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(-) Description

Title :  CRYSTAL STRUCTURE OF CED-4 BOUND CED-3 FRAGMENT
 
Authors :  W. J. Huang, T. Y. Jinag, W. Y. Choi, J. W. Wang, Y. G. Shi
Date :  15 Aug 13  (Deposition) - 23 Oct 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (4x)
Keywords :  Apoptosome, Apoptosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Huang, T. Jiang, W. Choi, S. Qi, Y. Pang, Q. Hu, Y. Xu, X. Gong, P. D. Jeffrey, J. Wang, Y. Shi
Mechanistic Insights Into Ced-4-Mediated Activation Of Ced-3.
Genes Dev. V. 27 2039 2013
PubMed-ID: 24065769  |  Reference-DOI: 10.1101/GAD.224428.113

(-) Compounds

Molecule 1 - CELL DEATH PROTEIN 4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CED-4, C35D10.9
    Organism Common: NEMATODE
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - CED-3 FRAGMENT
    Chains: C, D
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 40)

Asymmetric Unit (3, 40)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 152)
No.NameCountTypeFull Name
1ATP8Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MSE144Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:166 , LYS A:191 , ASP A:250 , ASP A:251 , ATP A:602BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWAREMSE A:128 , TYR A:131 , GLY A:162 , GLY A:164 , LYS A:165 , SER A:166 , VAL A:167 , GLN A:171 , ARG A:273 , PHE A:301 , TYR A:305 , PRO A:330 , ALA A:331 , MSE A:334 , THR A:367 , PRO A:368 , TYR A:369 , MG A:601BINDING SITE FOR RESIDUE ATP A 602
3AC3SOFTWARESER B:166 , ASP B:250 , ATP B:602BINDING SITE FOR RESIDUE MG B 601
4AC4SOFTWAREMSE B:128 , TYR B:131 , GLY B:162 , GLY B:164 , LYS B:165 , SER B:166 , VAL B:167 , GLN B:171 , ARG B:273 , PRO B:330 , ALA B:331 , MSE B:334 , THR B:367 , PRO B:368 , TYR B:369 , MG B:601BINDING SITE FOR RESIDUE ATP B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4M9Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Mse A:449 -Pro A:450
2Mse B:449 -Pro B:450

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 4M9Y)

(-) 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:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhh.........hhhhh..hhhhhhhhhh..........hhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhh............eeeeee......hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhh..eeeeee.hhhhhhhh...eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhh..hhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhhh.....eehhhhhh.........hhhhhhhhhhhhh............ee...hhhhhhhhh..hhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m9y A   1 mLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKmSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQmLDRKLLLGNVPKQmTCYIREYHVDRVIKKLDEmCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLmLKSEDDLLNFPSVEHVTSVVLKRmICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGmPmPVGEKEEDVLNKTIELSSGNPATLmmFFKSCEPKTFEKmAQLNNKLESRGLVGVECITPYSYKSLAmALQRCVEVLSDEDRSALAFAVVmPPGVDIPVKLWSCVIPVDEQLDDEVADRLKRLSKRGALLSGKRmPVLTFKIDHIIHmFLKHVVDAQTIANGISILEQRLLEIETVIRPEDFPKFmQLHQKFYDSLKNFACC 549
                            |       10        20        30        40      | 50        60        70        80        90       100       110   |   120       130       140      |150       160       170       180       190       200       210       220       230   |   240       250       260       270       280       290       300      |310       320       330   ||  340       350       360       370     | 380       390       400       410      |426       436       446  |    456     | 466       476       486||     529   |   539       549
                            |                                            47-MSE                                                            114-MSE       128-MSE            147-MSE                                                        210-MSE                 234-MSE                                                                  307-MSE                    334-MSE       348-MSE                     376-MSE                399-MSE           417|                      449-MSE      462-MSE                  487|         533-MSE            
                            1-MSE                                                                                                                                                                                                                                                                                                             309-MSE                   335-MSE                                                                            424                                                             521                            


Chain B from PDB  Type:PROTEIN  Length:511
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhh............hhhhhh.hhhhhhh..........hhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhh............eeeeee......hhhhhhhhhhhhhhh..............hhhhhhhhhhhhh.....eeeeeeee.hhhhhhhhhhh..eeeeee..hhhhhhh...eeeeee...hhhhhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.hhhhhhhhhhhhhh.....eehhhhhh......hhhhhhhhhhhhh.....ee.....ee...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m9y B   1 mLCEIECRALSTAHTRLIHDFEPRDALTYLEGKNIFTEDHSELISKmSTRLERIANFLRIYRRQASELGPLIDFFNYNNQSHLADFLEDYIDFAINEPDLLRPVVIAPQFSRQmLDRKLLLGNVPKQmTCYIREYHVDRVIKKLDEmCDLDSFFLFLHGRAGSGKSVIASQALSKSDQLIGINYDSIVWLKDSGTAPKSTFDLFTDILLmLKSEDDLLNFPSVEHVTSVVLKRmICNALIDRPNTLFVFDDVVQEETIRWAQELRLRCLVTTRDVEISNAASQTCEFIEVTSLEIDECYDFLEAYGmPmPVGEKEEDVLNKTIELSSGNPATLmmFFKSCEPKTFEKmAQLNNKLESRGLVGVECITPYSYKSLAmALQRCVEVLSDEDRSALAFAVVmPPGVDIPVKLWSCVIPVLDDEVADRLKRLSKRGALLSGKRmPVLTFKIDHIIHmFLKHVVDAQTIANGISILEQRLLEIGNNNETVIRPEDFPKFmQLHQKFYDSLKNFACC 549
                            |       10        20        30        40      | 50        60        70        80        90       100       110   |   120       130       140      |150       160       170       180       190       200       210       220       230   |   240       250       260       270       280       290       300      |310       320       330   ||  340       350       360       370     | 380       390       400       410     ||429       439       449       459  |    469       479       489 ||    528    |  538       548 
                            1-MSE                                        47-MSE                                                            114-MSE       128-MSE            147-MSE                                                        210-MSE                 234-MSE                                                                  307-MSE                    334-MSE       348-MSE                     376-MSE                399-MSE          416|                    449-MSE      462-MSE                      491|         533-MSE            
                                                                                                                                                                                                                                                                                                                                              309-MSE                   335-MSE                                                                           426                                                               521                            


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               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
                 4m9y C 748 PLFNFmG 754
                                 | 
                               753-MSE


Chain D 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
                 4m9y D 749 LFNFm 753
                                |
                                |
                              753-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 4M9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M9Y)

(-) Gene Ontology  (27, 27)

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 Related Entries

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        CED4_CAEEL | P30429: 2a5y 3lqq 3lqr 4m9s 4m9x 4m9z

(-) Related Entries Specified in the PDB File

4m9s 4m9x 4m9z