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(-) Description

Title :  CRYSTAL STRUCTURE OF LC3-LIR PEPTIDE COMPLEX
 
Authors :  K. Takagi, T. Mizushima, T. Johansen
Date :  18 Aug 15  (Deposition) - 21 Oct 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fyco1, Autophagy, Lc3, Lir, Protein Binding-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Olsvik, T. Lamark, K. Takagi, K. B. Larsen, G. Evjen, A. Vervatn, T. Mizushima, T. Johansen
Fyco1 Contains A C-Terminally Extended, Lc3A/B-Preferring Lc3-Interacting Region (Lir) Motif Required For Efficient Maturation Of Autophagosomes During Basal Autophagy
J. Biol. Chem. V. 290 29361 2015
PubMed-ID: 26468287  |  Reference-DOI: 10.1074/JBC.M115.686915

(-) Compounds

Molecule 1 - MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MAP1LC3B, MAP1ALC3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AUTOPHAGY-RELATED PROTEIN LC3 B,AUTOPHAGY-RELATED UBIQUITIN- LIKE MODIFIER LC3 B,MAP1 LIGHT CHAIN 3-LIKE PROTEIN 2,MAP1A/MAP1B LIGHT CHAIN 3 B,MAP1A/MAP1B LC3 B,MICROTUBULE-ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 BETA
 
Molecule 2 - PEPTIDE FROM FYVE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 1
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5D94)

(-) Sites  (0, 0)

(no "Site" information available for 5D94)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D94)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D94)

(-) Exons   (0, 0)

(no "Exon" information available for 5D94)

(-) 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    
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Chain A from PDB  Type:PROTEIN  Length:119
                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhh........eeee..ee......hhhhhhhhhh.....eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                5d94 A    5 KTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFGMKL  123
                                    14        24        34        44        54        64        74        84        94       104       114         


Chain B from PDB  Type:PROTEIN  Length:12
                                             
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ....ee.hhhhh Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                5d94 B 1277 DAVFDIITDEEL 1288
                                  1286
   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 5D94)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D94)

(-) Gene Ontology  (29, 33)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FYCO1_HUMAN | Q9BQS8: 5cx3
        MLP3B_HUMAN | Q9GZQ8: 1v49 2lue 2n9x 2zjd 3vtu 3vtv 3vtw 3wao 3x0w 4waa 5dcn 5gmv 5ms2 5ms5 5ms6 5v4k 5xac 5xad 5xae

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5D94)