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(-) Description

Title :  THE CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE ATG8-ATG19(412-415) COMPLEX
 
Authors :  N. N. Noda, F. Inagaki
Date :  17 Jul 08  (Deposition) - 09 Dec 08  (Release) - 30 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Ubiquitin Fold, Autophagy, Cytoplasmic Vesicle, Lipoprotein, Membrane, Protein Transport, Transport, Ubl Conjugation Pathway, Vacuole (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. N. Noda, H. Kumeta, H. Nakatogawa, K. Satoo, W. Adachi, J. Ishii, Y. Fujioka, Y. Ohsumi, F. Inagaki
Structural Basis Of Target Recognition By Atg8/Lc3 During Selective Autophagy
Genes Cells V. 13 1211 2008
PubMed-ID: 19021777  |  Reference-DOI: 10.1111/J.1365-2443.2008.01238.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AUTOPHAGY-RELATED PROTEIN 8
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHT1
    Expression System StrainBL21
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneATG8, APG8, AUT7, CVT5, YBL078C, YBL0732
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymAUTOPHAGY-RELATED UBIQUITIN-LIKE MODIFIER ATG8, CYTOPLASM TO VACUOLE TARGETING PROTEIN 5
 
Molecule 2 - SACCHAROMYCES CEREVISIAE ATG19(412-415)
    ChainsE, F, G, H
    EngineeredYES
    Other DetailsTHIS SEQUENCE CORRESPONDS TO RESIDUES 412- 415 OF SACCHAROMYCES CEREVISIAE ATG19.
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)A   E   
Biological Unit 2 (1x) B   F  
Biological Unit 3 (1x)  C   G 
Biological Unit 4 (1x)   D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:39 , ASP A:40 , ILE A:41 , GLY A:111BINDING SITE FOR RESIDUE SO4 A 117
2AC2SOFTWARELYS B:38 , SER B:39 , ASP B:40 , SER B:110 , GLY B:111 , GLU B:112BINDING SITE FOR RESIDUE SO4 B 117
3AC3SOFTWARESER C:39 , ASP C:40 , ILE C:41 , GLY C:111BINDING SITE FOR RESIDUE SO4 C 117
4AC4SOFTWARESER D:39 , ASP D:40 , SER D:110 , GLY D:111 , GLU D:112BINDING SITE FOR RESIDUE SO4 D 117
5AC5SOFTWARELYS A:66 , LYS B:66 , ARG B:67 , ALA D:88BINDING SITE FOR RESIDUE SO4 A 118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZPN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZPN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZPN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZPN)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZPN)

(-) 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:111
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
           ATG8_YEAST     1 MKSTFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSG 111
               SCOP domains d2zpna_ A: automated matches                                                                                    SCOP domains
               CATH domains 2zpnA00 A:1-111 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2zpn A   1 MKSTFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSG 111
                                    10        20        30        40        50        60        70        80        90       100       110 

Chain B from PDB  Type:PROTEIN  Length:109
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:109
                                    13        23        33        43        53        63        73        83        93       103         
           ATG8_YEAST     4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGE 112
               SCOP domains d2zpnb_ B: automated matches                                                                                  SCOP domains
               CATH domains 2zpnB00 B:4-112 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                            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
                 2zpn B   4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGE 112
                                    13        23        33        43        53        63        73        83        93       103         

Chain C from PDB  Type:PROTEIN  Length:108
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:108
                                    13        23        33        43        53        63        73        83        93       103        
           ATG8_YEAST     4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSG 111
               SCOP domains d2zpnc_ C: automated matches                                                                                 SCOP domains
               CATH domains 2zpnC00 C:4-111 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2zpn C   4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSG 111
                                    13        23        33        43        53        63        73        83        93       103        

Chain D from PDB  Type:PROTEIN  Length:109
 aligned with ATG8_YEAST | P38182 from UniProtKB/Swiss-Prot  Length:117

    Alignment length:109
                                    13        23        33        43        53        63        73        83        93       103         
           ATG8_YEAST     4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGE 112
               SCOP domains d2zpnd_ D: automated matches                                                                                  SCOP domains
               CATH domains 2zpnD00 D:4-112 Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2zpn D   4 TFKSEYPFEKRKAESERIADRFKNRIPVICEKAEKSDIPEIDKRKYLVPADLTVGQFVYVIRKRIMLPPEKAIFIFVNDTLPPTAALMSAIYQEHKDKDGFLYVTYSGE 112
                                    13        23        33        43        53        63        73        83        93       103         

Chain E from PDB  Type:PROTEIN  Length:4
 aligned with ATG19_YEAST | P35193 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:4
          ATG19_YEAST   412 WEEL 415
               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
                 2zpn E   1 WEEL   4

Chain F from PDB  Type:PROTEIN  Length:4
 aligned with ATG19_YEAST | P35193 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:4
          ATG19_YEAST   412 WEEL 415
               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
                 2zpn F   1 WEEL   4

Chain G from PDB  Type:PROTEIN  Length:4
 aligned with ATG19_YEAST | P35193 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:4
          ATG19_YEAST   412 WEEL 415
               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
                 2zpn G   1 WEEL   4

Chain H from PDB  Type:PROTEIN  Length:4
 aligned with ATG19_YEAST | P35193 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:4
          ATG19_YEAST   412 WEEL 415
               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
                 2zpn H   1 WEEL   4

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ZPN)

(-) Gene Ontology  (35, 44)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ATG8_YEAST | P38182)
molecular function
    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:0031386    protein tag    A molecular function exhibited by a protein that is covalently attached (AKA tagged or conjugated) to another protein where it acts as a marker, recognized by the cellular apparatus to target the tagged protein for some cellular process such as modification, sequestration, transport or degradation.
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    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:0034629    cellular protein complex localization    A protein complex localization process that takes place at the cellular level; as a result, a protein complex is transported to, or maintained in, a specific location within a cell.
    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:0044805    late nucleophagy    A type of nucleophagy, distinct from piecemeal microautophagy of the nucleus (PNM) where the nuclear material is delivered to the vacuole/lysosome for breakdown and recycling later than observed for PNM.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0034727    piecemeal microautophagy of nucleus    Degradation of a cell nucleus by lysosomal microautophagy.
    GO:0032258    protein localization by the CVT pathway    A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
    GO:0071211    protein targeting to vacuole involved in autophagy    The process of directing proteins towards the vacuole using signals contained within the protein, occurring as part of autophagy, the process in which cells digest parts of their own cytoplasm.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0061709    reticulophagy    The autophagic process in which parts of the endoplasmic reticulum are loaded into autophagosomes, delivered to the vacuole, and degraded in response to changing cellular conditions.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0033110    Cvt vesicle membrane    Either of the two lipid bilayers surrounding a Cvt vesicle, a vesicle that functions in the cytoplasm-to-vacuole targeting (Cvt) pathway.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0000329    fungal-type vacuole membrane    The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000407    pre-autophagosomal structure    Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
    GO:0005774    vacuolar membrane    The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Chain E,F,G,H   (ATG19_YEAST | P35193)
molecular function
    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:0030674    protein binding, bridging    The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
    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:0031503    protein complex localization    A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location.
    GO:0032258    protein localization by the CVT pathway    A cytoplasm to vacuole targeting pathway that uses machinery common with autophagy. The CVT vesicle is formed when the receptor protein, Atg19, binds to the complexes of the target protein (aminopeptidase or alpha-mannosidase homododecamers), forming the Cvt complex. Atg11 binds to Atg9 and transports the CVT complex to the pre-autophagosome (PAS). The phagophore membrane expands around the CVT complex (excluding bulk cytoplasm) forming the CVT vesicle. This pathway is mostly observed in yeast.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
    GO:0016050    vesicle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle.
cellular component
    GO:0034270    CVT complex    A protein complex that is involved in the CVT pathway. In budding yeast, the CVT complex consists of multimers of preApe1p.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0019898    extrinsic component of membrane    The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000407    pre-autophagosomal structure    Punctate structures proximal to the endoplasmic reticulum which are the sites where the Atg machinery assembles upon autophagy induction.
    GO:0034045    pre-autophagosomal structure membrane    A cellular membrane associated with the pre-autophagosomal structure.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATG19_YEAST | P351932kzb 5azf 5jge
        ATG8_YEAST | P381822kq7 2kwc 2li5 3rui 3vh3 3vh4 3vxw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2ZPN)