Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF AN ATG7-ATG10 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 :  2.90
Chains :  Asym./Biol. Unit :  A,B,Y,Z
Keywords :  Ubiquitin-Like Protein Activation Enzyme, Ubiquitin-Like Protein Transfer Enzyme, Protein Transport-Ligase Complex (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
    Mutation: YES
    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 - UBIQUITIN-LIKE-CONJUGATING ENZYME ATG10
    Chains: Y, Z
    EC Number: 6.3.2.-
    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: APG10, ATG10, YLL042C
    Mutation: YES
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: AUTOPHAGY-RELATED PROTEIN 10

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABYZ

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 701
2AC2SOFTWARECYS B:485 , CYS B:488 , CYS B:569 , CYS B:572BINDING SITE FOR RESIDUE ZN B 701

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:147 -Pro A:148
2Arg B:147 -Pro B:148
3Tyr Y:164 -Glu Y:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GSK)

(-) 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:570
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..ee.......eeeehhhhhhhhhhhhh...eeeeeeee............eeeehhhhh..........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhhhhhh....eeee.....ee..hhhhhhhhheeeee...........hhhhhhhhhhhhh....eeeeeee......eeeeeeee....eeeee..........eeee.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeee..hhhhhhhhhhhhhh...eeeeee......hhhhh....hhhhh..hhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhh..eeeeeee...eeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhh.................eeeee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gsk A   3 SERVLSYAPAFKSFLDTSFFQELSRLKLDVTSQPLTVNLDLHNIPKSADQVPLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDINKCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSKWVCILDADDEIVNYDKSIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKLLIIRQNEGSFALNATFASPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDAGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGQLGCYFCHRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKYSGSETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLS 605
                                    12        22        32|       47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466      |484    || 505       515       525       535       545       555       565       575       585       595       605
                                                        32|                                                                                                                                                                                                                       256|                                                                                                                                                                                                            473|    489|                                                                                                        
                                                         38                                                                                                                                                                                                                        266                                                                                                                                                                                                             482     501                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:572
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.......eeeehhhhhhhhhhhhh....eeeeeee............eeeehhhhhh.........eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeeeeeeeee....eeeeeee.hhhhhhhhhhhhhhhhh....eeee.....eee.hhhhhhhhheeeee...........hhhhhhhhhhhhh....eeeeeee......eeeeeeeee....eeeee..........eeee.hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhheeeee..hhhhhhhhhhhhhh...eeeee.......hhhhhh...hhhhh..hhhhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhh..eeeeeee...eeeeeee.....................hhhhhhhhhhhhhhhhhhhh....ee..ee...eeeee....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsk B   2 SSERVLSYAPAFKSFLDTSFFQELSRLKLDSTSQPLTVNLDLHNIPKSADQVPLFLTNRSFEKHNNKRTNEVPLQGSIFNFNVLDEFKNLDKQLFLHQRALECWEDGIKDINKCVSFVIISFADLKKYRFYYWLGVPCFQRPSSTVLHVRPEPSLKGLFSKCQKWFDVNYSKWVCILDADDEIVNYDKSIIRKTKVLAIRDTSTMENVPSALTKNFLSVLQYDVPDLIDFKLLIIRQNEGSFALNATFASIPDMKVSGWERNVQGKLAPRVVDLSSLLDPLKIADQSVDLNLKLMKWRILPDLNLDIIKNTKVLLLGAGTLGCYVSRALIAWGVRKITFVDNGTVSYSNPVRQALYNFEDAGKPKAELAAASLKRIFPLMDATGVKLSIPMIGHKLVNEEAQHKDFDRLRALIKEHDIIFLLVDSRESRWLPSLLSNIENKTVINAALGFDSYLVMRHGNKQLGCYFCHRTLDQMCTVTRPGVAMMASSLAVELMTSLLQTKETTVLGDIPHQIRGFLHNFSILKLETPAYEHCPACSPKVIEAFTDLGWEFVKKALEHPLYLEEISGLSVI 607
                                    11        21        31|       46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256||     274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474|      501       511       521       531 ||    545       555       565       575       585       595       605  
                                                        31|                                                                                                                                                                                                                         257|                                                                                                                                                                                                             474|     489|                             533|                                                                     
                                                         37                                                                                                                                                                                                                          266                                                                                                                                                                                                              481      501                              538                                                                     


Chain Y from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh........eeeeee......eeeee..hhhhhhhhhhh...eeeeeeeeeeee....eeeeeeeeeeeee....eeeeee...............ee.....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsk Y   1 MIPYQEWHSQLQSLYDSQIFHNWALSQDVHLNDEKDGLLLRLIPTRQLQKNTERIENKLLNHIELYLTYSKVYNEPLLLLRIWEEKSIDGIPMTKLMLPTDIESLLDVGSVWYSFHPMSTYLRRWVSIFIFSWLGYE 165
                                    10        20        30        40        50        60        70        80        90       100       125      |148       158       
                                                                                                                                     108|     132|                   
                                                                                                                                      124      146                   


Chain Z from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh........eeeeee......eeeee..hhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeeeeee....eeeeee............ee....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsk Z   2 IPYQEWHSQLQSLYDSQIFHNWALSQDVHLNDEKDGLLLRLIPTRQLQKNTERIENKLLNHIELYLTYSKVYNEPLLLLRIWEEKSIDGIPMTKLMLPTDIESLLSVWYSFHMSTYLRRWVSIFIFSWLGY 164
                                    11        21        31        41        51        61        71        81        91       101    || 129 ||    153       163 
                                                                                                                                  106|   131|                  
                                                                                                                                   125    146
   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 4GSK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 35)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:147 - Pro A:148   [ RasMol ]  
    Arg B:147 - Pro B:148   [ RasMol ]  
    Tyr Y:164 - Glu Y:165   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4gsk
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ATG10_YEAST | Q07879
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  ATG7_YEAST | P38862
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  6.3.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  ATG10_YEAST | Q07879
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  ATG7_YEAST | P38862
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ATG10_YEAST | Q07879: 4ebr
        ATG7_YEAST | P38862: 2li5 3rui 3ruj 3t7e 3t7f 3t7g 3t7h 3vh1 3vh2 3vh3 3vh4 4gsj 4gsl

(-) Related Entries Specified in the PDB File

4gsj 4gsl