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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ATG7-ATG3 CROSSLINKED COMPLEX
 
Authors :  S. E. Kaiser, K. Mao, A. M. Taherbhoy, S. Yu, J. L. Olszewski, D. M. Duda, I A. Deng, T. D. Fenn, D. J. Klionsky, B. A. Schulman
Date :  27 Aug 12  (Deposition) - 14 Nov 12  (Release) - 19 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ubiquitin-Like Protein Activation Enzyme, Ubiquitin-Like Protein Transfer Enzyme, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Kaiser, K. Mao, A. M. Taherbhoy, S. Yu, J. L. Olszewski, D. M. Duda, I. Kurinov, A. Deng, T. D. Fenn, D. J. Klionsky, B. A. Schulman
Noncanonical E2 Recruitment By The Autophagy E1 Revealed By Atg7-Atg3 And Atg7-Atg10 Structures.
Nat. Struct. Mol. Biol. V. 19 1242 2012
PubMed-ID: 23142976  |  Reference-DOI: 10.1038/NSMB.2415

(-) Compounds

Molecule 1 - UBIQUITIN-LIKE MODIFIER-ACTIVATING ENZYME ATG7
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-613
    Gene: APG7, ATG7, CVT2, YHR171W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ATG12-ACTIVATING ENZYME E1 ATG7, AUTOPHAGY-RELATED PROTEIN 7, CYTOPLASM TO VACUOLE TARGETING PROTEIN 2
 
Molecule 2 - AUTOPHAGY-RELATED PROTEIN 3
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APG3, ATG3, AUT1, N2040, YNR007C
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: AUTOPHAGY-RELATED E2-LIKE CONJUGATION ENZYME ATG3

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:485 , CYS A:488 , CYS A:569 , CYS A:572BINDING SITE FOR RESIDUE ZN A 700
2AC2SOFTWARECYS B:485 , CYS B:488 , CYS B:569 , CYS B:572BINDING SITE FOR RESIDUE ZN B 700

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Arg A:147 -Pro A:148
2Ser B:3 -Glu B:4
3Arg B:147 -Pro B:148
4Asp C:130 -Asp C:131
5Ala C:164 -Gln C:165
6Ile C:231 -His C:232
7Pro C:233 -Cys C:234
8Ala C:237 -Asn C:238
9Ala D:237 -Asn D:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GSL)

(-) 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:598
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.......eeeehhhhhhhhhhh........eeeeeeeeee............eeeehhhhhh.........eeeeeeeeee.hhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhh..eeeeeeee....eeeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhh....eeee.....eee.hhhhhhhhheeeee..........hhhhhhhhhhhhhh....eeeeeee......eeeeeeeee..........eeeee..........eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.eeeee..hhhhhhhhhhhhhh...eeeee.......hhhhh....hhhhh..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh..eeeeeee...eeeeee.................................hhhhhhhhhhhhhhhhhhhhh.......ee..ee...eeeee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsl A   3 SERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTCQPLTVNLDLHNIPKSADQVPLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDINKCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSKWVCILDADDEIVNYDKCIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKLLIIRQNEGSFALNATFASIDPQSSNPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNKQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLSVIK 608
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262|      274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474|      490       500       510       520       530       540       550       560       570       580       590       600        
                                                                                                                                                                                                                                                                                             262|                                                                                                                                                                                                              474|                                                                                                                               
                                                                                                                                                                                                                                                                                              265                                                                                                                                                                                                               481                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:592
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......eeeeehhhhhhhhhhhhhh......eeeeeeeee...........eeeeehhhhhh.........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeeeeeee....eeeeeee.....hhhhhhhhhhhhh....eeee.....ee..hhhhhhhhheeeee..........hhhhhhhhhhhhhh....eeeeeee......eeeeeeeee..........eeeee..........eeeehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhh.eeeee..hhhhhhhhhhhhhh...eeeee.......hhhhhh...hhhhh..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhh.eeeeeee...eeeeee.................................hhhhhhhhhhhhhhhhhhhh.......ee..ee...eeeee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsl B   3 SERVLSYAPAFKSFLDTSFFQELSRLKLDVLKLDSTCQPLTVNLDLHNIPKSADQVPLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDINKCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSKWVCILDADDEIVNYDKCIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKLLIIRQNEGSFALNATFASIDPQSSNPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDCGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNQLGCYFCHDVVAPTDSLTDRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISG 603
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262|      274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474|      491       501       511       521       531       541       551       561       571       581       591       601  
                                                                                                                                                                                                                                                                                             262|                                                                                                                                                                                                              474|                                                                                                                         
                                                                                                                                                                                                                                                                                              265                                                                                                                                                                                                               482                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhhhhhhh...ee.............hhhhh.eeeeeeee..hhhhh...hhhhhhhhh......eeeeeeeee......eeeeeeee.......hhhhhhh..hhhhhhhhheeee........eeeee......hhhhhhh...hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gsl C  21 TFLTTGQITPEEFVQAGDYLAHMFPTWKWNEESSDISYRDFLPKNKQFLIIRKVPADKRAEQAIDDIDELIQDMEIKMAQERYYDLYIAYSTSYRVPKMYIVGFNSNGSPLSPEQMFEDISADYRTKTATIEKLPFYKNSVLSVSIHPCKHANVMKILLDKLRVDQYLIVFLKFITSVTPSIQHDY 305
                                    30        40        50        60        70        80  ||   135      |165       175       185       195       205       215       225       235       245||     289       299      
                                                                                         83|          142|                                                                                246|                        
                                                                                         129           163                                                                                 281                        


Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhhhhhhh...ee..................eeeeeeeee..hhhhh.hhhhhhh.....eeeeeeeeee....eeeeeeeee.......hhhhhhhhhhhhhhh...eeee........eeeee......hhhhhhhh..hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gsl D  21 TFLTTGQITPEEFVQAGDYLAHMFPTWKWNEESSDISYRDFLPKNKQFLIIRKVPADKRAEQAIDELIQDMEIAQERYYDLYIAYSTSYRVPKMYIVGFNSNGSPLSPEQMFEDISADYRTKTATIEKLPFYKNSVLSVSIHPCKHANVMKILLDKVRVDQYLIVFLKFITSVTPSIQHD 304
                                    30        40        50        60        70        80  ||   138  ||   170       180       190       200       210       220       230       240      |284       294       304
                                                                                         83|      141|                                                                                247|                      
                                                                                         132       164                                                                                 282
   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 4GSL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 36)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ala C:164 - Gln C:165   [ RasMol ]  
    Ala C:237 - Asn C:238   [ RasMol ]  
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  ATG7_YEAST | P38862
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 Related Entries

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

UniProtKB/Swiss-Prot
        ATG3_YEAST | P40344: 2dyt 3t7g
        ATG7_YEAST | P38862: 2li5 3rui 3ruj 3t7e 3t7f 3t7g 3t7h 3vh1 3vh2 3vh3 3vh4 4gsj 4gsk

(-) Related Entries Specified in the PDB File

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