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(-) Description

Title :  STRUCTURE OF FRAGMENT OF HUMAN END-BINDING PROTEIN 1 (EB1) CONTAINING THE N-TERMINAL DOMAIN AT 1.35 A RESOLUTION
 
Authors :  X. Huang, L. L. Lovelace, D. Smith, L. Lebioda
Date :  11 Sep 07  (Deposition) - 23 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytoskeleton, Acetylation, Cell Cycle, Cell Division, Cytoplasm, Microtubule, Mitosis, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Huang, L. L. Lovelace, D. Smith, L. Lebioda
Structure Of Fragment Of Human End-Binding Protein 1 (Eb1) Containing The N-Terminal Domain At 1. 35 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    FragmentN-TERMINAL DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymAPC-BINDING PROTEIN EB1, END-BINDING PROTEIN 1, EB1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MOO1Ligand/IonMOLYBDATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MOO1Ligand/IonMOLYBDATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MOO-1Ligand/IonMOLYBDATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:16 , ARG A:17 , LYS B:34 , GLU B:36 , HOH B:270BINDING SITE FOR RESIDUE MOO A 269

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R8U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R8U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R8U)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.MARE1_HUMAN14-116
 
  2A:14-116
B:14-116
2EB1_CPS51230 EB1-C terminal (EB1-C) domain profile.MARE1_HUMAN185-255  1B:187-190
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.MARE1_HUMAN14-116
 
  1A:14-116
-
2EB1_CPS51230 EB1-C terminal (EB1-C) domain profile.MARE1_HUMAN185-255  0-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHPS50021 Calponin homology domain profile.MARE1_HUMAN14-116
 
  1-
B:14-116
2EB1_CPS51230 EB1-C terminal (EB1-C) domain profile.MARE1_HUMAN185-255  1B:187-190

(-) Exons   (4, 7)

Asymmetric Unit (4, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003755711ENSE00001467575chr20:31407699-31407834136MARE1_HUMAN-00--
1.2aENST000003755712aENSE00001467571chr20:31413731-31413854124MARE1_HUMAN1-41412A:1-41
B:1-41
41
41
1.3aENST000003755713aENSE00000661239chr20:31421523-31421668146MARE1_HUMAN41-89492A:41-89
B:41-89
49
49
1.4ENST000003755714ENSE00000661240chr20:31424440-31424647208MARE1_HUMAN90-159702A:90-131
B:90-132
42
43
1.5ENST000003755715ENSE00000661241chr20:31427541-31427662122MARE1_HUMAN159-199411-
B:187-190
-
4
1.6ENST000003755716ENSE00000661242chr20:31434424-31434576153MARE1_HUMAN200-250510--
1.7bENST000003755717bENSE00001950425chr20:31436478-314382111734MARE1_HUMAN251-268180--

(-) 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:131
 aligned with MARE1_HUMAN | Q15691 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
          MARE1_HUMAN     1 MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQ 131
               SCOP domains d2r8ua_ A: automated matches                                                                                                        SCOP domains
               CATH domains 2r8uA00 A:1-131 Actin-binding Protein, T-fimbrin; domain 1                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CH  PDB: A:14-116 UniProt: 14-116                                                                      --------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:1-41 UniProt: 1-41     ------------------------------------------------Exon 1.4  PDB: A:90-131 UniProt: 90-159    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3a  PDB: A:41-89 UniProt: 41-89           ------------------------------------------ Transcript 1 (2)
                 2r8u A   1 MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQ 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 

Chain B from PDB  Type:PROTEIN  Length:136
 aligned with MARE1_HUMAN | Q15691 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
          MARE1_HUMAN     1 MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQGQETAVAPSLVAPALNKPKKPLTSSSAAPQRPISTQRTAAAPKAGPGVVRKNPGVGNGD 190
               SCOP domains -d2r8ub1 B:2-131 Microtubule-associated protein eb1, N-terminal microtubule binding domain                                         ----------------------------------------------------------- SCOP domains
               CATH domains 2r8uB00 B:1-190 Actin-binding Protein, T-fimbrin; domain 1                                                                                                                                     CATH domains
           Pfam domains (1) ----------------CH-2r8uB01 B:17-116                                                                                 -------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------CH-2r8uB02 B:17-116                                                                                 -------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhh.hhhhhhhhhhhhhhhhhhhh.....hhhhhh..------------------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------CH  PDB: B:14-116 UniProt: 14-116                                                                      --------------------------------------------------------------------EB1_C  PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:1-41 UniProt: 1-41     ------------------------------------------------Exon 1.4  PDB: B:90-132 UniProt: 90-159 [INCOMPLETE]                  ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.3a  PDB: B:41-89 UniProt: 41-89           ---------------------------------------------------------------------Exon 1.5  PDB: B:187-190         Transcript 1 (2)
                 2r8u B   1 MAVNVYSTSVTSDNLSRHDMLAWINESLQLNLTKIEQLCSGAAYCQFMDMLFPGSIALKKVKFQAKLEHEYIQNFKILQAGFKRMGVDKIIPVDKLVKGKFQDNFEFVQWFKKFFDANYDGKDYDPVAARQG------------------------------------------------------GNGD 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 |       -         -         -         -         -      |190
                                                                                                                                                             132                                                    187   

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: CH (43)
(-)
Family: CH (43)
1aCH-2r8uB01B:17-116
1bCH-2r8uB02B:17-116

(-) Gene Ontology  (28, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MARE1_HUMAN | Q15691)
molecular function
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:1904527    negative regulation of microtubule binding    Any process that stops, prevents or reduces the frequency, rate or extent of microtubule binding.
    GO:0031115    negative regulation of microtubule polymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:1903033    positive regulation of microtubule plus-end binding    Any process that activates or increases the frequency, rate or extent of microtubule plus-end binding.
    GO:0035372    protein localization to microtubule    A process in which a protein is transported to, or maintained at, a microtubule.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
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:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0031253    cell projection membrane    The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection.
    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:0030981    cortical microtubule cytoskeleton    The portion of the microtubule cytoskeleton that lies just beneath the plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005881    cytoplasmic microtubule    Any microtubule in the cytoplasm of a cell.
    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:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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:0035371    microtubule plus-end    The growing (plus) end of a microtubule. In vitro, microtubules polymerize more quickly at the plus end than at the minus end. In vivo, microtubule growth occurs only at the plus end, and the plus end switches between periods of growth and shortening, a behavior known as dynamic instability.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MARE1_HUMAN | Q156911pa7 1txq 1ueg 1vka 1wu9 1yib 1yig 2hkq 2hl3 2hl5 2qjz 3gjo 3mtu 3mud 3tq7 4xa1 4xa3 4xa6 5jv3 5jvm 5jvp 5jvr 5jvs 5jvu 5jx1

(-) Related Entries Specified in the PDB File

1pa7 AMINO-TERMINAL DOMAIN OF EB1