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

(-) Description

Title :  STRUCTURE OF HUMAN MAD1 C-TERMINAL DOMAIN REVEALS ITS INVOLVEMENT IN KINETOCHORE TARGETING
 
Authors :  X. Luo, H. Sun, D. R. Tomchick
Date :  01 Mar 12  (Deposition) - 11 Apr 12  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Kinetochore, Mitosis, Spindle Checkpoint Protein, Mad2, Nucleus, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Kim, H. Sun, D. R. Tomchick, H. Yu, X. Luo
Structure Of Human Mad1 C-Terminal Domain Reveals Its Involvement In Kinetochore Targeting.
Proc. Natl. Acad. Sci. Usa V. 109 6549 2012
PubMed-ID: 22493223  |  Reference-DOI: 10.1073/PNAS.1118210109
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, UNP RESIDUES 597-718
    GeneMAD1, MAD1L1, TXBP181
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMITOTIC ARREST DEFICIENT 1-LIKE PROTEIN 1, MAD1-LIKE PROTEIN 1, MITOTIC CHECKPOINT MAD1 PROTEIN HOMOLOG, HSMAD1, HMAD1, TAX- BINDING PROTEIN 181

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4DZO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DZO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DZO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DZO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DZO)

(-) Exons   (3, 6)

Asymmetric/Biological Unit (3, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003996541bENSE00001539482chr7:2272609-2272507103MD1L1_HUMAN-00--
1.2aENST000003996542aENSE00001539480chr7:2270399-2270184216MD1L1_HUMAN-00--
1.3bENST000003996543bENSE00002145713chr7:2269778-2269619160MD1L1_HUMAN1-50500--
1.4bENST000003996544bENSE00001671509chr7:2265185-2265045141MD1L1_HUMAN51-97470--
1.6ENST000003996546ENSE00002162295chr7:2262389-2262210180MD1L1_HUMAN98-157600--
1.8bENST000003996548bENSE00000976254chr7:2259091-2258967125MD1L1_HUMAN158-199420--
1.9ENST000003996549ENSE00000976255chr7:2257678-225759782MD1L1_HUMAN199-226280--
1.10ENST0000039965410ENSE00000976256chr7:2255922-2255792131MD1L1_HUMAN227-270440--
1.11bENST0000039965411bENSE00000976257chr7:2255634-2255520115MD1L1_HUMAN270-308390--
1.12aENST0000039965412aENSE00002141654chr7:2252908-225284762MD1L1_HUMAN309-329210--
1.18ENST0000039965418ENSE00000976259chr7:2188873-218878787MD1L1_HUMAN329-358300--
1.24aENST0000039965424aENSE00001776916chr7:2108973-2108829145MD1L1_HUMAN358-406490--
1.25bENST0000039965425bENSE00001663966chr7:2054277-2054137141MD1L1_HUMAN407-453470--
1.26ENST0000039965426ENSE00001088371chr7:2041756-204170057MD1L1_HUMAN454-472190--
1.28bENST0000039965428bENSE00001088370chr7:2020176-202008889MD1L1_HUMAN473-502300--
1.29ENST0000039965429ENSE00002164012chr7:1997354-199726491MD1L1_HUMAN502-532310--
1.31ENST0000039965431ENSE00001790935chr7:1976533-1976323211MD1L1_HUMAN533-603712A:598-603
B:596-603 (gaps)
6
22
1.32bENST0000039965432bENSE00002141225chr7:1938026-1937836191MD1L1_HUMAN603-666642A:603-666
B:603-666
64
64
1.40dENST0000039965440dENSE00001678984chr7:1855864-1855430435MD1L1_HUMAN667-718522A:667-716 (gaps)
B:667-718 (gaps)
50
52

(-) 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:117
 aligned with MD1L1_HUMAN | Q9Y6D9 from UniProtKB/Swiss-Prot  Length:718

    Alignment length:119
                                   607       617       627       637       647       657       667       677       687       697       707         
          MD1L1_HUMAN   598 SKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEHPGDCLIFKATSPSGSKMQLLETEFSHTVGELIEVHLRRQDSIPAFLSSLTLELFSRQT 716
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeee...eeeeee.........eeeee..--...eeee...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.31  ---------------------------------------------------------------Exon 1.40d  PDB: A:667-716 (gaps) UniProt: 667-718 Transcript 1 (1)
           Transcript 1 (2) -----Exon 1.32b  PDB: A:603-666 UniProt: 603-666                     -------------------------------------------------- Transcript 1 (2)
                 4dzo A 598 SKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEHPGDCLIFKATS--GSKmQLLETEFSHTVGELIEVHLRRQDSIPAFLSSLTLELFSRQT 716
                                   607       617       627       637       647       657       667 |  |  677       687       697       707         
                                                                                                 669  |  |                                         
                                                                                                    672  |                                         
                                                                                                       675-MSE                                     

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with MD1L1_HUMAN | Q9Y6D9 from UniProtKB/Swiss-Prot  Length:718

    Alignment length:137
                                   591       601       611       621       631       641       651       661       671       681       691       701       711       
          MD1L1_HUMAN   582 GTVPADLEAAAASLPSSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEHPGDCLIFKATSPSGSKMQLLETEFSHTVGELIEVHLRRQDSIPAFLSSLTLELFSRQTVA 718
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeee.....eeeee.........eeeeee---..eeeee.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.31 [INCOMPLETE]---------------------------------------------------------------Exon 1.40d  PDB: B:667-718 (gaps) UniProt: 667-718   Transcript 1 (1)
           Transcript 1 (2) ---------------------Exon 1.32b  PDB: B:603-666 UniProt: 603-666                     ---------------------------------------------------- Transcript 1 (2)
                 4dzo B 596 G--------------SSKEVAELKKQVESAELKNQRLKEVFQTKIQEFRKACYTLTGYQIDITTENQYRLTSLYAEHPGDCLIFKAT---GSKmQLLETEFSHTVGELIEVHLRRQDSIPAFLSSLTLELFSRQTVA 718
                            |        -     | 601       611       621       631       641       651       661      |  -|  |   681       691       701       711       
                          596            597                                                                    668 672  |                                           
                                                                                                                       675-MSE                                       

   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 4DZO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DZO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DZO)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MD1L1_HUMAN | Q9Y6D9)
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).
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0007093    mitotic cell cycle checkpoint    A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
    GO:0007094    mitotic spindle assembly checkpoint    A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0090235    regulation of metaphase plate congression    Any process that modulates the rate, frequency, or extent of metaphase plate congression, the alignment of chromosomes at the metaphase plate, a plane halfway between the poles of the spindle.
    GO:1901990    regulation of mitotic cell cycle phase transition    Any process that modulates the frequency, rate or extent of mitotic cell cycle phase transition.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    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:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    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:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4dzo)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4dzo)
 

(-) 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
  4dzo
    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
  MD1L1_HUMAN | Q9Y6D9
    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
  MD1L1_HUMAN | Q9Y6D9
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MD1L1_HUMAN | Q9Y6D91go4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4DZO)