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(-) Description

Title :  CRYSTAL STRUCTURE OF NEDD4 LIR-FUSED HUMAN LC3B_2-119
 
Authors :  Y. Qiu, Y. Zheng, B. Schulman
Date :  09 Mar 17  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Autophagy, Ubiquitin E3 Ligase, Hect, Lir, Lc3, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Qiu, Y. Zheng, K. P. Wu, B. A. Schulman
Insights Into Links Between Autophagy And The Ubiquitin System From The Structure Of Lc3B Bound To The Lir Motif From The E3 Ligase Nedd4.
Protein Sci. 2017
PubMed-ID: 28470758  |  Reference-DOI: 10.1002/PRO.3186

(-) Compounds

Molecule 1 - MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B, MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B,MICROTUBULE- ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 2-119,UNP RESIDUES 2-119,UNP RESIDUES 2-119, UNP RESIDUES 2-119
    GeneMAP1LC3B, MAP1ALC3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAUTOPHAGY-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,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,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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:1026 , HIS A:1027 , PRO A:1028 , THR A:1029 , LYS A:1030binding site for residue GOL A 1201
2AC2SOFTWAREILE A:269 , GLY A:270 , ARG A:1069 , ARG A:1070binding site for residue SO4 A 1202
3AC3SOFTWARESER A:1087 , MET A:1088 , VAL A:1089 , SER A:1090 , MET B:1088 , VAL B:1089 , SER B:1090 , GLU B:1102binding site for residue GOL B 1201
4AC4SOFTWAREGLN B:1026 , HIS B:1027 , PRO B:1028 , THR B:1029 , LYS B:1030binding site for residue SO4 B 1202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V4K)

(-) Exons   (0, 0)

(no "Exon" information available for 5V4K)

(-) 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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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:125
                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhh........eeee..........hhhhhhhhhh.....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                5v4k A  264 ENWEIIGSPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQET 1118
                                  1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113     
                                 271|                                                                                                                    
                                 1002                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:124
                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhhh.......eeee..........hhhhhhhhhh.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                5v4k B  264 ENWEIIGSPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRRLQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQE 1117
                                  1003      1013      1023      1033      1043      1053      1063      1073      1083      1093      1103      1113    
                                 271|                                                                                                                   
                                 1002                                                                                                                   

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  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 5V4K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V4K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V4K)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MLP3B_HUMAN | Q9GZQ81v49 2lue 2n9x 2zjd 3vtu 3vtv 3vtw 3wao 3x0w 4waa 5d94 5dcn 5gmv 5ms2 5ms5 5ms6 5xac 5xad 5xae

(-) Related Entries Specified in the PDB File

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