3RB5 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CALCIUM BINDING DOMAIN CBD12 OF CALX1.1

Authors :   M. Wu, L. Zheng

Date :   28 Mar 11 (Deposition) - 02 Nov 11 (Release) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Cbd12, Calcium Binding And Regulation, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Wu, S. Tong, J. Gonzalez, V. Jayaraman, J. L. Spudich, L. Zheng
Structural Basis Of The Ca(2+) Inhibitory Mechanism Of Drosophila Na(+)/Ca(2+) Exchanger Calx And Its Modification By Alternative Splicing.
Structure V. 19 1509 2011
PubMed-ID: 22000518 | Reference-DOI: 10.1016/J.STR.2011.07.008

Molecule 1 - NA/CA EXCHANGE PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CALX, NCX, CG5685
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A (1x)	B (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:490 , GLU A:520 , GLU A:523	BINDING SITE FOR RESIDUE CA A 1
02	AC2	SOFTWARE	GLU A:455 , ASP A:515 , ASP A:516 , ASP A:551 , ASP A:552	BINDING SITE FOR RESIDUE CA A 2
03	AC3	SOFTWARE	GLU A:455 , ASP A:516 , VAL A:518 , GLU A:520 , ASP A:550 , ASP A:552	BINDING SITE FOR RESIDUE CA A 3
04	AC4	SOFTWARE	HOH A:18 , GLU A:455 , ASP A:490 , GLU A:520 , GLU A:523 , ILE A:548	BINDING SITE FOR RESIDUE CA A 4
05	AC5	SOFTWARE	TYR A:689 , GLN B:481 , ILE B:543	BINDING SITE FOR RESIDUE MPD A 4984
06	AC6	SOFTWARE	LYS A:620 , PHE A:621 , ARG B:572	BINDING SITE FOR RESIDUE SO4 A 731
07	AC7	SOFTWARE	GLY A:449 , HIS A:450	BINDING SITE FOR RESIDUE SO4 A 732
08	AC8	SOFTWARE	PRO A:448 , GLU A:461 , ARG A:463 , ARG A:508	BINDING SITE FOR RESIDUE SO4 A 7
09	AC9	SOFTWARE	ASP B:490 , GLU B:520 , GLU B:523	BINDING SITE FOR RESIDUE CA B 1
10	BC1	SOFTWARE	GLU B:455 , ASP B:515 , ASP B:516 , ASP B:551 , ASP B:552 , ARG B:584	BINDING SITE FOR RESIDUE CA B 2
11	BC2	SOFTWARE	GLU B:455 , ASP B:516 , VAL B:518 , GLU B:520 , ASP B:550 , ASP B:552	BINDING SITE FOR RESIDUE CA B 3
12	BC3	SOFTWARE	GLU B:455 , ASP B:490 , ILE B:514 , ASP B:516 , GLU B:520	BINDING SITE FOR RESIDUE CA B 4
13	BC4	SOFTWARE	PRO B:448 , GLY B:449 , HIS B:450	BINDING SITE FOR RESIDUE SO4 B 731
14	BC5	SOFTWARE	ARG B:467 , GLY B:468	BINDING SITE FOR RESIDUE SO4 B 6
15	BC6	SOFTWARE	ARG A:572 , LYS B:620 , PHE B:621	BINDING SITE FOR RESIDUE SO4 B 5

(no "SS Bond" information available for 3RB5)

Asymmetric Unit

No.	Residues
1	Glu A:447	-	Pro A:448
2	Val A:540	-	Pro A:541
3	Ala A:554	-	Gly A:555
4	Leu A:624	-	Phe A:625
5	Glu B:447	-	Pro B:448
6	Val B:540	-	Pro B:541
7	Ala B:554	-	Gly B:555
8	Val B:570	-	Gly B:571
9	Val B:636	-	Ser B:637

(no "SAP(SNP)/Variant" information available for 3RB5)

(no "PROSITE Motif" information available for 3RB5)

(no "Exon" information available for 3RB5)

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:238
 aligned with Q24413_DROME | Q24413 from UniProtKB/TrEMBL  Length:950

    Alignment length:252
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691  
         Q24413_DROME   442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEESSYEKDVSFKVHIGEPRLAPDDGLAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRIR 693
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeee.....ee..eee.......eeeeeeeee............eeeeee.....ee..ee...........eeeeeeee......ee....eeeeeee......eee....eeee......eeeeeeee......eeeeeeeeee-----......eeeeee.....eeeeee.---------.eeeeeee...ee...hhhhhhhhhhh.......hhhhhhhhh...ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rb5 A 442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTEND-----KDYEGARGELVFENNESEKFIDLF---------DVSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRIR 693
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591    |    -|      611       621   |     -   |   641       651       661       671       681       691  
                                                                                                                                                                                    596   602                    625       635

Chain A from PDB  Type:PROTEIN  Length:238
 aligned with Q9VDG5_DROME | Q9VDG5 from UniProtKB/TrEMBL  Length:950

    Alignment length:252
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691  
         Q9VDG5_DROME   442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEESSYEKDVSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRIR 693
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeee.....ee..eee.......eeeeeeeee............eeeeee.....ee..ee...........eeeeeeee......ee....eeeeeee......eee....eeee......eeeeeeee......eeeeeeeeee-----......eeeeee.....eeeeee.---------.eeeeeee...ee...hhhhhhhhhhh.......hhhhhhhhh...ee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rb5 A 442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTEND-----KDYEGARGELVFENNESEKFIDLF---------DVSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRIR 693
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591    |    -|      611       621   |     -   |   641       651       661       671       681       691  
                                                                                                                                                                                    596   602                    625       635

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q24413_DROME | Q24413 from UniProtKB/TrEMBL  Length:950

    Alignment length:251
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691 
         Q24413_DROME   442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEESSYEKDVSFKVHIGEPRLAPDDGLAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRI 692
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeee....eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee..........eeeeeeee............eeeeeee......eeee...eee......eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee....------..eeeee...ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rb5 B 442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEE------VSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRI 692
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       | -    |  641       651       661       671       681       691 
                                                                                                                                                                                                                     629    636

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q9VDG5_DROME | Q9VDG5 from UniProtKB/TrEMBL  Length:950

    Alignment length:251
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691 
         Q9VDG5_DROME   442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEESSYEKDVSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRI 692
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeee....eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee..........eeeeeeee............eeeeeee......eeee...eee......eeeeeeeee......eeeeeeee.............eeeeee.....eeeeeee....------..eeeee...ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rb5 B 442 IRMYFEPGHYTVMENCGEFEVRVVRRGDISTYASVEYETQDGTASAGTDFVGRKGLLSFPPGVDEQRFRIEVIDDDVFEEDECFYIRLFNPSEGVKLAVPMIATVMILDDDHAGIFAFTDSVFEITESVGRFELKVMRYSGARGTVIVPYWTENDTATESKDYEGARGELVFENNESEKFIDLFILEE------VSFKVHIGEPRLAPDDELAAKIKEVEKKPVQDLTELDRILLLSKPRNGELTTAYVRI 692
                                   451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       | -    |  641       651       661       671       681       691 
                                                                                                                                                                                                                     629    636

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 3RB5)

(no "CATH Domain" information available for 3RB5)

(no "Pfam Domain" information available for 3RB5)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9VDG5_DROME | Q9VDG5)

molecular function
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	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:0050884	neuromuscular process controlling posture	Any process in which an organism voluntarily modulates its posture, the alignment of its anatomical parts.
	GO:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	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:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B (Q24413_DROME | Q24413)

molecular function
	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).
biological process
	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:0050884	neuromuscular process controlling posture	Any process in which an organism voluntarily modulates its posture, the alignment of its anatomical parts.
	GO:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	GO:0034976	response to endoplasmic reticulum stress	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 stress acting at the endoplasmic reticulum. ER stress usually results from the accumulation of unfolded or misfolded proteins in the ER lumen.
	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:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:554 - Gly A:555	[ RasMol ]
		Ala B:554 - Gly B:555	[ RasMol ]
		Glu A:447 - Pro A:448	[ RasMol ]
		Glu B:447 - Pro B:448	[ RasMol ]
		Leu A:624 - Phe A:625	[ RasMol ]
		Val A:540 - Pro A:541	[ RasMol ]
		Val B:540 - Pro B:541	[ RasMol ]
		Val B:570 - Gly B:571	[ RasMol ]
		Val B:636 - Ser B:637	[ RasMol ]

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	3rb5
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	Q24413_DROME \| Q24413
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	Q9VDG5_DROME \| Q9VDG5
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	Q24413_DROME \| Q24413
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	Q9VDG5_DROME \| Q9VDG5
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UniProtKB/Swiss-Prot
	Q24413_DROME \| Q24413	:	3e9t 3ead 3rb7
UniProtKB/TrEMBL
	Q24413_DROME \| Q24413	:	3e9u
	Q9VDG5_DROME \| Q9VDG5	:	3e9t 3ead 3rb7

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 23)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File