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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN LC3A_2-121
 
Authors :  H. Suzuki, K. Tabata, E. Morita, M. Kawasaki, R. Kato, R. C. J. Dobson, T. Yoshimori, S. Wakatsuki
Date :  06 May 13  (Deposition) - 25 Dec 13  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Ubiquitin-Like Fold, Autophagy, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Suzuki, K. Tabata, E. Morita, M. Kawasaki, R. Kato, R. C. Dobson, T. Yoshimori, S. Wakatsuki
Structural Basis Of The Autophagy-Related Lc3/Atg13 Lir Complex: Recognition And Interaction Mechanism.
Structure V. 22 47 2014
PubMed-ID: 24290141  |  Reference-DOI: 10.1016/J.STR.2013.09.023

(-) Compounds

Molecule 1 - MICROTUBULE-ASSOCIATED PROTEINS 1A/1B LIGHT CHAIN 3A
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAP1LC3A
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAUTOPHAGY-RELATED PROTEIN LC3 A, AUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER LC3 A, MAP1 LIGHT CHAIN 3-LIKE PROTEIN 1, MAP1A/MAP1B LIGHT CHAIN 3 A, MAP1A/MAP1B LC3 A, MICROTUBULE- ASSOCIATED PROTEIN 1 LIGHT CHAIN 3 ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MLT1Ligand/IonD-MALATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:12 , PHE A:17 , ARG A:20 , ASP A:108 , HOH A:320 , HOH A:373BINDING SITE FOR RESIDUE MLT A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WAL)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WAL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WAL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WAL)

(-) Exons   (0, 0)

(no "Exon" information available for 3WAL)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:115
 aligned with MLP3A_HUMAN | Q9H492 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:115
                                    14        24        34        44        54        64        74        84        94       104       114     
          MLP3A_HUMAN     5 RPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETF 119
               SCOP domains d3wala_ A: automated matches                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.............eeeee...hhhhhhhhhhhhhh.......eeee..ee......hhhhhhhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3wal A   9 RPFKQRRSFADRCKEVQQIRDQHPSKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELVKIIRRRLQLNPTQAFFLLVNQHSMVSVSTPIADIYEQEKDEDGFLYMVYASQETF 123
                                    18        28        38        48        58        68        78        88        98       108       118     

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WAL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WAL)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MLP3A_HUMAN | Q9H492)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0008429    phosphatidylethanolamine binding    Interacting selectively and non-covalently with phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
    GO:0005543    phospholipid binding    Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0000045    autophagosome assembly    The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0000422    autophagy of mitochondrion    The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
    GO:0006995    cellular response to nitrogen starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nitrogen.
    GO:0016236    macroautophagy    The major inducible pathway for the general turnover of cytoplasmic constituents in eukaryotic cells, it is also responsible for the degradation of active cytoplasmic enzymes and organelles during nutrient starvation. Macroautophagy involves the formation of double-membrane-bounded autophagosomes which enclose the cytoplasmic constituent targeted for degradation in a membrane-bounded structure. Autophagosomes then fuse with a lysosome (or vacuole) releasing single-membrane-bounded autophagic bodies that are then degraded within the lysosome (or vacuole). Though once thought to be a purely non-selective process, it appears that some types of macroautophagy, e.g. macropexophagy, macromitophagy, may involve selective targeting of the targets to be degraded.
cellular component
    GO:0005776    autophagosome    A double-membrane-bounded compartment that engulfs endogenous cellular material as well as invading microorganisms to target them to the vacuole/lysosome for degradation as part of macroautophagy.
    GO:0000421    autophagosome membrane    The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0031090    organelle membrane    A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MLP3A_HUMAN | Q9H4923eci 3wan 4zdv 5cx3 5dpr

(-) Related Entries Specified in the PDB File

3vtu 3vtv 3vtw 3wam 3wan 3wao 3wap