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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ATG5-ATG16N69
 
Authors :  J. H. Kim, S. B. Hong, H. K. Song
Date :  10 Jun 14  (Deposition) - 11 Mar 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Autophagy Protein Complex, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Kim, S. B. Hong, J. K. Lee, S. Han, K. H. Roh, K. E. Lee, Y. K. Kim, E. J. Choi, H. K. Song
Insights Into Autophagosome Maturation Revealed By The Structures Of Atg5 With Its Interacting Partners
Autophagy V. 11 75 2015
PubMed-ID: 25484072  |  Reference-DOI: 10.4161/15548627.2014.984276

(-) Compounds

Molecule 1 - AUTOPHAGY PROTEIN 5
    ChainsA, C, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    GeneATG5, APG5L, ASP
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPG5-LIKE,APOPTOSIS-SPECIFIC PROTEIN
 
Molecule 2 - AUTOPHAGY-RELATED PROTEIN 16-1
    ChainsB, D, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 1-69
    GeneATG16L1, APG16L, UNQ9393/PRO34307
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPG16-LIKE 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4TQ0)

(-) Sites  (0, 0)

(no "Site" information available for 4TQ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TQ0)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:96 -Pro A:97
2Gln A:272 -Pro A:273
3Leu C:96 -Pro C:97
4Gln C:272 -Pro C:273
5Phe D:10 -Pro D:11
6Glu E:73 -Gly E:74
7Leu E:96 -Pro E:97
8Asp E:209 -Gly E:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4TQ0)

(-) 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:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.eeeeeeee......eeeeee...hhhhhhhhhhhhh.....eeeee..ee.....hhhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhh......eeeee......................hhhhhhhhhhhhhh.eeee..........hhhhhhhhh......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tq0 A   4 DKDVLRDVWFGRIPTCFTLYQEAEPYYLLLPRVSYLTLVTDKVKKHFQKVMEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQP 273
                                    13        23||      39        49        59||      75        85        95       105 ||    122       132       142       152       162       172       182       192       202       212       222    || 239       249       259       269    
                                               24|                           60|                                     107|                                                                                                             227|                                      
                                                31                            67                                      115                                                                                                              235                                      

Chain B from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 4tq0 B  10 FPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLH  49
                                    19        29        39        49

Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhheeeeeeee............eeeeee...hhhhhhhhhhhhhhh...eeeee..ee.....hhhhhhhhhh......eeeeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhh......eeeee......................hhhhhhhhhhhhhh.eeee..........hhhhhhhhh......eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tq0 C   4 DKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQP 273
                                    13        23        33        43        53      ||69        79        89        99      |118       128       138       148       158       168       178       188       198       208       218       235       245       255       265        
                                                                                   60|                                    106|                                                                                                            227|                                      
                                                                                    67                                     116                                                                                                             235                                      

Chain D from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 4tq0 D  10 FPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKS  46
                                    19        29        39       

Chain E from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhheeeeeeee............eeeeee...hhhhhhhhhhhhhhh...eeee..ee.....hhhhhhhhhh......eeeeee.hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhh.............eeeee..............ee...ee.hhhhhhhhhh...eeee..........hhhhhhhhh......eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tq0 E   4 DKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPT 274
                                    13        23        33        43        53      ||70        80        90       100  ||   122       132       142       152       162       172       182       192       202       212       222  ||   241       251       261       271   
                                                                                   60|                                103|                                                                                                          225|                                       
                                                                                    68                                 116                                                                                                           235                                       

Chain F from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 4tq0 F  10 FPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLLEKSDLH  49
                                    19        29        39        49

   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 4TQ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TQ0)

(-) Gene Ontology  (53, 64)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4tq0)
 
  Cis Peptide Bonds
    Asp E:209 - Gly E:210   [ RasMol ]  
    Gln A:272 - Pro A:273   [ RasMol ]  
    Gln C:272 - Pro C:273   [ RasMol ]  
    Glu E:73 - Gly E:74   [ RasMol ]  
    Leu A:96 - Pro A:97   [ RasMol ]  
    Leu C:96 - Pro C:97   [ RasMol ]  
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    Phe D:10 - Pro D:11   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        A16L1_HUMAN | Q676U54gdk 4gdl 4naw 5d7g
        ATG5_HUMAN | Q9H1Y04gdk 4gdl 4naw 4tq1 5d7g

(-) Related Entries Specified in the PDB File

4tq1