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(-) Description

Title :  THE STRUCTURE OF THE AXH DOMAIN OF ATAXIN-1.
 
Authors :  M. Rees, Y. W. Chen, C. De Chiara, A. Pastore
Date :  05 Apr 12  (Deposition) - 27 Mar 13  (Release) - 17 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Rna Binding Protein, Rna Binding, Ob-Fold, High Mobility Group Homology, Hmg, Dimerization (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. De Chiara, M. Rees, R. P. Menon, K. Pauwels, C. Lawrence, P. V. Konarev, D. I. Svergun, S. R. Martin, Y. W. Chen, A. Pastore
Self-Assembly And Conformational Heterogeneity Of The Axh Domain Of Ataxin-1: An Unusual Example Of A Chameleon Fold
Biophys. J. V. 104 1304 2013
PubMed-ID: 23528090  |  Reference-DOI: 10.1016/J.BPJ.2013.01.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATAXIN-1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM30
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantPLYSS
    Expression System Vector TypePLASMID
    FragmentAXH DOMAIN, RESIDUES 566-688
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSPINOCEREBELLAR ATAXIA TYPE 1 PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:655 , ALA D:603 , SER D:606 , LEU D:609BINDING SITE FOR RESIDUE NA D1690

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (2, 8)

Asymmetric Unit (2, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1gENST000002447691gENSE00001168411chr6:16761687-16761529159ATX1_HUMAN-00--
1.2ENST000002447692ENSE00001279756chr6:16754322-1675427449ATX1_HUMAN-00--
1.3aENST000002447693aENSE00001989379chr6:16753578-16753464115ATX1_HUMAN-00--
1.7ENST000002447697ENSE00001279744chr6:16658132-16658007126ATX1_HUMAN-00--
1.9ENST000002447699ENSE00001279736chr6:16586138-16586011128ATX1_HUMAN-00--
1.10ENST0000024476910ENSE00001279728chr6:16522919-1652285862ATX1_HUMAN-00--
1.11aENST0000024476911aENSE00001279724chr6:16486341-16486203139ATX1_HUMAN-00--
1.14aENST0000024476914aENSE00000848097chr6:16328701-163266252077ATX1_HUMAN1-6396394A:565-640
B:565-640
C:565-640
D:565-640
76
76
76
76
1.15bENST0000024476915bENSE00001279802chr6:16307090-162993437748ATX1_HUMAN640-8151764A:641-689
B:641-689
C:641-689
D:641-688
49
49
49
48

(-) 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:125
 aligned with ATX1_HUMAN | P54253 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:125
                                   573       583       593       603       613       623       633       643       653       663       673       683     
           ATX1_HUMAN   564 AAAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 688
               SCOP domains d4apta_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...eee.....eee.hhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeeee....eeeeeeee....eee...eeee.hhhhhhhhh....ee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.14a  PDB: A:565-640 UniProt: 1-639 [INCOMPLETE]                      Exon 1.15b  PDB: A:641-689 UniProt: 640-815       Transcript 1
                 4apt A 565 AMAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 689
                                   574       584       594       604       614       624       634       644       654       664       674       684     

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with ATX1_HUMAN | P54253 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:125
                                   573       583       593       603       613       623       633       643       653       663       673       683     
           ATX1_HUMAN   564 AAAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 688
               SCOP domains d4aptb_ B: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..eee.....eee.hhhhhhhhhh.......eeeeeeeeeeeee.....eeeeeeee....eeeeeeee....eee...eeee.hhhhhhhhhh...ee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.14a  PDB: B:565-640 UniProt: 1-639 [INCOMPLETE]                      Exon 1.15b  PDB: B:641-689 UniProt: 640-815       Transcript 1
                 4apt B 565 AMAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 689
                                   574       584       594       604       614       624       634       644       654       664       674       684     

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with ATX1_HUMAN | P54253 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:125
                                   573       583       593       603       613       623       633       643       653       663       673       683     
           ATX1_HUMAN   564 AAAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 688
               SCOP domains d4aptc_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...eee.....eee.hhhhhhhhhhhhhhh..eeeeeeeeeeeee.....eeeeeee......eeeeeee....eee...eeee.hhhhhhhhhh...ee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.14a  PDB: C:565-640 UniProt: 1-639 [INCOMPLETE]                      Exon 1.15b  PDB: C:641-689 UniProt: 640-815       Transcript 1
                 4apt C 565 AMAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTLK 689
                                   574       584       594       604       614       624       634       644       654       664       674       684     

Chain D from PDB  Type:PROTEIN  Length:124
 aligned with ATX1_HUMAN | P54253 from UniProtKB/Swiss-Prot  Length:815

    Alignment length:124
                                   573       583       593       603       613       623       633       643       653       663       673       683    
           ATX1_HUMAN   564 AAAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTL 687
               SCOP domains d4aptd_ D: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhh..eee.....eee.hhhhhhhhhhhhhhh...eeeeeeeeeeee.....eeeeeeee.....eeeeeee....eee...eeee.hhhhhhhhhh...ee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.14a  PDB: D:565-640 UniProt: 1-639 [INCOMPLETE]                      Exon 1.15b  PDB: D:641-688 UniProt: 640-815      Transcript 1
                 4apt D 565 AMAPPTLPPYFMKGSIIQLANGELKKVEDLKTEDFIQSAEISNDLKIDSSTVERIEDSHSPGVAVIQFAVGEHRAQVSVEVLVEYPFFVFGQGWSSCCPERTSQLFDLPCSKLSVGDVCISLTL 688
                                   574       584       594       604       614       624       634       644       654       664       674       684    

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (ATX1_HUMAN | P54253)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0034046    poly(G) binding    Interacting selectively and non-covalently with a sequence of guanine residues in an RNA molecule.
    GO:0008266    poly(U) RNA binding    Interacting selectively and non-covalently with a sequence of uracil residues in an RNA molecule.
    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).
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
biological process
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051168    nuclear export    The directed movement of substances out of the nucleus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0042272    nuclear RNA export factor complex    A protein complex that contains two proteins (know in several organisms, including Drosophila, as NXF1 and NXF2) and is required for the export of the majority of mRNAs from the nucleus to the cytoplasm; localized in the nucleoplasm and at both the nucleoplasmic and cytoplasmic faces of the nuclear pore complex; shuttles between the nucleus and the cytoplasm.
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ATX1_HUMAN | P542531oa8 2m41 4aqp 4j2j 4j2l

(-) Related Entries Specified in the PDB File

1oa8 AXH DOMAIN OF HUMAN SPINOCEREBELLAR ATAXIN-1
4aqp THE STRUCTURE OF THE AXH DOMAIN OF ATAXIN-1.