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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF CA2+/CAM-CAV2.2 IQ DOMAIN (WITHOUT CLONING ARTIFACT, HM TO TV) COMPLEX

Authors :   E. Y. Kim, C. H. Rumpf, Y. Fujiwara, E. S. Cooley, F. Van Petegem, D. L. Mi

Date :   18 Jul 08 (Deposition) - 04 Nov 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Calmodulin, Calcium Channel, Iq Domain, Inactivation, Facilitation, Calcium-Dependent, Voltage-Gated, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Y. Kim, C. H. Rumpf, Y. Fujiwara, E. S. Cooley, F. Van Petegem, D. L. Minor
Structures Of Ca(V)2 Ca(2+)/Cam-Iq Domain Complexes Reveal Binding Modes That Underlie Calcium-Dependent Inactivation And Facilitation.
Structure V. 16 1455 2008
PubMed-ID: 18940602 | Reference-DOI: 10.1016/J.STR.2008.07.010

Molecule 1 - CALMODULIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEGST
	Expression System Strain	:	BL21(DE3)-PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CAM

Molecule 2 - VOLTAGE-DEPENDENT N-TYPE CALCIUM CHANNEL SUBUNIT ALPHA-1B
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B-HMT
	Expression System Strain	:	BL21(DE3)-PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1853-1873
	Gene	:	CACNA1B, CACH5, CACNL1A5
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	VOLTAGE-GATED CALCIUM CHANNEL SUBUNIT ALPHA CAV2.2, CALCIUM CHANNEL, L TYPE, ALPHA-1 POLYPEPTIDE ISOFORM 5, BRAIN CALCIUM CHANNEL III, BIII

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:20 , ASP A:22 , ASP A:24 , THR A:26 , GLU A:31	BINDING SITE FOR RESIDUE CA A 501
2	AC2	SOFTWARE	ASP A:56 , ASP A:58 , ASN A:60 , THR A:62 , GLU A:67	BINDING SITE FOR RESIDUE CA A 502
3	AC3	SOFTWARE	ASP A:93 , ASP A:95 , ASN A:97 , TYR A:99 , GLU A:104	BINDING SITE FOR RESIDUE CA A 503
4	AC4	SOFTWARE	ASP A:129 , ASP A:131 , ASP A:133 , GLN A:135 , GLU A:140	BINDING SITE FOR RESIDUE CA A 504

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

(no "Cis Peptide Bond" information available for 3DVJ)

Asymmetric/Biological Unit (15, 15)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_069222	N	54	I	CALM1_HUMAN	Disease (CPVT4)	267607276	A	N	53	I
02	UniProt	VAR_073275	F	90	L	CALM1_HUMAN	Disease (LQT14)	730882253	A	F	89	L
03	UniProt	VAR_073276	D	96	V	CALM2_HUMAN	Disease (LQT15)	730882254	A	D	95	V
04	UniProt	VAR_073277	N	98	I	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	I
05	UniProt	VAR_078541	N	98	S	CALM1_HUMAN	Disease (CPVT4)	398124647	A	N	97	S
06	UniProt	VAR_078543	N	98	S	CALM2_HUMAN	Disease (LQT15)	398124647	A	N	97	S
07	UniProt	VAR_078261	A	103	V	CALM3_HUMAN	Disease	---	A	A	102	V
08	UniProt	VAR_078542	D	130	G	CALM1_HUMAN	Disease (LQT14)	730882252	A	D	129	G
09	UniProt	VAR_078544	D	130	G	CALM2_HUMAN	Disease (LQT15)	730882252	A	D	129	G
10	UniProt	VAR_078262	D	130	V	CALM2_HUMAN	Disease (LQT15)	---	A	D	129	V
11	UniProt	VAR_073279	D	132	E	CALM2_HUMAN	Disease (LQT15)	398124648	A	D	131	E
12	UniProt	VAR_073280	D	134	H	CALM2_HUMAN	Disease (LQT15)	398124650	A	D	133	H
13	UniProt	VAR_073281	Q	136	P	CALM2_HUMAN	Disease (LQT15)	398124649	A	Q	135	P
14	UniProt	VAR_078263	E	141	G	CALM1_HUMAN	Disease (LQT14)	---	A	E	140	G
15	UniProt	VAR_073282	F	142	L	CALM1_HUMAN	Disease (LQT14)	11551462	A	F	141	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	CALM1_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-77 A:82-115 A:116-147
				CALM2_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-77 A:82-115 A:116-147
				CALM3_HUMAN	8-43 44-79 81-116 117-149	4	A:7-42 A:43-77 A:82-115 A:116-147
2	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CALM1_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM2_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141
				CALM3_HUMAN	21-33 57-69 94-106 130-142	4	A:20-32 A:56-68 A:93-105 A:129-141

(no "Exon" information available for 3DVJ)

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:140
 aligned with CALM1_HUMAN | P0DP23 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
         CALM1_HUMAN      5 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  148
               SCOP domains d3dvja_ A: Calmodulin                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.----hhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ---EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-77             -EF_HAND_2  PDB: A:82-115            EF_HAND_2  PDB: A:116-147        PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (5)
                PROSITE (6) ----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (6)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3dvj A    4 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMK----EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  147
                                    13        23        33        43        53        63        73   |    83        93       103       113       123       133       143    
                                                                                                    77   82

Chain A from PDB  Type:PROTEIN  Length:140
 aligned with CALM2_HUMAN | P0DP24 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
         CALM2_HUMAN      5 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  148
               SCOP domains d3dvja_ A: Calmodulin                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.----hhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                PROSITE (1) ---EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-77             -EF_HAND_2  PDB: A:82-115            EF_HAND_2  PDB: A:116-147        PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                PROSITE (5) ----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (5)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3dvj A    4 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMK----EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  147
                                    13        23        33        43        53        63        73   |    83        93       103       113       123       133       143    
                                                                                                    77   82

Chain A from PDB  Type:PROTEIN  Length:140
 aligned with CALM3_HUMAN | P0DP25 from UniProtKB/Swiss-Prot  Length:149

    Alignment length:144
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    
         CALM3_HUMAN      5 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  148
               SCOP domains d3dvja_ A: Calmodulin                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhhh.----hhhhhhhhhhhh.....eehhhhhhhhhhhh....hhhhhhhhhhhhh......eehhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------------I-----------------------------------L-----V-I----V--------------------------G-E-H-P----GL------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------S-------------------------------G------------------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------------------S-------------------------------V------------------ SAPs(SNPs) (3)
                PROSITE (2) ---EF_HAND_2  PDB: A:7-42 UniProt: 8-43EF_HAND_2  PDB: A:43-77             -EF_HAND_2  PDB: A:82-115            EF_HAND_2  PDB: A:116-147        PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ----------------EF_HAND_1    -----------------------EF_HAND_1    ------------------------EF_HAND_1    -----------------------EF_HAND_1    ------ PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3dvj A    4 LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMK----EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA  147
                                    13        23        33        43        53        63        73   |    83        93       103       113       123       133       143    
                                                                                                    77   82

Chain B from PDB  Type:PROTEIN  Length:21
 aligned with CAC1B_RABIT | Q05152 from UniProtKB/Swiss-Prot  Length:2339

    Alignment length:21
                                  1862      1872 
         CAC1B_RABIT   1853 TVGKVYAALMIFDFYKQNKTS 1873
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                3dvj B 1853 TVGKVYAALMIFDFYKQNKTS 1873
                                  1862      1872

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)

Human (Homo sapiens) [TaxId: 9606] (74)

d3dvja_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CALM1_HUMAN | P0DP23)

Chain A (CALM2_HUMAN | P0DP24)

Chain A (CALM3_HUMAN | P0DP25)

Chain B (CAC1B_RABIT | Q05152)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005216	ion channel activity	Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0005245	voltage-gated calcium channel activity	Enables the transmembrane transfer of a calcium ion by a voltage-gated channel. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
	GO:0005244	voltage-gated ion channel activity	Enables the transmembrane transfer of an ion by a voltage-gated channel. An ion is an atom or group of atoms carrying an electric charge by virtue of having gained or lost one or more electrons. A voltage-gated channel is a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
biological process
	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: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:0034765	regulation of ion transmembrane transport	Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other.
	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:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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:0005891	voltage-gated calcium channel complex	A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dvj)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (15, 15)

PROSITE Motifs (2, 8)

Exons (0, 0)

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SCOP Domains (1, 1)

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