1XA5 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF CALMODULIN IN COMPLEX WITH KAR-2, A BIS-INDOL ALKALOID

Authors :   I. Horvath, V. Harmat, E. Hlavanda, G. Naray-Szabo, J. Ovadi

Date :   25 Aug 04 (Deposition) - 21 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.12

Chains :   Asym./Biol. Unit : A

Keywords :   Calmodulin, Vinca Alkaloid, Kar-2, Drug Binding, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Horvath, V. Harmat, A. Perczel, V. Palfi, L. Nyitrai, A. Nagy, E. Hlavanda, G. Naray-Szabo, J. Ovadi
The Structure Of The Complex Of Calmodulin With Kar-2: A Novel Mode Of Binding Explains The Unique Pharmacology Of The Drug
J. Biol. Chem. V. 280 8266 2005
PubMed-ID: 15596444 | Reference-DOI: 10.1074/JBC.M410353200

Molecule 1 - CALMODULIN
	Chains	:	A
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Tissue	:	BRAIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	KAR	1	Ligand/Ion	3"-(BETA-CHLOROETHYL)-2",4"-DIOXO-3, 5"-SPIRO-OXAZOLIDINO-4-DEACETOXY-VINBLASTINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31 , HOH A:188	BINDING SITE FOR RESIDUE CA A 149
2	AC2	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104 , HOH A:196	BINDING SITE FOR RESIDUE CA A 151
3	AC3	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140 , HOH A:168	BINDING SITE FOR RESIDUE CA A 152
4	AC4	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67 , HOH A:159	BINDING SITE FOR RESIDUE CA A 150
5	AC5	SOFTWARE	GLN A:3 , LEU A:18 , PHE A:19 , LEU A:39 , PHE A:68 , MET A:72 , ILE A:85 , MET A:109 , MET A:144 , MET A:145 , ALA A:147 , LYS A:148 , HOH A:155 , HOH A:180	BINDING SITE FOR RESIDUE KAR A 153

(no "SS Bond" information available for 1XA5)

(no "Cis Peptide Bond" information available for 1XA5)

(no "SAP(SNP)/Variant" information available for 1XA5)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CALM_BOVIN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-78 A:80-115 A:116-148
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM_BOVIN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

Asymmetric/Biological Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.7	ENSBTAT00000019411	7	ENSBTAE00000320796	chr18:53531460-53531549	90	CALM_BOVIN	1-1	1	0	-	-
1.8	ENSBTAT00000019411	8	ENSBTAE00000157831	chr18:53535790-53535820	31	CALM_BOVIN	2-12	11	1	A:3-11	9
1.9	ENSBTAT00000019411	9	ENSBTAE00000428812	chr18:53537981-53538124	144	CALM_BOVIN	12-60	49	1	A:11-59	49
1.10	ENSBTAT00000019411	10	ENSBTAE00000416563	chr18:53538265-53538371	107	CALM_BOVIN	60-95	36	1	A:59-94 (gaps)	36
1.11	ENSBTAT00000019411	11	ENSBTAE00000389868	chr18:53538749-53538884	136	CALM_BOVIN	96-141	46	1	A:95-140	46
1.12	ENSBTAT00000019411	12	ENSBTAE00000245541	chr18:53538967-53540533	1567	CALM_BOVIN	141-149	9	1	A:140-148	9

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:144
 aligned with CALM_BOVIN | P62157 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:146
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           CALM_BOVIN     4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 149
               SCOP domains d1xa5a_ A: Calmodulin                                                                                                                              SCOP domains
               CATH domains 1xa5A00 A:3-148 EF-hand                                                                                                                            CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------EF_hand_5-1xa5A01 A:84-145                                    --- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------EF_hand_5-1xa5A02 A:84-145                                    --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhh.........hhhhhhhhhhh--....hhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-78             -EF_HAND_2  PDB: A:80-115            EF_HAND_2  PDB: A:116-148         PROSITE (1)
                PROSITE (2) -----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------- PROSITE (2)
           Transcript 1 (1) Exon 1.8 -----------------------------------------------Exon 1.10  PDB: A:59-94 (gaps)      Exon 1.11  PDB: A:95-140 UniProt: 96-141      -------- Transcript 1 (1)
           Transcript 1 (2) --------Exon 1.9  PDB: A:11-59 UniProt: 12-60            --------------------------------------------------------------------------------Exon 1.12 Transcript 1 (2)
                 1xa5 A   3 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR--KDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTAK 148
                                    12        22        32        42        52        62        72 |  |   82        92       102       112       122       132       142      
                                                                                                  74 77

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: EF Hand-like (739)

Superfamily: EF-hand (657)

Family: Calmodulin-like (356)

Protein domain: Calmodulin (152)

Cow (Bos taurus) [TaxId: 9913] (16)

d1xa5a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Recoverin; domain 1 (474)

Homologous Superfamily: EF-hand (412)

Cattle (Bos taurus) (44)

1xa5A00

A:3-148

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EF_hand (270)

Family: EF_hand_5 (126)

Bos taurus (Bovine) (4)

1a	EF_hand_5-1xa5A01	A:84-145
1b	EF_hand_5-1xa5A02	A:84-145

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM_BOVIN | P62157)

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.
	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).
biological process
	GO:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0000086	G2/M transition of mitotic cell cycle	The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
	GO:0006936	muscle contraction	A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
	GO:0060315	negative regulation of ryanodine-sensitive calcium-release channel activity	Any process that decreases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0043388	positive regulation of DNA binding	Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
	GO:0060316	positive regulation of ryanodine-sensitive calcium-release channel activity	Any process that increases the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
	GO:0010880	regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
	GO:0022400	regulation of rhodopsin mediated signaling pathway	Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
	GO:0000922	spindle pole	Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.
	GO:0008076	voltage-gated potassium channel complex	A protein complex that forms a transmembrane channel through which potassium ions may cross a cell membrane in response to changes in membrane potential.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 1XA5)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (5, 5)

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