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

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN RUN AND FYVE DOMAIN-CONTAINING PROTEIN
 
Authors :  H. Wang, S. Kishishita, K. Murayama, C. Takemoto, T. Terada, M. Shirouzu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Apr 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structure Genomics, Fyve Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wang, S. Kishishita, T. Murayama, C. Takemoto, T. Terada, L. Chen, Z. Q. Fu, J. Chrzas, B. C. Wang, M. Shirouzu, S. Yokoyama
Crystal Structure Of Human Run And Fyve Domain-Containing Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RUN AND FYVE DOMAIN-CONTAINING PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System Plasmid: PK060327-08
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 627-708
    Gene: RUFY1, RABIP4, ZFYVE12
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS
    Synonym: FYVE-FINGER PROTEIN EIP1, ZINC FINGER FYVE DOMAIN- CONTAINING PROTEIN 12, LA-BINDING PROTEIN 1, RAB4- INTERACTING PROTEIN, MS1309 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:38 , CYS A:41 , CYS A:66 , CYS A:69BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWARECYS A:22 , CYS A:25 , CYS A:46 , CYS A:49BINDING SITE FOR RESIDUE ZN A 301
3AC3SOFTWAREHIS A:36 , HIS A:37 , ARG A:39 , ARG A:64BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YW8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.RUFY1_HUMAN642-700  1A:16-74

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003194491aENSE00001372451chr5:178977559-178977880322RUFY1_HUMAN1-1041040--
1.3dENST000003194493dENSE00001770679chr5:178987026-178987199174RUFY1_HUMAN104-162590--
1.4aENST000003194494aENSE00001240095chr5:178989548-178989665118RUFY1_HUMAN162-201400--
1.5aENST000003194495aENSE00001240088chr5:178994462-178994563102RUFY1_HUMAN201-235350--
1.6bENST000003194496bENSE00001240082chr5:178996303-178996426124RUFY1_HUMAN235-276420--
1.7aENST000003194497aENSE00001240078chr5:179004076-17900413762RUFY1_HUMAN277-297210--
1.8ENST000003194498ENSE00001240074chr5:179007948-17900801366RUFY1_HUMAN297-319230--
1.9ENST000003194499ENSE00001240067chr5:179012797-17901286670RUFY1_HUMAN319-342240--
1.11bENST0000031944911bENSE00001795047chr5:179016547-179016648102RUFY1_HUMAN343-376340--
1.13ENST0000031944913ENSE00001649014chr5:179018626-179018742117RUFY1_HUMAN377-415390--
1.14bENST0000031944914bENSE00001689103chr5:179020479-179020646168RUFY1_HUMAN416-471560--
1.15bENST0000031944915bENSE00001689109chr5:179021867-17902196498RUFY1_HUMAN472-504330--
1.16cENST0000031944916cENSE00001644060chr5:179023563-179023682120RUFY1_HUMAN504-544410--
1.17ENST0000031944917ENSE00001742098chr5:179025693-179025822130RUFY1_HUMAN544-587440--
1.18aENST0000031944918aENSE00001666679chr5:179028893-17902898795RUFY1_HUMAN588-619320--
1.19aENST0000031944919aENSE00001750822chr5:179032877-17903292549RUFY1_HUMAN619-635170--
1.20dENST0000031944920dENSE00001696739chr5:179034583-17903466078RUFY1_HUMAN636-661261A:15-3521
1.22gENST0000031944922gENSE00001515319chr5:179036377-179037027651RUFY1_HUMAN662-708471A:36-7540

(-) 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
(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:61
 aligned with RUFY1_HUMAN | Q96T51 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:61
                                   650       660       670       680       690       700 
          RUFY1_HUMAN   641 KDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLLQ 701
               SCOP domains d2yw8a_ A: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains FYVE-2yw8A01 A:15-75                                          Pfam domains
         Sec.struct. author .....................ee......ee.hhhhheee........eeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_FYVE  PDB: A:16-74 UniProt: 642-700                     - PROSITE
               Transcript 1 Exon 1.20d           Exon 1.22g  PDB: A:36-75 [INCOMPLETE]    Transcript 1
                 2yw8 A  15 KDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELALPSYPKPVRVCDSCHTLLLQ  75
                                    24        34        44        54        64        74
   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
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YW8)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: zf-FYVE-PHD (57)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUFY1_HUMAN | Q96T51)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008565    protein transporter activity    Enables the directed movement of proteins into, out of or within a cell, or between cells.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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:0030100    regulation of endocytosis    Any process that modulates the frequency, rate or extent of endocytosis.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2yw8)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2yw8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RUFY1_HUMAN | Q96T51
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RUFY1_HUMAN | Q96T51
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RUFY1_HUMAN | Q96T51: 2yqm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YW8)