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(-) Description

Title :  STRUCTURE OF THE TANDEM PH DOMAINS OF RTT106 (RESIDUES 68-315)
 
Authors :  D. Su, J. R. Thompson, G. Mer
Date :  20 Sep 11  (Deposition) - 01 Feb 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tandem Pleckstrin-Homology Domains, Chromosomal Protein, Nucleus, Phosphoprotein, Transcription, Transcription Regulation, Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Su, Q. Hu, Q. Li, J. R. Thompson, G. Cui, A. Fazly, B. A. Davies, M. V. Botuyan, Z. Zhang, G. Mer
Structural Basis For Recognition Of H3K56-Acetylated Histon H3-H4 By The Chaperone Rtt106.
Nature V. 483 104 2012
PubMed-ID: 22307274  |  Reference-DOI: 10.1038/NATURE10861

(-) Compounds

Molecule 1 - HISTONE CHAPERONE RTT106
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTEV
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 68-315
    Gene: N1346, RTT106, YNL206C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: REGULATOR OF TY1 TRANSPOSITION PROTEIN 106

 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, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3TVV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Ser A:83 -Pro A:84
2Lys A:246 -Pro A:247
3Ser B:83 -Pro B:84
4Gly B:243 -Phe B:244
5Lys B:246 -Pro B:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TVV)

(-) 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:233
 aligned with RT106_YEAST | P40161 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:244
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306    
          RT106_YEAST    67 ISETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKMASFLPVPEKPNLIYLFMTYTSCEDNKFSEPVVMTLNKENTLNQFKNLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFVNSTLVDTDAEKINSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSMIDQTEYAKIDDYVKRKQMKDKSMSE 310
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee...eeeeeeeee......eeeeeee..eeeeeeehhhhheeeeeeee......eeeeeeee..hhhhh....eeeeeehhhhhhhhhhh.........hhhhhhhhhhhhhhhh........-----------...eeeeeee..eeeeeee...eeee......eeee...eeeeeee.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tvv A   0 mSETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKmASFLPVPEKPNLIYLFmTYTSCEDNKFSEPVVmTLNKENTLNQFKKLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFV-----------INSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSmIDQTEYAKIDDYVKRKQmKDKSmSE 310
                            ||      76        86        96       106       116       126       136     | 146       156 |     166       176       186       196        |-         -|      226       236       246       256       266       276       286       296      |306 |  
                            ||                                                      125-MSE          142-MSE         158-MSE                                        205         217                                                                 285-MSE           303-MSE|  
                            0-MSE                                                                                                                                                                                                                                          308-MSE
                            68                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:235
 aligned with RT106_YEAST | P40161 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:246
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      
          RT106_YEAST    66 EISETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKMASFLPVPEKPNLIYLFMTYTSCEDNKFSEPVVMTLNKENTLNQFKNLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFVNSTLVDTDAEKINSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSMIDQTEYAKIDDYVKRKQMKDKSMSEE 311
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeeee...eeeeeeeee......eeeeeee..eeeeee.hhhhheeeeeeee......eeeeeeee.........eeeeeeeehhhhhhhhhhh........hhhhhhhhhhhhhhhh.........-----------...eeeeeee..eeeeeee...eeeee.....eeee...eeeeeee.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tvv B  -1 HmSETNTIFKLEGVSVLSPLRKKLDLVFYLSNVDGSPVITLLKGNDRELSIYQLNKNIKmASFLPVPEKPNLIYLFmTYTSCEDNKFSEPVVmTLNKENTLNQFKKLGLLDSNVTDFEKCVEYIRKQAILTGFKISNPFV-----------INSFHLQCHRGTKEGTLYFLPDHIIFGFKKPILLFDASDIESITYSSITRLTFNASLVTKDGEKYEFSmIDQTEYAKIDDYVKRKQmKDKSmSEE 311
                             ||     75        85        95       105       115       125       135      |145       155  |    165       175       185       195       205         - |     225       235       245       255       265       275       285       295       305  |   
                             ||                                                      125-MSE          142-MSE         158-MSE                                        205         217                                                                 285-MSE           303-MSE|   
                             0-MSE                                                                                                                                                                                                                                          308-MSE
                             68
   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 3TVV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RT106_YEAST | P40161)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0070869    heterochromatin assembly involved in chromatin silencing    Any process that results in the assembly of chromatin into heterochromatin and contributes to 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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0032196    transposition    Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.
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: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.

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  Cis Peptide Bonds
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  RT106_YEAST | P40161
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 Related Entries

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

UniProtKB/Swiss-Prot
        RT106_YEAST | P40161: 2lh0 3fss 3gyo 3gyp 3to1 3tw1

(-) Related Entries Specified in the PDB File

3fss 3hkh 3tw1