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(-) Description

Title :  CRYSTAL STRUCTURE OF RAP1/DNA COMPLEX
 
Authors :  B. Matot, Y. -V. Le Bihan, S. Gasparini, M. H. Ledu
Date :  09 Nov 11  (Deposition) - 07 Dec 11  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Double Myb, Transcription Regulation, Telomeres Length Regulation, Telomeres Protection, Nucleus, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Matot, Y. V. Le Bihan, R. Lescasse, J. Perez, S. Miron, G. David, B. Castaing, P. Weber, B. Raynal, S. Zinn-Justin, S. Gasparini, M. H. Le Du
The Orientation Of The C-Terminal Domain Of The Saccharomyces Cerevisiae Rap1 Protein Is Determined By Its Binding To Dna.
Nucleic Acids Res. V. 40 3197 2012
PubMed-ID: 22139930  |  Reference-DOI: 10.1093/NAR/GKR1166

(-) Compounds

Molecule 1 - DNA-BINDING PROTEIN RAP1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentDNA BINDING DOMAIN, UNP RESIDUES 360-601
    GeneRAP1, GRF1, TUF1, YNL216W, N1310
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymREPRESSOR/ACTIVATOR SITE-BINDING PROTEIN, SBF-E, TUF
 
Molecule 2 - TELOMERIC DNA
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - TELOMERIC DNA
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:503 , GLY A:504 , GLU A:506BINDING SITE FOR RESIDUE CA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UKG)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Phe A:424 -Gly A:425
2Lys A:426 -Leu A:427
3Pro A:474 -Asp A:475
4Pro A:499 -Asn A:500
5Asn A:500 -His A:501
6Asn A:508 -Phe A:509
7Gly A:519 -Pro A:520
8Ala A:596 -Lys A:597

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UKG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UKG)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YNL216W1YNL216W.1XIV:241690-2441732484RAP1_YEAST1-8278271A:360-601 (gaps)242

(-) 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:223
 aligned with RAP1_YEAST | P11938 from UniProtKB/Swiss-Prot  Length:827

    Alignment length:242
                                   369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599  
           RAP1_YEAST   360 KASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSKRLEYVYEVDKFGKLVRDDDGNLIKTKVLPPSIKRKFSADEDYTLAIAVKKQFYRDLFQIDPDTGRSLITDEDTPTAIARRNMTMDPNHVPGSEPNFAAYRTQSRRGPIAREFFKHFAEEHAAHTENAWRDRFRKFLLAYGIDDYISYYEAEKAQNREPEPMKNLTNRPKRPGVPTPGNYNSAAKRARN 601
               SCOP domains d3ukga1 A:360-445 automated matches                                                   d3ukga2 A:446-601 automated matche                   s                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhhh..ee.................ee...........hhhhhhhhhhhhhhhhhhhhhh........-------------------.......................hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:360-601 (gaps) UniProt: 1-827 [INCOMPLETE]                                                                                                                                                                                        Transcript 1
                 3ukg A 360 KASFTDEEDEFILDVVRKNPTRRTTHTLYDEISHYVPNHTGNSIRHRFRVYLSKRLEYVYEVDKFGKLVRDDDGNLIKTKVLPPSIKRKFSADEDYTLAIAVKKQFYRDLFQIDPDTGRS-------------------PNHVPGSEPNFAAYRTQSRRGPIAREFFKHFAEEHAAHTENAWRDRFRKFLLAYGIDDYISYYEAEKAQNREPEPMKNLTNRPKRPGVPTPGNYNSAAKRARN 601
                                   369       379       389       399       409       419       429       439       449       459       469       479         -       499       509       519       529       539       549       559       569       579       589       599  
                                                                                                                                                 479                 499                                                                                                      

Chain C from PDB  Type:DNA  Length:31
                                                               
                 3ukg C   1 GAACACCACACAACACCCACACACCAGGTGT  31
                                    10        20        30 

Chain D from PDB  Type:DNA  Length:31
                                                               
                 3ukg D   1 ACCTGGTGTGTGGGTGTTGTGTGGTGTTCAC  31
                                    10        20        30 

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UKG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UKG)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RAP1_YEAST | P11938)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0051880    G-quadruplex DNA binding    Interacting selectively and non-covalently with G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad. The stacking of guanine tetrads results in G-quadruplex DNA structures. G-quadruplex DNA can form under physiological conditions from some G-rich sequences, such as those found in telomeres, immunoglobulin switch regions, gene promoters, fragile X repeats, and the dimerization domain in the human immunodeficiency virus (HIV) genome.
    GO:0001132    RNA polymerase II transcription factor activity, TBP-class protein binding    Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well.
    GO:0001094    TFIID-class transcription factor binding    Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor.
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    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:0042162    telomeric DNA binding    Interacting selectively and non-covalently with a telomere, a specific structure at the end of a linear chromosome required for the integrity and maintenance of the end.
    GO:0000982    transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    GO:0001076    transcription factor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0071919    G-quadruplex DNA formation    A DNA metabolic process that results in the formation of G-quadruplex DNA structures, in which groups of four guanines adopt a flat, cyclic Hoogsteen hydrogen-bonding arrangement known as a guanine tetrad or G-quartet. The stacking of several layers of G-quartets forms G-quadruplexes, in which one or more DNA single strands are assembled in parallel and/or antiparallel, with interactions that can be either intra- or intermolecular in nature.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0006348    chromatin silencing at telomere    Repression of transcription of telomeric DNA by altering the structure of chromatin.
    GO:0035390    establishment of chromatin silencing at telomere    The initial formation of a transcriptionally silent chromatin structure such as heterochromatin at the telomere.
    GO:0071169    establishment of protein localization to chromatin    The directed movement of a protein to a part of a chromosome that is organized into chromatin.
    GO:0070200    establishment of protein localization to telomere    The directed movement of a protein to a specific location in the telomeric region of a chromosome.
    GO:0031936    negative regulation of chromatin silencing    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0031848    protection from non-homologous end joining at telomere    A process that prevents non-homologous end joining at telomere, thereby ensuring that telomeres do not fuse.
    GO:0072363    regulation of glycolytic process by positive regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of glycolysis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0010833    telomere maintenance via telomere lengthening    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins and lengthening the telomeric DNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    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:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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:0070187    shelterin complex    A nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase. The complex is known to contain TERF1, TERF2, POT1, RAP1, TINF2 and ACD in mammalian cells, and Pot1, Tpz1, Rap1, Rif1, Rif2 and Taz1 in Schizosaccharomyces. Taz1 and Rap1 (or their mammalian equivalents) form a dsDNA-binding subcomplex, Pot1 and Tpz1 form an ssDNA-binding subcomplex, and the two subcomplexes are bridged by Poz1, which acts as an effector molecule along with Ccq1.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RAP1_YEAST | P119381ign 2l42 3cz6 3owt 4bj5 4bj6 4bjt 4gfb

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3UKG)