Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  N-TERMINAL DOMAIN OF SEC18P
 
Authors :  S. M. Babor, D. Fass
Date :  13 Aug 99  (Deposition) - 22 Dec 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Double-Psi Beta Barrel, Vesicle Fusion, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Babor, D. Fass
Crystal Structure Of The Sec18P N-Terminal Domain.
Proc. Natl. Acad. Sci. Usa V. 96 14759 1999
PubMed-ID: 10611286  |  Reference-DOI: 10.1073/PNAS.96.26.14759
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEC18P (RESIDUES 22 - 210)
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAED4
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1NEN6Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NEN2Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NEN2Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NEN2Ligand/Ion1-ETHYL-PYRROLIDINE-2,5-DIONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:34 , PRO A:35 , ASN A:36 , TYR A:39 , SER A:71 , ASP A:73BINDING SITE FOR RESIDUE NEN A 601
2AC2SOFTWARELEU A:41 , ALA A:42 , ARG A:145 , CYS A:146 , HOH A:454BINDING SITE FOR RESIDUE NEN A 602
3AC3SOFTWARECYS B:34 , PRO B:35 , ASN B:36 , TYR B:39 , SER B:71 , ASP B:73 , HOH B:333BINDING SITE FOR RESIDUE NEN B 603
4AC4SOFTWARELEU B:41 , ALA B:42 , ARG B:145 , CYS B:146BINDING SITE FOR RESIDUE NEN B 604
5AC5SOFTWARECYS C:34 , PRO C:35 , ASN C:36 , TYR C:39 , ALA C:46 , SER C:71 , ASP C:73BINDING SITE FOR RESIDUE NEN C 605
6AC6SOFTWARELEU C:41 , ALA C:42 , ARG C:145 , CYS C:146 , HOH C:359BINDING SITE FOR RESIDUE NEN C 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CR5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CR5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CR5)

(-) Exons   (1, 3)

Asymmetric Unit (1, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR080C1YBR080C.1II:400884-3986082277SEC18_YEAST1-7587583A:26-210 (gaps)
B:23-207 (gaps)
C:26-208 (gaps)
185
185
183

(-) 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:178
 aligned with SEC18_YEAST | P18759 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:185
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
          SEC18_YEAST    26 TRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFKGR 210
               SCOP domains d1cr5a1 A:26-107 N-terminal domain of NSF-N, NSF-Nn                               d1cr5a2 A:108-210        C-terminal domain of NSF-N, NSF-Nc                                             SCOP domains
               CATH domains 1cr5A01 A:26-102  [code=2.40.40.20, no name defined]                         1cr5A02 A:103-210  [cod       e=3.10.330.10, no name defined]                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhh..eeee.........eeee...eeeeeee.......eeeehhhhhhhhh.....eeeeee.hhhhhhh...eeeeeeeeeee..-------..hhhhhhhhhhhhhh..ee....eeeeee..eeeeeeeeeeeee..................ee.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:26-210 (gaps) UniProt: 1-758 [INCOMPLETE]                                                                                                                                Transcript 1
                 1cr5 A  26 TRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRA-------VFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFKGR 210
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     
                                                                                                                             125     133                                                                             

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with SEC18_YEAST | P18759 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:185
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
          SEC18_YEAST    23 DTRTRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFF 207
               SCOP domains d1cr5b1 B:23-107 N-terminal domain of NSF-N, NSF-Nn                                  d1cr5b2 B:108-207          C-terminal domain of NSF-N, NSF-Nc                                        SCOP domains
               CATH domains ---1cr5B01 B:26-102  [code=2.40.40.20, no name defined]                         1cr5B02 B:103-206  [cod         e=3.10.330.10, no name defined]                                         - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhh..eeee.........eeee...eeeeeee.......eeeehhhhhhhhh.....eeeeee.hhhhhhhhhh.eeeeeeeeee..---------hhhhhhhhhhhhhh..ee....eeeeee..eeeeeeeeeeee...................ee.....eeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:23-207 (gaps) UniProt: 1-758 [INCOMPLETE]                                                                                                                                Transcript 1
                 1cr5 B  23 DTRTRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRA---------DQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFF 207
                                    32        42        52        62        72        82        92       102       112       122  |      -  |    142       152       162       172       182       192       202     
                                                                                                                                125       135                                                                        

Chain C from PDB  Type:PROTEIN  Length:175
 aligned with SEC18_YEAST | P18759 from UniProtKB/Swiss-Prot  Length:758

    Alignment length:183
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   
          SEC18_YEAST    26 TRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFK 208
               SCOP domains d1cr5c1 C:26-107 N-terminal domain of NSF-N, NSF-Nn                               d1cr5c2 C:108-208         C-terminal domain of NSF-N, NSF-Nc                                          SCOP domains
               CATH domains 1cr5C01 C:26-102  [code=2.40.40.20, no name defined]                         1cr5C02 C:103-207  [co        de=3.10.330.10, no name defined]                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhh..eeee.........eeee...eeeeeee.......eeeehhhhhhhhh.....eeeeee.hhhhhhh..eeeeeeeeeeee.--------..hhhhhhhhhhhhhh..ee....eeeeee..eeeeeeeeeeeeee.................ee.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:26-208 (gaps) UniProt: 1-758 [INCOMPLETE]                                                                                                                              Transcript 1
                 1cr5 C  26 TRHLKVSNCPNNSYALANVAAVSPNDFPNNIYIIIDNLFVFTTRHSNDIPPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFR--------VFDQDELAKQFVRCYESQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFFK 208
                                    35        45        55        65        75        85        95       105       115        |-       135       145       155       165       175       185       195       205   
                                                                                                                            124      133                                                                           

   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  (2, 6)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CR5)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SEC18_YEAST | P18759)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0043001    Golgi to plasma membrane protein transport    The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane.
    GO:0048211    Golgi vesicle docking    The initial attachment of a Golgi transport vesicle membrane to a target membrane, mediated by proteins protruding from the membrane of the Golgi vesicle and the target membrane.
    GO:0035494    SNARE complex disassembly    The disaggregation of the SNARE protein complex into its constituent components. The SNARE complex is a protein complex involved in membrane fusion; a stable ternary complex consisting of a four-helix bundle, usually formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers.
    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:0048219    inter-Golgi cisterna vesicle-mediated transport    The directed movement of substances from one Golgi cisterna to another, mediated by small transport vesicles.
    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.
    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:0042144    vacuole fusion, non-autophagic    The fusion of two vacuole membranes to form a single vacuole.
    GO:0048280    vesicle fusion with Golgi apparatus    The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi.
    GO:0016192    vesicle-mediated transport    A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005795    Golgi stack    The set of thin, flattened membrane-bounded compartments, called cisternae, that form the central portion of the Golgi complex. The stack usually comprises cis, medial, and trans cisternae; the cis- and trans-Golgi networks are not considered part of the stack.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    NEN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cr5)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1cr5
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SEC18_YEAST | P18759
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  SEC18_YEAST | P18759
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1CR5)

(-) Related Entries Specified in the PDB File

1qcs N-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR
1qdn N-TERMINAL DOMAIN OF N-ETHYLMALEIMIDE SENSITIVE FACTOR