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(-) Description

Title :  SOLUTION STRUCTURE OF THE EEA1 FYVE DOMAIN COMPLEXED WITH INOSITOL 1,3-BISPHOSPHATE
 
Authors :  T. Kutateladze, M. Overduin
Date :  19 Jan 01  (Deposition) - 14 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Beta Sheet, Alpha Helix, Zinc Cluster, Ptdins(3)P, Endocytosis/Exocytosis Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kutateladze, M. Overduin
Structural Mechanism Of Endosome Docking By The Fyve Domain.
Science V. 291 1793 2001
PubMed-ID: 11230696  |  Reference-DOI: 10.1126/SCIENCE.291.5509.1793
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOSOME-ASSOCIATED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX
    Expression System Strain: BL21PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FYVE DOMAIN (RESIDUES 1346-1410)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (2, 3)
No.NameCountTypeFull Name
1ITP1Ligand/IonPHOSPHORIC ACID MONO-(2,3,4,6-TETRAHYDROXY-5-PHOSPHONOOXY-CYCLOHEXYL) ESTER
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:12 , CYS A:15 , CYS A:36 , CYS A:39BINDING SITE FOR RESIDUE ZN A 66
2AC2SOFTWARECYS A:28 , CYS A:31 , CYS A:56 , CYS A:59BINDING SITE FOR RESIDUE ZN A 67
3AC3SOFTWAREARG A:25 , HIS A:26 , HIS A:27 , ARG A:29 , ARG A:54BINDING SITE FOR RESIDUE ITP A 68

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_FYVEPS50178 Zinc finger FYVE/FYVE-related type profile.EEA1_HUMAN1352-1410  1A:6-64

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003223491ENSE00001477661chr12:93323107-93322819289EEA1_HUMAN1-880--
1.3ENST000003223493ENSE00001282982chr12:93285497-9328540593EEA1_HUMAN9-39310--
1.4ENST000003223494ENSE00000676847chr12:93258763-93258636128EEA1_HUMAN40-82430--
1.5ENST000003223495ENSE00000676849chr12:93251261-9325120755EEA1_HUMAN82-100190--
1.6ENST000003223496ENSE00000676865chr12:93251116-9325105166EEA1_HUMAN101-122220--
1.7ENST000003223497ENSE00000676885chr12:93247730-9324769140EEA1_HUMAN123-136140--
1.8ENST000003223498ENSE00000676904chr12:93246801-93246688114EEA1_HUMAN136-174390--
1.9ENST000003223499ENSE00000676922chr12:93246072-93245951122EEA1_HUMAN174-214410--
1.10ENST0000032234910ENSE00000676940chr12:93245042-93244887156EEA1_HUMAN215-266520--
1.11ENST0000032234911ENSE00000676942chr12:93236357-93236241117EEA1_HUMAN267-305390--
1.12ENST0000032234912ENSE00000921615chr12:93226626-93226288339EEA1_HUMAN306-4181130--
1.13ENST0000032234913ENSE00000676944chr12:93221837-93221688150EEA1_HUMAN419-468500--
1.14ENST0000032234914ENSE00000676945chr12:93220061-93219942120EEA1_HUMAN469-508400--
1.15ENST0000032234915ENSE00000921614chr12:93213287-93213084204EEA1_HUMAN509-576680--
1.16ENST0000032234916ENSE00000921613chr12:93210176-93209976201EEA1_HUMAN577-643670--
1.17ENST0000032234917ENSE00000921612chr12:93206869-93206756114EEA1_HUMAN644-681380--
1.18ENST0000032234918ENSE00000921611chr12:93205210-93205055156EEA1_HUMAN682-733520--
1.19ENST0000032234919ENSE00000921610chr12:93202932-93202793140EEA1_HUMAN734-780470--
1.20ENST0000032234920ENSE00000921609chr12:93196510-93196180331EEA1_HUMAN780-8901110--
1.21ENST0000032234921ENSE00000921608chr12:93195477-93195376102EEA1_HUMAN891-924340--
1.22ENST0000032234922ENSE00000921607chr12:93192862-93192668195EEA1_HUMAN925-989650--
1.23ENST0000032234923ENSE00000921606chr12:93181825-93181643183EEA1_HUMAN990-1050610--
1.24ENST0000032234924ENSE00000921605chr12:93175911-93175726186EEA1_HUMAN1051-1112620--
1.25ENST0000032234925ENSE00000921604chr12:93174187-93174056132EEA1_HUMAN1113-1156440--
1.26ENST0000032234926ENSE00000921603chr12:93173076-93172891186EEA1_HUMAN1157-1218620--
1.27ENST0000032234927ENSE00000921602chr12:93171955-93171717239EEA1_HUMAN1219-1298800--
1.28ENST0000032234928ENSE00000921601chr12:93171439-93171319121EEA1_HUMAN1298-1338410--
1.29ENST0000032234929ENSE00000921600chr12:93170718-9317062099EEA1_HUMAN1339-1371331A:1-2525
1.30bENST0000032234930bENSE00001198267chr12:93169909-931662863624EEA1_HUMAN1372-1411401A:26-6540

(-) Sequences/Alignments

NMR Structure
   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:65
 aligned with EEA1_HUMAN | Q15075 from UniProtKB/Swiss-Prot  Length:1411

    Alignment length:65
                                  1356      1366      1376      1386      1396      1406     
          EEA1_HUMAN   1347 RKWAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACFNDLQG 1411
               SCOP domains d1hyia_ A: Eea1                                                   SCOP domains
               CATH domains 1hyiA00 A:1-65 Zinc/RING finger domain, C3HC4 (zinc finger)       CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................eee......eee.....eeeee....eeeeehhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----ZF_FYVE  PDB: A:6-64 UniProt: 1352-1410                    - PROSITE
               Transcript 1 Exon 1.29  PDB: A:1-25   Exon 1.30b  PDB: A:26-65                 Transcript 1
                1hyi A    1 RKWAEDNEVQNCMACGKGFSVTVRRHHCRQCGNIFCAECSAKNALTPSSKKPVRVCDACFNDLQG   65
                                    10        20        30        40        50        60
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 23)

NMR Structure(hide GO term definitions)
Chain A   (EEA1_HUMAN | Q15075)
molecular function
    GO:0005545    1-phosphatidylinositol binding    Interacting selectively and non-covalently with phosphatidylinositol, any glycophospholipid with its sn-glycerol 3-phosphate residue is esterified to the 1-hydroxyl group of 1D-myo-inositol.
    GO:0030742    GTP-dependent 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) using energy from the hydrolysis of GTP.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045022    early endosome to late endosome transport    The directed movement of substances, in membrane-bounded vesicles, from the early sorting endosomes to the late sorting endosomes; transport occurs along microtubules and can be experimentally blocked with microtubule-depolymerizing drugs.
    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:0016189    synaptic vesicle to endosome fusion    Fusion of a synaptic vesicle with an endosome.
    GO:0006906    vesicle fusion    Fusion of the membrane of a transport vesicle with its target membrane.
cellular component
    GO:0044308    axonal spine    A spine that originates from the axon, usually from the initial segment.
    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:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma 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:0055037    recycling endosome    An organelle consisting of a network of tubules that functions in targeting molecules, such as receptors transporters and lipids, to the plasma membrane.
    GO:0005969    serine-pyruvate aminotransferase complex    An enzyme complex that catalyzes the formation of hydroxypyruvate and alanine from serine and pyruvate.

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  1hyi
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 Related Entries

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

UniProtKB/Swiss-Prot
        EEA1_HUMAN | Q15075: 1hyj 1joc 3mjh

(-) Related Entries Specified in the PDB File

1hyj 1HYJ CONTAINS THE FYVE DOMAIN WITHOUT INOSITOL 1,3- BISPHOSPHATE