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(-) Description

Title :  STRUCTURE OF CALPAIN DOMAIN 6 IN COMPLEX WITH CALPASTATIN DIC
 
Authors :  B. Todd, D. Moore, C. C. S. Deivanayagam, G. -D. Lin, D. Chattopadhyay, M K. K. W. Wang, S. V. L. Narayana
Date :  07 Feb 03  (Deposition) - 19 Aug 03  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Calcium Binding, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Todd, D. Moore, C. C. S. Deivanayagam, G. -D. Lin, D. Chattopadhyay, M. Maki, K. K. W. Wang, S. V. L. Narayana
A Structural Model For The Inhibition Of Calpain By Calpastatin: Crystal Structures Of The Native Domain Vi Of Calpain And Its Complexes With Calpastatin Peptide And A Small Molecule Inhibitor.
J. Mol. Biol. V. 328 131 2003
PubMed-ID: 12684003  |  Reference-DOI: 10.1016/S0022-2836(03)00274-2

(-) Compounds

Molecule 1 - CALCIUM-DEPENDENT PROTEASE, SMALL SUBUNIT
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DOMAIN VI
    Gene: CAPNS1 OR CAPN4
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: CALPAIN REGULATORY SUBUNIT, CALCIUM-ACTIVATED NEUTRAL PROTEINASE, CANP
 
Molecule 2 - CALPASTATIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: DIC, RESIDUES 230-241
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: CALPAIN INHIBITOR
 
Molecule 3 - SMALL MOLECULE INHIBITOR
    Chains: E
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:107 , ASP A:110 , GLU A:112 , GLU A:117BINDING SITE FOR RESIDUE CA A 900
2AC2SOFTWAREASP A:150 , ASP A:152 , THR A:154 , LYS A:156 , GLU A:161 , HOH A:1069BINDING SITE FOR RESIDUE CA A 901
3AC3SOFTWAREASP A:180 , ASP A:182 , SER A:184 , THR A:186 , GLU A:191 , HOH A:1168BINDING SITE FOR RESIDUE CA A 902
4AC4SOFTWAREALA B:407 , ASP B:410 , GLU B:412 , GLU B:417BINDING SITE FOR RESIDUE CA B 903
5AC5SOFTWAREASP B:450 , ASP B:452 , THR B:454 , LYS B:456 , GLU B:461 , HOH B:1115BINDING SITE FOR RESIDUE CA B 904
6AC6SOFTWAREASP B:480 , VAL B:481 , ASP B:482 , SER B:484 , THR B:486 , GLU B:491BINDING SITE FOR RESIDUE CA B 905
7AC7SOFTWARELEU A:102 , LEU A:106 , ILE A:121 , ARG A:128 , HIS A:129 , LEU A:132 , TRP A:166 , LYS A:170 , GLN A:173 , ALA A:174 , GLU A:197 , PHE A:224 , HOH A:1059 , HOH A:1090 , HOH A:1102 , HOH A:1116 , HOH A:1177 , HOH C:1006 , HOH C:1020 , HOH C:1071 , HOH C:1080 , HOH C:1131BINDING SITE FOR CHAIN C OF CALPASTATIN
8AC8SOFTWARELEU B:402 , LEU B:406 , ILE B:421 , VAL B:425 , ARG B:428 , HIS B:429 , TRP B:466 , LYS B:470 , GLN B:473 , ALA B:474 , LYS B:477 , HOH D:1023BINDING SITE FOR CHAIN D OF CALPASTATIN
9AC9SOFTWAREASP A:131 , GLY A:200 , PHE A:201 , HIS A:202 , ASP A:235 , PHE A:238 , LYS A:242 , ILE B:556 , HOH C:1071 , HOH E:1070 , HOH E:1076 , HOH E:1079BINDING SITE FOR CHAIN E OF SMALL MOLECULE INHIBITOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NX0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NX0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NX0)

(-) PROSITE Motifs  (2, 10)

Asymmetric/Biological Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EF_HAND_1PS00018 EF-hand calcium-binding domain.CPNS1_PIG150-162
 
180-192
 		  4A:150-162
B:450-462
A:180-192
B:480-492
2EF_HAND_2PS50222 EF-hand calcium-binding domain profile.CPNS1_PIG167-202
 
137-165
 
232-266
 		  6A:167-202
B:467-502
A:137-165
B:437-465
A:232-266
B:532-566

(-) Exons   (0, 0)

(no "Exon" information available for 1NX0)

(-) Sequences/Alignments

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_PIG | P04574 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:173
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
            CPNS1_PIG    94 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 266
               SCOP domains d1nx0a_ A: Calpain small (regulatory) subunit (domain VI)                                                                                                                     SCOP domains
               CATH domains 1nx0A00 A:94-266 EF-hand                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PDB: A:232-266           PROSITE (1)
                PROSITE (2) -------------------------------------------EF_HAND_2  PDB: A:137-165    -EF_HAND_2  PDB: A:167-202           ---------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx0 A  94 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 266
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   


Chain B from PDB  Type:PROTEIN  Length:173
 aligned with CPNS1_PIG | P04574 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:173
                                   103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263   
            CPNS1_PIG    94 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 266
               SCOP domains d1nx0b_ B: Calpain small (regulatory) subunit (domain VI)                                                                                                                     SCOP domains
               CATH domains 1nx0B00 B:394-566 EF-hand                                                                                                                                                     CATH domains
           Pfam domains (1) ---------------EF_hand_6-1nx0B03 B:409-468                                 --EF_hand_4-1nx0B01 B:471-501    ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------EF_hand_6-1nx0B04 B:409-468                                 --EF_hand_4-1nx0B02 B:471-501    ----------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.........hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------EF_HAND_1    -----------------EF_HAND_1    ---------------------------------------EF_HAND_2  PDB: B:532-566           PROSITE (1)
                PROSITE (2) -------------------------------------------EF_HAND_2  PDB: B:437-465    -EF_HAND_2  PDB: B:467-502           ---------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nx0 B 394 EEVRQFRRLFAQLAGDDMEVSATELMNILNKVVTRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDVDRSGTIGSSELPGAFEAAGFHLNEHLYSMIIRRYSDEGGNMDFDNFISCLVRLDAMFRAFKSLDKDGTGQIQVNIQEWLQLTMYS 566
                                   403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563   


Chain C from PDB  Type:PROTEIN  Length:12
 aligned with ICAL_CHLAE | P49342 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:12
                                   239  
           ICAL_CHLAE   230 DAIDALSSDFTC 241
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 1nx0 C 601 DAIDALSSDFTS 612
                                   610  


Chain C from PDB  Type:PROTEIN  Length:12
 aligned with ICAL_PIG | P12675 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:20
                                   658       668
             ICAL_PIG   649 DPIDALSGDFDRCPSTTETS 668
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author hhhhhhhh..--------.. Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
                 Transcript -------------------- Transcript
                 1nx0 C 601 DAIDALSSDF--------TS 612
                                   610       612
                                   610      611 


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with ICAL_CHLAE | P49342 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:11
                                   239 
           ICAL_CHLAE   230 DAIDALSSDFT 240
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1nx0 D 701 DAIDALSSDFT 711
                                   710 


Chain D from PDB  Type:PROTEIN  Length:11
 aligned with ICAL_PIG | P12675 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:11
                                   240 
             ICAL_PIG   231 DAIDALSLDLT 241
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1nx0 D 701 DAIDALSSDFT 711
                                   710 


Chain E from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 1nx0 E 801 AKAIA 805
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: EF_hand (270)

(-) Gene Ontology  (14, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CPNS1_PIG | P04574)
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.
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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.

Chain C,D   (ICAL_CHLAE | P49342)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

Chain C,D   (ICAL_PIG | P12675)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CPNS1_PIG | P04574: 1alv 1alw 1nx1 1nx2 1nx3 4phn
        ICAL_CHLAE | P49342: 1nx1
        ICAL_PIG | P12675: 1nx1

(-) Related Entries Specified in the PDB File

1nx1 1nx2 1nx3