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(-) Description

Title :  CRYSTAL STRUCTURE OF ATG13(17BR)-ATG17-ATG29-ATG31 COMPLEX
 
Authors :  Y. Fujioka, N. N. Noda
Date :  27 Feb 14  (Deposition) - 07 May 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fujioka, S. W. Suzuki, H. Yamamoto, C. Kondo-Kakuta, Y. Kimura, H. Hirano, R. Akada, F. Inagaki, Y. Ohsumi, N. N. Noda
Structural Basis Of Starvation-Induced Assembly Of The Autophagy Initiation Complex.
Nat. Struct. Mol. Biol. V. 21 513 2014
PubMed-ID: 24793651  |  Reference-DOI: 10.1038/NSMB.2822

(-) Compounds

Molecule 1 - ATG29
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-86
    Gene: KLTH0D11660G
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS
    Organism Taxid: 559295
    Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284
    Synonym: KLTH0C07942P
 
Molecule 2 - ATG31
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KLTH0C07942G
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS
    Organism Taxid: 559295
    Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284
    Synonym: KLTH0D11660P
 
Molecule 3 - ATG17
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PACYCDUET-1
    Expression System Strain: BL21(DE)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KLTH0D15642G
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS
    Organism Taxid: 559295
    Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284
    Synonym: KLTH0D15642P
 
Molecule 4 - ATG13 17BR
    Chains: G
    Engineered: YES
    Fragment: UNP RESIDUES 392-404
    Organism Common: YEAST
    Organism Scientific: LACHANCEA THERMOTOLERANS
    Organism Taxid: 559295
    Synonym: KLTH0A00704P
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 60)

Asymmetric/Biological Unit (1, 60)
No.NameCountTypeFull Name
1UNK60Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 4P1W)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P1W)

(-) Exons   (0, 0)

(no "Exon" information available for 4P1W)

(-) 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:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee..............hhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 4p1w A   1 MNSENTIVYVRVAGRNGFVDPLKFYWDLERDRSLWSSVSKLxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  82
                                    10    ||  22        32        42||||||||60||||||||70||||||||80||
                                         15|                       43|||||||60-UNK|||69-UNK|||78-UNK
                                          18                        52-UNK|||61-UNK|||70-UNK|||79-UNK
                                                                     53-UNK|| 62-UNK|| 71-UNK|| 80-UNK
                                                                      54-UNK|  63-UNK|  72-UNK|  81-UNK
                                                                       55-UNK   64-UNK   73-UNK   82-UNK
                                                                        56-UNK   65-UNK   74-UNK    
                                                                         57-UNK   66-UNK   75-UNK   
                                                                          58-UNK   67-UNK   76-UNK  
                                                                           59-UNK   68-UNK   77-UNK 


Chain B from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....................eeee..eeeee................eeeeee........eeeeee...ee...eee...eeeeeee.....hhhhh..hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1w B   9 VLEPFTVTVVDRNVKHQVEGEPEEPDHEVQGVMFATNVKYIFEDDQELLPEQEDPAIENVVIIEADESLRVTQVELISDQFKQVGYEVRDGNEVCIDALSRFETPRQLGNLPLEKLVQLYKLQNDQLHSLFNTLH 146
                                    18        28   ||   41        51        61        71        81        91       101       111       121       131       141     
                                                  32|                                                                                                              
                                                   36                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..........eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1w C   2 NEAVIEKLLENSRKFLTGAKLICQESNDHLTTTKLRIREWQKFQSKLHFVLDCIQQQTKFLSEILLREGIGRNLIEEEWSQTVLVRLVNDMKFWQNEITKMMNKLDNITNEIDQQHNSKLGDFISRDSSHILDSKLNEIPTIRKQVENITRQYQTMLAKVQSQLVESRMKGLRDLKLNEEFTNEADQLEQELADFLKSFTDHFDKCSALSSRSVSPEDAQNLFEIVERDDKDLAAINSLLQDAAIDVASFVRKVNMLLDERDADKAKMQATLSKLLTELRKHEEYISVFEGISALIQKFKASCLEDIRQTRNLLDFYANFERSYHNLLKEVKRRKETAAKLSQILKSCETQLEQINTADLRERQMFLLENGNYLPETIWPDEIGSLSPLYTLNYEVRKV 413
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171   ||  194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         
                                                                                                                                                                                                       175|                                                                                                                                                                                                                                
                                                                                                                                                                                                        189                                                                                                                                                                                                                                


Chain D from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee..........hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4p1w D   1 MNSENTIVYVRVAGRDPLKFYWDLERDRSLWSSVSKLxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  80
                                    10    ||  26        36      ||54||||||||64||||||||74||||||
                                         15|                   43|||||||60-UNK|||69-UNK|||78-UNK
                                          22                    52-UNK|||61-UNK|||70-UNK|||79-UNK
                                                                 53-UNK|| 62-UNK|| 71-UNK|| 80-UNK
                                                                  54-UNK|  63-UNK|  72-UNK|   
                                                                   55-UNK   64-UNK   73-UNK   
                                                                    56-UNK   65-UNK   74-UNK  
                                                                     57-UNK   66-UNK   75-UNK 
                                                                      58-UNK   67-UNK   76-UNK
                                                                       59-UNK   68-UNK   77-UNK


Chain E from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee..............eeee..eeeee.............eeeeee........eeeeee...ee...eee...eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p1w E   9 VLEPFTVTVVDRNVKHQVPDHEVQGVMFATNVKYIFEDLLPEQEDPAIENVVIIEADESLRVTQVELISDQFKQVGYEVRDGNEVCIDALSRFETPRQLGNLPLEKLVQLYKLQNDQLHSLFNTLH 146
                                    18       |37        47       |60        70        80        90       100       110       120       130       140      
                                            26|                 55|                                                                                       
                                             36                  59                                                                                       


Chain F from PDB  Type:PROTEIN  Length:389
                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhh....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1w F   2 NEAVIEKLLENSRKFLTGAKLICQESNDHLTTTKLRIREWQKFQSKLHFVLDCIQQQTKFLSEILLREGIGRNLIEEEWSQTVLVRLVNDMKFWQNEITKMMNKLDNITNEIDQQHNSKLGDFISRDSSHILDSKLNEIPTIRKQVENITRQYQTMLAKVQSQLVESRMKGLRDEFKLNEEFTNEADQLEQELADFLKSFTDHFDKCSALSSFEIVERDDKDLAAINSLLQDAAIDVASFVRKVNMLLDERDADKAKMQATLSKLLTELRKHEEYISVFEGISALIQKFKASCLEDIRQTRNLLDFYANFERSYHNLLKEVKRRKETAAKLSQILKSCETQLEQINTADLRERQMFLLENGNYLPETIWPDEIGSLSPLYTLNYEVRKV 413
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     ||193       203       213       223 ||    244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404         
                                                                                                                                                                                                         177|                                225|                                                                                                                                                                                
                                                                                                                                                                                                          190                                 237                                                                                                                                                                                


Chain G from PDB  Type:PROTEIN  Length:6
                                      
               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
                 4p1w G 396 SSFGRL 401
   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 4P1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P1W)

(-) Gene Ontology  (23, 39)

Asymmetric/Biological Unit(hide GO term definitions)

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

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        C5DB94_LACTC | C5DB94: 4j2g 5jhf
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(-) Related Entries Specified in the PDB File

4p1n