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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ATG12~ATG5 CONJUGATE IN COMPLEX WITH AN N-TERMINAL FRAGMENT OF ATG16L1
 
Authors :  C. Otomo, Z. Metlagel, G. Takaesu, T. Otomo
Date :  31 Jul 12  (Deposition) - 05 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.88
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Protein Conjugate, Protein-Protein Complex, Ubiquitin-Like Protein, Autophagy, E3 Ligase, Ubiquitin-Like Fold, Structural Protein, Isopeptide Bond, Cytoplasm And Autophagosomal Membranes, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Otomo, Z. Metlagel, G. Takaesu, T. Otomo
Structure Of The Human Atg12~Atg5 Conjugate Required For Lc Lipidation In Autophagy.
Nat. Struct. Mol. Biol. V. 20 59 2013
PubMed-ID: 23202584  |  Reference-DOI: 10.1038/NSMB.2431

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE PROTEIN ATG12
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC DUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APG12, APG12L, ATG12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AUTOPHAGY-RELATED PROTEIN 12, APG12-LIKE
 
Molecule 2 - AUTOPHAGY PROTEIN 5
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYC DUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APG5L, ASP, ATG5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APG5-LIKE, APOPTOSIS-SPECIFIC PROTEIN
 
Molecule 3 - AUTOPHAGY-RELATED PROTEIN 16-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APG16L, ATG16L1, UNQ9393/PRO34307
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: APG16-LIKE 1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:95 , PRO B:97 , ASN B:99BINDING SITE FOR RESIDUE NA B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:63 -Asp A:64
2Leu B:96 -Pro B:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GDL)

(-) 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:88
                                                                                                                        
               SCOP domains d4gdla_ A: automated matches                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........eeeee...hhhhhhhhhhhhh........eeee..........hhhhhhhhhh...eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 4gdl A  53 KKIDILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLKLVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCKSQAWG 140
                                    62        72        82        92       102       112       122       132        


Chain B from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eeeeeeee............eeeeee...hhhhh.hhhhhhhhh..........eeee..ee.....hhhhhhhhhh......eeeeee.............hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhh............eeee.......................hhhhhhhhhh.....eeee..........hhhhhhhhh......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gdl B   3 DDKDVLRDVWFGRIPTCFTLYQDEITEREAEPYYLLLPRVSYLTLVTDKVKKHFQKVMRQEDISEIWFEYEGTPLKWHYPIGLLFDLLASSSALPWNITVHFKSFPEKDLLHCPSKDAIEAHFMSCMKEADALKHKSQVINEMQKKDHKQLWMGLQNDRFDQFWAINRKLMEYPAEENGFRYIPFRIYQTTTERPFIQKLFRPVAADGQLHTLGDLLKEVCPSAIKNQVMIHGIEPMLETPLQWLSEHLSYPDNFLHISIIPQPT 274
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    || 239       249       259       269     
                                                                                                                                                                                                                                                          227|                                       
                                                                                                                                                                                                                                                           235                                       


Chain C from PDB  Type:PROTEIN  Length:34
                                                                  
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 4gdl C  10 MPRWKRHISEQLRRRDRLQRQAFEEIILQYNKLL  43
                                    19        29        39
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (54, 81)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4gdl
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  A16L1_HUMAN | Q676U5
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  ATG12_HUMAN | O94817
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  ATG5_HUMAN | Q9H1Y0
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 Related Entries

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

UniProtKB/Swiss-Prot
        A16L1_HUMAN | Q676U5: 4gdk 4naw 4tq0 5d7g
        ATG12_HUMAN | O94817: 4gdk 4naw
        ATG5_HUMAN | Q9H1Y0: 4gdk 4naw 4tq0 4tq1 5d7g

(-) Related Entries Specified in the PDB File

4gdk THE STRUCTURE OF THE SAME COMPLEX IN A DIFFERENT SPACE GROUP.