1DVI - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CALPAIN DOMAIN VI WITH CALCIUM BOUND

Authors :   M. Cygler, H. Blanchard, P. Grochulski

Date :   15 May 97 (Deposition) - 27 May 98 (Release) - 02 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Calcium-Dependent Protease, Small Subunit (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Blanchard, P. Grochulski, Y. Li, J. S. Arthur, P. L. Davies, J. S. Elce, M. Cygler
Structure Of A Calpain Ca(2+)-Binding Domain Reveals A Nove Ef-Hand And Ca(2+)-Induced Conformational Changes.
Nat. Struct. Biol. V. 4 532 1997
PubMed-ID: 9228945 | Reference-DOI: 10.1038/NSB0797-532
(for further references see the PDB file header)

Molecule 1 - CALPAIN
	Cell Line	:	BL21
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Gene	:	CAPN4
	Expression System Plasmid	:	PT7-7F-21K
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PT7
	Fragment	:	SMALL (REGULATORY) SUBUNIT, DOMAIN VI, RESIDUES 87 - 270
	Gene	:	CAPN4
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Tissue	:	LIVER

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	CA	8	Ligand/Ion	CALCIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:111 , ASP A:114 , GLU A:116 , GLU A:121 , HOH A:284 , HOH A:296	BINDING SITE FOR RESIDUE CA A 271
2	AC2	SOFTWARE	ASP A:154 , ASP A:156 , THR A:158 , LYS A:160 , GLU A:165 , HOH A:275	BINDING SITE FOR RESIDUE CA A 272
3	AC3	SOFTWARE	ASP A:184 , ASP A:186 , SER A:188 , THR A:190 , GLU A:195 , HOH A:278	BINDING SITE FOR RESIDUE CA A 273
4	AC4	SOFTWARE	ASP A:139 , ASP A:227 , ASP A:229 , ASN A:230 , HOH B:282 , HOH B:285	BINDING SITE FOR RESIDUE CA A 274
5	AC5	SOFTWARE	ALA B:111 , ASP B:114 , GLU B:116 , GLU B:121 , HOH B:302 , HOH B:314	BINDING SITE FOR RESIDUE CA B 275
6	AC6	SOFTWARE	ASP B:154 , ASP B:156 , THR B:158 , LYS B:160 , GLU B:165 , HOH B:292	BINDING SITE FOR RESIDUE CA B 276
7	AC7	SOFTWARE	ASP B:184 , ASP B:186 , SER B:188 , THR B:190 , GLU B:195 , HOH B:295	BINDING SITE FOR RESIDUE CA B 277
8	AC8	SOFTWARE	ASP B:139 , ASP B:227 , ASP B:229 , ASN B:230 , HOH B:301 , HOH B:315	BINDING SITE FOR RESIDUE CA B 278

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

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

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

Asymmetric/Biological Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EF_HAND_1	PS00018	EF-hand calcium-binding domain.	CPNS1_RAT	154-166 184-196	4	A:154-166 B:154-166 A:184-196 B:184-196
2	EF_HAND_2	PS50222	EF-hand calcium-binding domain profile.	CPNS1_RAT	171-206 141-169 236-270	6	A:171-206 B:171-206 A:141-169 B:141-169 A:236-270 B:236-270

(no "Exon" information available for 1DVI)

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:173
 aligned with CPNS1_RAT | Q64537 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:173
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   
            CPNS1_RAT    98 EEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS 270
               SCOP domains d1dvia_ A: Calpain small (regulatory) subunit (domain VI)                                                                                                                     SCOP domains
               CATH domains 1dviA00 A:98-270 EF-hand                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.......eehhhhhhhhhh......hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PDB: A:236-270           PROSITE (1)
                PROSITE (2) -------------------------------------------EF_HAND_2  PDB: A:141-169    -EF_HAND_2  PDB: A:171-206           ---------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dvi A  98 EEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTSRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS 270
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with CPNS1_RAT | Q64537 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:173
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267   
            CPNS1_RAT    98 EEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS 270
               SCOP domains d1dvib_ B: Calpain small (regulatory) subunit (domain VI)                                                                                                                     SCOP domains
               CATH domains 1dviB00 B:98-270 EF-hand                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh..........hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhh.....hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PDB: B:236-270           PROSITE (1)
                PROSITE (2) -------------------------------------------EF_HAND_2  PDB: B:141-169    -EF_HAND_2  PDB: B:171-206           ---------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dvi B  98 EEERQFRKLFVQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTSRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQGIYKRFDTDRSGTIGSNELPGAFEAAGFHLNQHIYSMIIRRYSDETGNMDFDNFISCLVRLDAMFRAFRSLDKNGTGQIQVNIQEWLQLTMYS 270
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

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: Penta-EF-hand proteins (30)

Protein domain: Calpain small (regulatory) subunit (domain VI) (16)

Norway rat (Rattus norvegicus) [TaxId: 10116] (8)

1a	d1dvia_	A:
1b	d1dvib_	B:

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)

Norway rat (Rattus norvegicus) (37)

1a	1dviA00	A:98-270
1b	1dviB00	B:98-270

(no "Pfam Domain" information available for 1DVI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (CPNS1_RAT | Q64537)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004198	calcium-dependent cysteine-type endopeptidase activity	Catalysis of the hydrolysis of nonterminal peptide bonds in a polypeptide chain by a mechanism using a cysteine residue at the enzyme active center, and requiring the presence of calcium.
	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).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1dvi)

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	CPNS1_RAT \| Q64537	:	1aj5 1df0 1np8 1u5i 3bow 3df0

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 10)

Exons (0, 0)

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