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(-) Description

Title :  GABARAP-L1 ATG4B LIR COMPLEX
 
Authors :  S. Mouilleron, M. Skytte Rasmussen, B. Kumar Shrestha, M. Wirth, K. B Larsen, Y. Abudu Princely, E. Sjottem, S. Tooze, T. Lamark, T. Johans
Date :  21 Sep 16  (Deposition) - 08 Feb 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.44
Chains :  Asym./Biol. Unit :  B,C,D,E
Keywords :  Lir, Gabarap, Atg8, Lc3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Skytte Rasmussen, S. Mouilleron, B. Kumar Shrestha, M. Wirth, R. Lee, K. Bowitz Larsen, Y. Abudu Princely, N. O'Reilly, E. Sjttem, S. A. Tooze, T. Lamark, T. Johansen
Atg4B Contains A C-Terminal Lir Motif Important For Binding And Efficient Cleavage Of Mammalian Orthologs Of Yeast Atg8
Autophagy V. 13 834 2017
PubMed-ID: 28287329  |  Reference-DOI: 10.1080/15548627.2017.1287651

(-) Compounds

Molecule 1 - GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN-LIKE 1
    Chains: D, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Gene: GABARAPL1, GEC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EARLY ESTROGEN-REGULATED PROTEIN,GABA(A) RECEPTOR-ASSOCIATED PROTEIN-LIKE 1,GLANDULAR EPITHELIAL CELL PROTEIN 1,GEC-1
 
Molecule 2 - CYSTEINE PROTEASE ATG4B
    Chains: C, E
    EC Number: 3.4.22.-
    Engineered: YES
    Fragment: UNP RESIDUES 384-393
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AUT-LIKE 1 CYSTEINE ENDOPEPTIDASE,AUTOPHAGIN-1,AUTOPHAGY- RELATED CYSTEINE ENDOPEPTIDASE 1,AUTOPHAGY-RELATED PROTEIN 4 HOMOLOG B,HAPG4B
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : BCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric/Biological Unit (6, 11)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MG3Ligand/IonMAGNESIUM ION
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PER2Ligand/IonPEROXIDE ION
5PGE2Ligand/IonTRIETHYLENE GLYCOL
6SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP D:45 , HIS D:69 , HOH D:304 , HOH D:317 , HOH D:340 , HOH D:343 , HOH D:348binding site for residue MG D 201
2AC2SOFTWARETYR D:61 , ARG D:65 , ALA D:75 , LEU D:76 , PHE D:77 , PHE D:78 , ILE D:84 , THR D:87 , PGE D:203 , HOH D:323binding site for residue PGE D 202
3AC3SOFTWAREVAL D:57 , TYR D:61 , ARG D:65 , ALA D:75 , PHE D:77 , ILE D:84 , PRO D:85 , THR D:87 , PGE D:202 , HOH D:323 , HOH D:339binding site for residue PGE D 203
4AC4SOFTWAREGLN D:59 , PHE D:62 , LEU D:63 , HOH D:310binding site for residue EDO D 204
5AC5SOFTWAREARG B:28 , TYR D:25 , PRO D:26 , ASP D:27 , ARG D:28binding site for residue PER D 205
6AC6SOFTWARETYR B:25 , PRO B:26 , ASP B:27 , ARG B:28 , ARG D:28binding site for residue PER D 206
7AC7SOFTWAREHIS B:69 , ASN B:98 , HOH B:308 , HOH B:313 , HOH B:320 , HOH B:336binding site for residue MG B 201
8AC8SOFTWAREASP B:54 , HOH B:302 , HOH B:306 , HOH B:323 , HOH B:332 , SEP C:392binding site for residue MG B 202
9AC9SOFTWARETYR B:61 , ALA B:75 , PHE B:77 , THR B:87 , HOH B:301binding site for residue PEG B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LXI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LXI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LXI)

(-) Exons   (0, 0)

(no "Exon" information available for 5LXI)

(-) 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 B from PDB  Type:PROTEIN  Length:116
                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxi B   1 MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYG 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....ee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5lxi C 384 EDEDFEILsL 393
                                   393
                                  392-SEP


Chain D from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhhh.......eee..........hhhhhhhhhh.....eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxi D   1 MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain E from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...ee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 5lxi E 386 EDFEILsL 393
                                  | 
                                392-SEP
   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 5LXI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LXI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LXI)

(-) Gene Ontology  (40, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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  3.4.22.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        ATG4B_HUMAN | Q9Y4P1: 2cy7 2d1i 2z0d 2z0e 2zzp 5lxh
        GBRL1_HUMAN | Q9H0R8: 2l8j 2r2q 5dpt 5lxh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LXI)