3GIN - JenaLib

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Title :   CRYSTAL STRUCTURE OF E454K-CBD1

Authors :   V. Chaptal, G. Mercado-Besserer, J. Abramson

Date :   05 Mar 09 (Deposition) - 21 Apr 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Cbd1, Cbd2, Ncx, Calcium Binding Domain 1, Antiport, Calcium Transport, Calmodulin-Binding, Cell Membrane, Glycoprotein, Ion Transport, Membrane, Phosphoprotein, Sodium Transport, Transmembrane, Transport, Metal Transport, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Chaptal, M. Ottolia, G. Mercado-Besserer, D. A. Nicoll, K. D. Philipson, J. Abramson
Structure And Functional Analysis Of A Ca2+ Sensor Mutant O The Na+/Ca2+ Exchanger
J. Biol. Chem. V. 284 14688 2009
PubMed-ID: 19332552 | Reference-DOI: 10.1074/JBC.C900037200

Molecule 1 - SODIUM/CALCIUM EXCHANGER 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	HMS174(DE3)
	Expression System Taxid	:	562
	Expression System Vector	:	PET47B(+)
	Fragment	:	CALX-BETA 1 DOMAIN
	Gene	:	SLC8A1
	Mutation	:	YES
	Organism Common	:	DOG
	Organism Scientific	:	CANIS LUPUS FAMILIARIS
	Organism Taxid	:	9615
	Synonym	:	NA(+)/CA(2+)-EXCHANGE PROTEIN 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	CA	7	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:385 , ASP A:447 , ILE A:449 , ASP A:498 , ASP A:500	BINDING SITE FOR RESIDUE CA A 1
2	AC2	SOFTWARE	GLU A:385 , ASP A:446 , ASP A:447 , ASP A:499 , ASP A:500	BINDING SITE FOR RESIDUE CA A 2
3	AC3	SOFTWARE	HOH A:22 , HOH A:44 , HOH A:45 , HOH A:46 , HOH A:48	BINDING SITE FOR RESIDUE CA A 5
4	AC4	SOFTWARE	GLU A:385 , ASP A:421 , ASP A:447 , GLU A:451	BINDING SITE FOR RESIDUE CA A 7
5	AC5	SOFTWARE	HOH B:2 , CA B:4 , GLU B:385 , ASP B:446 , ASP B:447 , ASP B:499 , ASP B:500	BINDING SITE FOR RESIDUE CA B 3
6	AC6	SOFTWARE	CA B:3 , GLU B:385 , ASP B:447 , ILE B:449 , ASP B:498 , ASP B:500	BINDING SITE FOR RESIDUE CA B 4
7	AC7	SOFTWARE	HOH B:95 , GLU B:385 , ASP B:421 , ASP B:447 , GLU B:451	BINDING SITE FOR RESIDUE CA B 6

Asymmetric Unit

No.	Residues
1	A:485	-	B:485

Asymmetric Unit

No.	Residues
1	Ser A:488	-	Pro A:489
2	Ser B:488	-	Pro B:489

(no "SAP(SNP)/Variant" information available for 3GIN)

(no "PROSITE Motif" information available for 3GIN)

(no "Exon" information available for 3GIN)

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:116
 aligned with NAC1_CANLF | P23685 from UniProtKB/Swiss-Prot  Length:970

    Alignment length:132
                                   411       421       431       441       451       461       471       481       491       501       511       521       531  
           NAC1_CANLF   402 PVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDENFLVHLSNVKVSSEASEDGILEANHVSALACLGSPSTATVTIFDDDH 533
               SCOP domains d3gina_ A: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...eeeee....eeeeeeeee.......eeeeeeeee............eeeeee.....eeeeeee..........eeeeeeeeeee.----------------.eeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gin A 370 PVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDKNFLVHLSNVKV----------------ALACLGSPSTATVTIFDDDH 501
                                   379       389       399       409       419       429       439       449       459     |   -         -  |    489       499  
                                                                                                                         465              482

Chain B from PDB  Type:PROTEIN  Length:116
 aligned with NAC1_CANLF | P23685 from UniProtKB/Swiss-Prot  Length:970

    Alignment length:132
                                   411       421       431       441       451       461       471       481       491       501       511       521       531  
           NAC1_CANLF   402 PVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDENFLVHLSNVKVSSEASEDGILEANHVSALACLGSPSTATVTIFDDDH 533
               SCOP domains d3ginb_ B: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeee....eeeeeeeee......eeeeeeeeee............eeeeee.....eeeeeee..........eeeeeeeeeeeee----------------.eee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gin B 370 PVSKIFFEQGTYQCLENCGTVALTIIRRGGDLTNTVFVDFRTEDGTANAGSDYEFTEGTVVFKPGETQKEIRVGIIDDDIFEEDKNFLVHLSNVKVS----------------LACLGSPSTATVTIFDDDH 501
                                   379       389       399       409       419       429       439       449       459      |  -         -   |   489       499  
                                                                                                                          466              483

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: CalX-like (13)

Family: CalX-beta domain (7)

Protein domain: automated matches (4)

Canis lupus [TaxId: 9615] (1)

1a	d3gina_	A:
1b	d3ginb_	B:

(no "CATH Domain" information available for 3GIN)

(no "Pfam Domain" information available for 3GIN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAC1_CANLF | P23685)

molecular function
	GO:0030506	ankyrin binding	Interacting selectively and non-covalently with ankyrin, a 200 kDa cytoskeletal protein that attaches other cytoskeletal proteins to integral membrane proteins.
	GO:0015297	antiporter activity	Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. The reaction is: solute A(out) + solute B(in) = solute A(in) + solute B(out).
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005432	calcium:sodium antiporter activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Ca2+(in) + Na+(out) = Ca2+(out) + Na+(in).
	GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
	GO:0008092	cytoskeletal protein binding	Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:1901660	calcium ion export	The directed movement of calcium ion out of a cell or organelle.
	GO:0070509	calcium ion import	The directed movement of calcium ions into a cell or organelle.
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0007154	cell communication	Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment.
	GO:0034614	cellular response to reactive oxygen species	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 a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
	GO:0006883	cellular sodium ion homeostasis	Any process involved in the maintenance of an internal steady state of sodium ions at the level of a cell.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0030501	positive regulation of bone mineralization	Any process that activates or increases the frequency, rate or extent of bone mineralization.
	GO:0098735	positive regulation of the force of heart contraction	Any process that increases the force of heart muscle contraction.
	GO:0035994	response to muscle stretch	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 myofibril being extended beyond its slack length.
	GO:0071436	sodium ion export	The directed movement of sodium ions out of a cell or organelle.
	GO:0097369	sodium ion import	The directed movement of sodium ions into a cell or organelle.
	GO:0035725	sodium ion transmembrane transport	A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006814	sodium ion transport	The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	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: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:0031226	intrinsic component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in 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:0042383	sarcolemma	The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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	Cis Peptide Bonds
		Ser A:488 - Pro A:489	[ RasMol ]
		Ser B:488 - Pro B:489	[ RasMol ]

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	NAC1_CANLF \| P23685	:	2dpk 2fws 2fwu 2qvk 2qvm 3us9

2dpk	WILD-TYPE CBD1
2qvm	WILD-TYPE CBD2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (1, 1)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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