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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SECOND ZINC FINGER FROM ZRANB2/ZNF265 BOUND TO 6 NT SSRNA SEQUENCE AGGUAA
 
Authors :  F. E. Loughlin, A. P. Mcgrath, M. Lee, J. M. Guss, J. P. Mackay
Date :  15 Feb 09  (Deposition) - 03 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Zinc Finger, Zranb2, Znf265, Rna, Protein-Rna Complex, Transcription- Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. E. Loughlin, R. E. Mansfield, P. M. Vaz, A. P. Mcgrath, S. Setiyaputra, R. Gamsjaeger, E. S. Chen, B. J. Morris, J. M. Guss, J. P. Mackay
The Zinc Fingers Of The Sr-Like Protein Zranb2 Are Single-Stranded Rna-Binding Domains That Recognize 5' Splic Site-Like Sequences
Proc. Natl. Acad. Sci. Usa V. 106 5581 2009
PubMed-ID: 19304800  |  Reference-DOI: 10.1073/PNAS.0802466106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER RAN-BINDING DOMAIN-CONTAINING PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: BL21 ROSETTA2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER DOMAIN
    Gene: ZRANB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ZINC FINGER PROTEIN 265, ZINC FINGER, SPLICING
 
Molecule 2 - RNA (5'-R(*AP*GP*GP*UP*AP*A)-3')
    Chains: C
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED 6 NT SSRNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:71 , CYS A:74 , CYS A:85 , CYS A:88BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G9Y)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G9Y)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RANBP2_1PS01358 Zinc finger RanBP2-type signature.ZRAB2_HUMAN13-34
69-88		  1-
A:69-88

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003709201aENSE00001954996chr1:71546980-71546623358ZRAB2_HUMAN1-19190--
1.2ENST000003709202ENSE00000903869chr1:71544391-7154433953ZRAB2_HUMAN19-37190--
1.3ENST000003709203ENSE00000903868chr1:71544248-71544140109ZRAB2_HUMAN37-73371A:67-737
1.4ENST000003709204ENSE00000903867chr1:71542560-7154247883ZRAB2_HUMAN73-101291A:73-9523
1.5ENST000003709205ENSE00000903866chr1:71538231-7153815577ZRAB2_HUMAN101-126260--
1.6ENST000003709206ENSE00000903865chr1:71537938-71537804135ZRAB2_HUMAN127-171450--
1.7ENST000003709207ENSE00000995752chr1:71536679-71536510170ZRAB2_HUMAN172-228570--
1.8bENST000003709208bENSE00000995751chr1:71535045-7153495987ZRAB2_HUMAN228-257300--
1.9dENST000003709209dENSE00000903863chr1:71532617-71532459159ZRAB2_HUMAN257-310540--
1.10fENST0000037092010fENSE00001867543chr1:71530820-715289741847ZRAB2_HUMAN310-330210--

(-) 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:29
 aligned with ZRAB2_HUMAN | O95218 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:29
                                    76        86         
           ZRAB2_HUMAN   67 NDWQCKTCSNVNWARRSECNMCNTPKYAK 95
               SCOP domains ----------------------------- SCOP domains
               CATH domains ----------------------------- CATH domains
               Pfam domains ----------------------------- Pfam domains
         Sec.struct. author ..ee......ee................. Sec.struct. author
                 SAPs(SNPs) ----------------------------- SAPs(SNPs)
                    PROSITE --ZF_RANBP2_1         ------- PROSITE
           Transcript 1 (1) 1.3    ---------------------- Transcript 1 (1)
           Transcript 1 (2) ------Exon 1.4  PDB: A:73-95  Transcript 1 (2)
                  3g9y A 67 NDWQCKTCSNVNWARRSECNMCNTPKYAK 95
                                    76        86         


Chain C from PDB  Type:RNA  Length:6
                                     
                  3g9y C  1 AGGUAA  6
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3G9Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3G9Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G9Y)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ZRAB2_HUMAN | O95218)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    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
        ZRAB2_HUMAN | O95218: 1n0z 2k1p

(-) Related Entries Specified in the PDB File

2k1p SOLUTION STRUCTURE OF THE SECOND ZINC FINGER DOMAIN OF ZRANB2/ZNF265