASP A:207 , ASP A:210 , ASP A:243 , CA A:327	BINDING SITE FOR RESIDUE CA A 328

(no "SS Bond" information available for 2A62)

Asymmetric Unit

No.	Residues
1	Gly A:231	-	Thr A:232
2	Ser A:267	-	Asp A:268
3	Asp A:273	-	Gly A:274

(no "SAP(SNP)/Variant" information available for 2A62)

Asymmetric Unit (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CADHERIN_2	PS50268	Cadherins domain profile.	CADH8_MOUSE	87-167 168-276 277-391 392-496 496-618	3	A:26-106 A:107-215 A:216-322 - -
2	CADHERIN_1	PS00232	Cadherin domain signature.	CADH8_MOUSE	155-165 264-274 484-494	2	A:94-104 A:203-213 -

Biological Unit 1 (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CADHERIN_2	PS50268	Cadherins domain profile.	CADH8_MOUSE	87-167 168-276 277-391 392-496 496-618	6	A:26-106 A:107-215 A:216-322 - -
2	CADHERIN_1	PS00232	Cadherin domain signature.	CADH8_MOUSE	155-165 264-274 484-494	4	A:94-104 A:203-213 -

(no "Exon" information available for 2A62)

Asymmetric 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:319
 aligned with CADH8_MOUSE | P97291 from UniProtKB/Swiss-Prot  Length:799

    Alignment length:322
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381  
          CADH8_MOUSE    62 GWVWNQMFVLEEFSGPEPILVGRLHTDLDPGSKKIKYILSGDGAGTIFQINDITGDIHAIKRLDREEKAEYTLTAQAVDFETNKPLEPPSEFIIKVQDINDNAPEFLNGPYHATVPEMSILGTSVTNVTATDADDPVYGNSAKLVYSILEGQPYFSIEPETAIIKTALPNMDREAKEEYLVVIQAKDMGGHSGGLSGTTTLTVTLTDVNDNPPKFAQSLYHFSVPEDVVLGTAIGRVKANDQDIGENAQSSYDIIDGDGTALFEITSDAQAQDGVIRLRKPLDFETKKSYTLKVEAANIHIDPRFSSRGPFKDTATVKIVVE 383
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee..........ee...............eeeeee......eeee....eeee.............eeeeee......eeeeeeee.ee..............eeeeee............................eeeeeee....eee......eee.....hhhhh.eeeeeeeeee...........eeeeeee.............eeeeee........eeeeee.....hhhhh..eeee.---..............eeeee...........eeeeeeeee..................eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------CADHERIN_2  PDB: A:26-106 UniProt: 87-167                                        CADHERIN_2  PDB: A:107-215 UniProt: 168-276                                                                  CADHERIN_2  PDB: A:216-322 UniProt: 277-391                                                                 PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------CADHERIN_1 --------------------------------------------------------------------------------------------------CADHERIN_1 ------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a62 A   1 SWVWNQMFVLEEFSGPEPILVGRLHTDLDPGSKKIKYILSGDGAGTIFQINDITGDIHAIKRLDREEKAEYTLTAQAVDFETNKPLEPPSEFIIKVQDINDNAPEFLNGPYHATVPEMSILGTSVTNVTATDADDPVYGNSAKLVYSILEGQPYFSIEPETAIIKTALPNMDREAKEEYLVVIQAKDMGGHSGGLSGTTTLTVTLTDVNDNPPKFAQSLYHFSVPEDVVLGTAIGRVKANDQDIGENAQSSYDII---GTALFEITSDAQAQDGVIRLRKPLDFETKKSYTLKVEAANIHIDPRFSSRGPFKDTATVKIVVE 322
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250    |  260       270       280       290       300       310       320  
                                                                                                                                                                                                                                                                                        255 259

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 '\|'

(no "SCOP Domain" information available for 2A62)

(no "CATH Domain" information available for 2A62)

(no "Pfam Domain" information available for 2A62)

Asymmetric Unit(hide GO term definitions)

Chain A (CADH8_MOUSE | P97291)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0007268	chemical synaptic transmission	The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
	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:0009409	response to cold	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
	GO:0035249	synaptic transmission, glutamatergic	The vesicular release of glutamate from a presynapse, across a chemical synapse, the subsequent activation of glutamate receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
cellular component
	GO:0043679	axon terminus	Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it.
	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: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.
	GO:0043083	synaptic cleft	The narrow gap that separates the presynaptic and postsynaptic membranes, into which neurotransmitter is released.

Asymmetric Unit
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		AC5	[ RasMol ]	+environment [ RasMol ]
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	Cis Peptide Bonds
		Asp A:273 - Gly A:274	[ RasMol ]
		Gly A:231 - Thr A:232	[ RasMol ]
		Ser A:267 - Asp A:268	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2a62
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	CADH8_MOUSE \| P97291
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	CADH8_MOUSE \| P97291
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	CADH8_MOUSE \| P97291	:	1zxk

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 5)

Exons (0, 0)

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