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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 :  1.58
Chains :  Asym. Unit :  A,B,C,E,F,G
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
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: A, B, C
    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: E, F, G
    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

  123456
Asymmetric Unit : ABCEFG
Biological Unit 1 (1x): A  E  
Biological Unit 2 (1x):  B  F 
Biological Unit 3 (1x):   C  G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:45 , LYS A:46 , ARG A:47 , LYS A:48 , HOH A:303 , HOH A:341 , HIS B:69 , ASP E:387binding site for residue SO4 A 201
02AC2SOFTWAREHIS A:69 , ASP B:45 , LYS B:46 , ARG B:47 , LYS B:48 , SO4 B:203 , HOH B:333 , ASP F:387binding site for residue SO4 B 201
03AC3SOFTWAREARG B:14 , GLU C:101binding site for residue SO4 B 202
04AC4SOFTWARETYR B:5 , ASP B:8 , HIS B:9 , LYS B:48 , SO4 B:201 , HOH B:311 , HOH B:319 , THR C:83binding site for residue SO4 B 203
05AC5SOFTWAREPHE B:79 , VAL B:80 , ASN B:81 , ASN B:82 , TYR B:106 , ALA B:108 , HOH B:302 , HOH B:315 , HOH B:363binding site for residue GOL B 204
06AC6SOFTWAREHOH A:315 , ARG B:22 , GLU B:96 , TYR B:103 , HOH B:301 , HOH B:334binding site for residue GOL B 205
07AC7SOFTWAREGLN A:93 , GLU A:96 , LYS C:46 , ARG C:47 , LYS C:48 , SO4 C:202 , HOH C:302 , ASP G:387binding site for residue SO4 C 201
08AC8SOFTWARETYR C:5 , ASP C:8 , HIS C:9 , LYS C:48 , SO4 C:201 , HOH C:302binding site for residue SO4 C 202
09AC9SOFTWAREARG C:71 , GLU C:73 , ASP C:74 , SER C:113 , VAL C:114 , TYR C:115 , GLY C:116 , LYS C:117binding site for residue SO4 C 203
10AD1SOFTWAREGLU C:34 , LYS C:35 , ARG C:47 , HOH C:310 , HOH C:334binding site for residue GOL C 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LXH)

(-) Sequences/Alignments

Asymmetric 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:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.hhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhhh.......eee..........hhhhhhhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxh A   0 SMKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESV 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhh.....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 5lxh B   1 MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVY 115
                                    10        20        30        40        50        60        70        80        90       100       110     


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhhhhhhhhh..eeeeeeee.........eeeee...hhhhhhhhhhhhhh....eeeeee..........hhhhhhhhhh.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5lxh C   1 MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHLRPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK 117
                                    10        20        30     || 43        53        63        73        83        93       103       113    
                                                              36|                                                                             
                                                               40                                                                             


Chain E from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author hhhhhee... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5lxh E 384 EDEDFEILSL 393
                                   393


Chain F 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
                 5lxh F 384 EDEDFEILSL 393
                                   393


Chain G 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
                 5lxh G 384 EDEDFEILSL 393
                                   393
   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 5LXH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 47)

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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 5lxi
        GBRL1_HUMAN | Q9H0R8: 2l8j 2r2q 5dpt 5lxi

(-) Related Entries Specified in the PDB File

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