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(-) Description

Title :  X-RAY CRYSTAL STRUCTURAL ANALYSIS OF THE COMPLEX BETWEEN ALG-2 AND SEC31A PEPTIDE
 
Authors :  T. Takahashi, H. Suzuki, M. Kawasaki, H. Shibata, S. Wakatsuki, M. Maki
Date :  29 Jul 14  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Penta-Ef-Hand Protein, Endoplasmic Reticulum, Membrane, Transport, Apoptosis, Calcium Binding, Apoptosis-Transport Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Takahashi, K. Kojima, W. Zhang, K. Sasaki, M. Ito, H. Suzuki, M. Kawasaki, S. Wakatsuki, T. Takahara, H. Shibata, M. Maki
Structural Analysis Of The Complex Between Penta-Ef-Hand Alg-2 Protein And Sec31A Peptide Reveals A Novel Target Recognition Mechanism Of Alg-2
Int J Mol Sci V. 16 3677 2015
PubMed-ID: 25667979  |  Reference-DOI: 10.3390/IJMS16023677

(-) Compounds

Molecule 1 - PROGRAMMED CELL DEATH PROTEIN 6
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3D
    Expression System StrainBL21 DE3 PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 20-191
    GenePDCD6, ALG2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPOPTOSIS-LINKED GENE 2 PROTEIN, PROBABLE CALCIUM-BINDING PROTEIN ALG-2
 
Molecule 2 - PROTEIN TRANSPORT PROTEIN SEC31A
    ChainsC, D
    EngineeredYES
    FragmentALG-2 BINDING SITE, UNP RESIDUES 837-848
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS SEQUENCE OCCURS NATURALLY IN HUMANS.
    SynonymABP125, ABP130, SEC31-LIKE PROTEIN 1, SEC31-RELATED PROTEIN A, WEB1-LIKE PROTEIN
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1ZN10Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:36 , ASP A:38 , SER A:40 , VAL A:42 , GLU A:47BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREASP A:103 , ASP A:105 , SER A:107 , MET A:109 , ASP A:111 , GLU A:114 , ZN A:203BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWAREASP A:105 , ASP A:111 , GLN A:145 , ZN A:202BINDING SITE FOR RESIDUE ZN A 203
04AC4SOFTWAREASP A:171 , ASP A:173BINDING SITE FOR RESIDUE ZN A 204
05AC5SOFTWAREASP B:36 , ASP B:38 , SER B:40 , VAL B:42 , GLU B:47 , HOH B:311BINDING SITE FOR RESIDUE ZN B 201
06AC6SOFTWAREASP B:103 , ASP B:105 , SER B:107 , MET B:109 , GLU B:114 , ZN B:203BINDING SITE FOR RESIDUE ZN B 202
07AC7SOFTWAREASP B:105 , SER B:107 , ASP B:111 , GLN B:145 , ZN B:202BINDING SITE FOR RESIDUE ZN B 203
08AC8SOFTWAREARG B:104 , ASP B:171 , ASP B:173 , HOH B:306 , HOH B:310BINDING SITE FOR RESIDUE ZN B 204
09AC9SOFTWAREASN C:1 , ASN C:12 , ASN D:1 , ZN D:101BINDING SITE FOR RESIDUE ZN C 101
10BC1SOFTWAREASN C:1 , ZN C:101 , ASN D:1 , HIS D:10 , GLY D:11BINDING SITE FOR RESIDUE ZN D 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WXA)

(-) Sequences/Alignments

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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......eehhhhhh.ee.......hhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wxa A  25 QSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV 191
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       

Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhh.ee.......hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wxa B  25 QSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV 191
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .....ee..... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3wxa C   1 NPPPPGFIMHGN  12
                                    10  

Chain D from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author .....ee..... Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 3wxa D   1 NPPPPGFIMHGN  12
                                    10  

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 3WXA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 60)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDCD6_HUMAN | O753402zn8 2zn9 2znd 2zne 2zrs 2zrt 3aaj 3aak 5gqq

(-) Related Entries Specified in the PDB File

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