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(-) Description

Title :  CRYSTAL STRUCTURE OF APAF-1 CARD AND CASPASE-9 CARD COMPLEX
 
Authors :  Q. Hu, D. Wu, C. Yan, Y. Shi
Date :  03 Oct 14  (Deposition) - 15 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Death Domain Superfamily, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Hu, D. Wu, W. Chen, Z. Yan, C. Yan, T. He, Q. Liang, Y. Shi
Molecular Determinants Of Caspase-9 Activation By The Apaf- Apoptosome
Proc. Natl. Acad. Sci. Usa 2014
PubMed: search

(-) Compounds

Molecule 1 - APOPTOTIC PROTEASE-ACTIVATING FACTOR 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCARD DOMAIN
    GeneAPAF1, KIAA0413
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPAF-1
 
Molecule 2 - CASPASE-9
    ChainsE, F
    EC Number3.4.22.62
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCARD DOMAIN
    GeneCASP9, MCH6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCASP-9, APOPTOTIC PROTEASE MCH-6, APOPTOTIC PROTEASE- ACTIVATING FACTOR 3, APAF-3, ICE-LIKE APOPTOTIC PROTEASE 6, ICE-LAP6, CASPASE-9 SUBUNIT P35, CASPASE-9 SUBUNIT P10

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO47Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:21 , THR A:22 , SER A:23 , ARG A:44 , GLN A:49 , ARG A:52 , HOH A:202 , HOH A:209BINDING SITE FOR RESIDUE SO4 A 101
2AC2SOFTWAREHIS A:28 , SER A:31 , HOH A:210 , HOH A:216 , HIS C:77 , ARG F:36BINDING SITE FOR RESIDUE SO4 A 102
3AC3SOFTWARELYS B:21 , THR B:22 , SER B:23 , ARG B:52BINDING SITE FOR RESIDUE SO4 B 101
4AC4SOFTWARETHR B:48 , GLN B:49 , ARG B:52 , THR D:48 , GLN D:49 , ARG D:52BINDING SITE FOR RESIDUE SO4 B 102
5AC5SOFTWARELYS C:21 , THR C:22 , SER C:23 , ARG C:44 , GLN C:49 , ARG C:52 , HOH C:204 , HOH C:208 , HOH C:209BINDING SITE FOR RESIDUE SO4 C 101
6AC6SOFTWAREHIS A:77 , HOH A:248 , HIS C:28 , SER C:31 , HOH C:203 , HOH C:256 , ARG E:36BINDING SITE FOR RESIDUE SO4 C 102
7AC7SOFTWARELYS D:21 , THR D:22 , SER D:23 , GLN D:49 , ARG D:52 , HOH D:203BINDING SITE FOR RESIDUE SO4 D 101
8AC8SOFTWARESER D:38BINDING SITE FOR RESIDUE CL D 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RHW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RHW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RHW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RHW)

(-) Exons   (0, 0)

(no "Exon" information available for 4RHW)

(-) 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:95
                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  4rhw A  1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS 95
                                    10        20        30        40        50        60        70        80        90     

Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4rhw B  1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIP 92
                                    10        20        30        40        50        60        70        80        90  

Chain C from PDB  Type:PROTEIN  Length:95
                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  4rhw C  1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIPVVS 95
                                    10        20        30        40        50        60        70        80        90     

Chain D from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  4rhw D  1 MDAKARNCLLQHREALEKDIKTSYIMDHMISDGFLTISEEEKVRNEPTQQQRAAMLIKMILKKDNDSYVSFYNALLHEGYKDLAALLHDGIP 92
                                    10        20        30        40        50        60        70        80        90  

Chain E from PDB  Type:PROTEIN  Length:95
                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  4rhw E  1 MDEADRRLLRRCRLRLVEELQVDQLWDALLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQA 95
                                    10        20        30        40        50        60        70        80        90     

Chain F from PDB  Type:PROTEIN  Length:95
                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  4rhw F  1 MDEADRRLLRRCRLRLVEELQVDQLWDALLSRELFRPHMIEDIQRAGSGSRRDQARQLIIDLETRGSQALPLFISCLEDTGQDMLASFLRTNRQA 95
                                    10        20        30        40        50        60        70        80        90     

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

(no "SCOP Domain" information available for 4RHW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RHW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RHW)

(-) Gene Ontology  (63, 75)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        APAF_HUMAN | O147271c15 1cww 1cy5 1z6t 2p1h 2ygs 3j2t 3jbt 3ygs 5juy 5wvc 5wve
        CASP9_HUMAN | P552111jxq 1nw9 2ar9 3d9t 3v3k 3ygs 5juy 5wve

(-) Related Entries Specified in the PDB File

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