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(-) Description

Title :  CRYSTAL STRUCTURE OF A DEATH DOMAIN OF HUMAN ANKRYN PROTEIN
 
Authors :  Ihsanawati, Y. Bessho, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yok Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  12 Apr 07  (Deposition) - 15 Apr 08  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Homo Sapiens, Death Domain, Monomer, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Ihsanawati, Y. Bessho, L. Chen, Z. J. Liu, B. C. Wang, M. Shirouzu, S. Yokoyama
Crystal Structure Of A Death Domain Of Human Ankryn Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANKYRIN-1
    ChainsA
    EngineeredYES
    Expression System PlasmidPK060123-20
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 1394-1497, DEATH DOMAIN
    GeneANK1, ANK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE SYSTEM
    SynonymERYTHROCYTE ANKYRIN, ANKYRIN-R, DEATH DOMAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2 , SER A:1397 , THR A:1401 , GLU A:1402 , GLN A:1403 , ALA A:1404 , TRP A:1419 , ALA A:1420 , ARG A:1437 , GLN A:1447BINDING SITE FOR RESIDUE GOL A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.ANK1_HUMAN1403-1487  1A:1404-1485
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.ANK1_HUMAN1403-1487  1A:1404-1485
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEATH_DOMAINPS50017 Death domain profile.ANK1_HUMAN1403-1487  2A:1404-1485

(-) Exons   (3, 3)

Asymmetric Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003475282aENSE00001381881chr8:41655140-41655030111ANK1_HUMAN1-990--
1.4ENST000003475284ENSE00001252297chr8:41615655-41615554102ANK1_HUMAN10-43340--
1.5ENST000003475285ENSE00001252286chr8:41591587-4159148999ANK1_HUMAN44-76330--
1.6ENST000003475286ENSE00001252279chr8:41585524-4158542699ANK1_HUMAN77-109330--
1.7ENST000003475287ENSE00001252268chr8:41584866-4158476899ANK1_HUMAN110-142330--
1.8ENST000003475288ENSE00001252255chr8:41583464-41583279186ANK1_HUMAN143-204620--
1.9ENST000003475289ENSE00001252247chr8:41582072-4158197499ANK1_HUMAN205-237330--
1.10ENST0000034752810ENSE00001252241chr8:41581151-4158105399ANK1_HUMAN238-270330--
1.11ENST0000034752811ENSE00001252233chr8:41580741-4158064399ANK1_HUMAN271-303330--
1.12ENST0000034752812ENSE00001252224chr8:41577376-41577179198ANK1_HUMAN304-369660--
1.13ENST0000034752813ENSE00001252214chr8:41575722-4157562499ANK1_HUMAN370-402330--
1.14ENST0000034752814ENSE00001252205chr8:41575220-4157512299ANK1_HUMAN403-435330--
1.15ENST0000034752815ENSE00001252199chr8:41574569-4157447199ANK1_HUMAN436-468330--
1.16ENST0000034752816ENSE00000692080chr8:41573367-41573170198ANK1_HUMAN469-534660--
1.17ENST0000034752817ENSE00001252194chr8:41572592-4157249499ANK1_HUMAN535-567330--
1.18ENST0000034752818ENSE00001252187chr8:41571772-4157167499ANK1_HUMAN568-600330--
1.19ENST0000034752819ENSE00000532984chr8:41566493-41566296198ANK1_HUMAN601-666660--
1.20aENST0000034752820aENSE00000692050chr8:41563759-4156366199ANK1_HUMAN667-699330--
1.21ENST0000034752821ENSE00000692046chr8:41561990-4156189299ANK1_HUMAN700-732330--
1.22ENST0000034752822ENSE00000532987chr8:41561657-4156155999ANK1_HUMAN733-765330--
1.23ENST0000034752823ENSE00001252162chr8:41559662-4155957093ANK1_HUMAN766-796310--
1.24ENST0000034752824ENSE00001252155chr8:41559140-4155906873ANK1_HUMAN797-821250--
1.26ENST0000034752826ENSE00001252145chr8:41557066-4155697097ANK1_HUMAN821-853330--
1.27ENST0000034752827ENSE00001252137chr8:41555639-4155556179ANK1_HUMAN853-879270--
1.29ENST0000034752829ENSE00001252128chr8:41554291-4155419498ANK1_HUMAN880-912330--
1.30ENST0000034752830ENSE00001191945chr8:41554105-41553881225ANK1_HUMAN912-987760--
1.31ENST0000034752831ENSE00001252111chr8:41552849-41552695155ANK1_HUMAN987-1039530--
1.32aENST0000034752832aENSE00001252103chr8:41552321-41552110212ANK1_HUMAN1039-1109710--
1.33ENST0000034752833ENSE00000532996chr8:41551620-41551416205ANK1_HUMAN1110-1178690--
1.34ENST0000034752834ENSE00000692020chr8:41550719-4155062397ANK1_HUMAN1178-1210330--
1.35aENST0000034752835aENSE00000532998chr8:41550394-41550166229ANK1_HUMAN1210-1286770--
1.36ENST0000034752836ENSE00001252076chr8:41548117-41547992126ANK1_HUMAN1287-1328420--
1.37aENST0000034752837aENSE00001252070chr8:41547864-41547745120ANK1_HUMAN1329-1368400--
1.38ENST0000034752838ENSE00000692006chr8:41546107-4154602979ANK1_HUMAN1369-1395270--
1.39ENST0000034752839ENSE00000533002chr8:41545748-4154567475ANK1_HUMAN1395-1420261A:1397-142125
1.40ENST0000034752840ENSE00000691993chr8:41543801-41543670132ANK1_HUMAN1420-1464451A:1421-146545
1.41ENST0000034752841ENSE00000691972chr8:41542208-41542062147ANK1_HUMAN1464-1513501A:1465-148521
1.43bENST0000034752843bENSE00000691945chr8:41530430-41529872559ANK1_HUMAN1513-16991870--
1.44bENST0000034752844bENSE00000691941chr8:41526082-41525785298ANK1_HUMAN1699-17981000--
1.47ENST0000034752847ENSE00001252325chr8:41521260-4152117784ANK1_HUMAN1799-1826280--
1.48cENST0000034752848cENSE00001361299chr8:41519459-41519319141ANK1_HUMAN1827-1873470--
1.49eENST0000034752849eENSE00001851591chr8:41513272-415107392534ANK1_HUMAN1874-188180--

(-) 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:89
 aligned with ANK1_HUMAN | P16157 from UniProtKB/Swiss-Prot  Length:1881

    Alignment length:89
                                  1405      1415      1425      1435      1445      1455      1465      1475         
          ANK1_HUMAN   1396 SLSGTEQAEMKMAVISEHLGLSWAELARELQFSVEDINRIRVENPNSLLEQSVALLNLWVIREGQNANMENLYTALQSIDRGEIVNMLE 1484
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------Death-2yviA01 A:1405-1485                                                         Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------DEATH_DOMAIN  PDB: A:1404-1485 UniProt: 1403-1487                                  PROSITE
           Transcript 1 (1) Exon 1.39 [INCOMPLETE]   -------------------------------------------Exon 1.41             Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.40  PDB: A:1421-1465                  -------------------- Transcript 1 (2)
                2yvi A 1397 SLSGTEQAEMKMAVISEHLGLSWAELARELQFSVEDINRIRVENPNSLLEQSVALLNLWVIREGQNANMENLYTALQSIDRGEIVNMLE 1485
                                  1406      1416      1426      1436      1446      1456      1466      1476         

   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  (0, 0)

(no "SCOP Domain" information available for 2YVI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Death (18)

(-) Gene Ontology  (30, 30)

Asymmetric Unit(hide GO term definitions)
Chain A   (ANK1_HUMAN | P16157)
molecular function
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0008093    cytoskeletal adaptor activity    The binding activity of a molecule that brings together a cytoskeletal protein and one or more other molecules, permitting them to function in a coordinated way.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0030507    spectrin binding    Interacting selectively and non-covalently with spectrin, a protein that is the major constituent of the erythrocyte cytoskeletal network. It associates with band 4.1 (see band protein) and actin to form the cytoskeletal superstructure of the erythrocyte plasma membrane. It is composed of nonhomologous chains, alpha and beta, which aggregate side-to-side in an antiparallel fashion to form dimers, tetramers, and higher polymers.
    GO:0005200    structural constituent of cytoskeleton    The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
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:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0045199    maintenance of epithelial cell apical/basal polarity    The maintenance of the apicobasal polarity of an epithelial cell.
    GO:0010638    positive regulation of organelle organization    Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle.
    GO:0072661    protein targeting to plasma membrane    The process of directing proteins towards the plasma membrane; usually uses signals contained within the protein.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0031672    A band    The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    GO:0030018    Z disc    Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
    GO:0030673    axolemma    The portion of the plasma membrane surrounding an axon; it is a specialized trilaminar random mosaic of protein molecules floating within a fluid matrix of highly mobile phospholipid molecules, 7-8 nm in thickness.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0045211    postsynaptic membrane    A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0016529    sarcoplasmic reticulum    A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
    GO:0014731    spectrin-associated cytoskeleton    The part of the cytoskeleton composed of spectrin, protein 4.1 and ankyrin. Spectrin-associated cytoskeleton is associated with the plasma membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANK1_HUMAN | P161571n11 2yqf 3f59 3kbt 3kbu 3ud1 3ud2

(-) Related Entries Specified in the PDB File

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