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(-) Description

Title :  SOLUTION STRUCTURE OF THE SECOND ZINC FINGER DOMAIN OF ZRANB2/ZNF265
 
Authors :  F. E. Loughlin, J. P. Mackay
Date :  13 Mar 08  (Deposition) - 17 Mar 09  (Release) - 17 Mar 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Zinc Finger, Znf265, Rna Binding, Ranbp2, Rbz, Zis, Alternative Splicing, Metal-Binding, Mrna Processing, Mrna Splicing, Nucleus, Phosphoprotein, Polymorphism, Rna- Binding, Zinc-Finger, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. E. Loughlin, R. E. Mansfield, P. M. Vaz, W. Leung, S. Setiyaputra, R. P. Grant, E. S. Chen, R. Gamsjaeger, J. P. Mackay
The Zinc Fingers Of The Sr-Proein Zranb2 Recognize 5'Splice Site-Like Sequences And Constitute A Distinct Class Of Rna Binding Domain
To Be Published
PubMed: search
(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 Taxid: 562
    Expression System Vector: PGEX2T
    Fragment: RANBP2-TYPE 2, RESIDUES 65-95
    Gene: ZRANB2, ZIS, ZNF265
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ZINC FINGER PROTEIN 265, ZINC FINGER, SPLICING

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:71 , THR A:73 , CYS A:74 , MET A:87BINDING SITE FOR RESIDUE ZN A 96

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2K1P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2K1P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2K1P)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RANBP2_2PS50199 Zinc finger RanBP2 type profile.ZRAB2_HUMAN9-40
65-94		  1-
A:65-94
2ZF_RANBP2_1PS01358 Zinc finger RanBP2-type signature.ZRAB2_HUMAN13-34
69-88		  1-
A:69-88

(-) Exons   (2, 2)

NMR Structure (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:63-73 (gaps)25
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

NMR Structure
   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:33
 aligned with ZRAB2_HUMAN | O95218 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:47
                                    58        68        78        88       
           ZRAB2_HUMAN   49 GTEIGKTLAEKSRGLFSANDWQCKTCSNVNWARRSECNMCNTPKYAK 95
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------zf-RanBP-2k1pA01 A:65-94      - Pfam domains
         Sec.struct. author ..--------------............................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------ZF_RANBP2_2  PDB: A:65-94     - PROSITE (1)
                PROSITE (2) --------------------ZF_RANBP2_1         ------- PROSITE (2)
           Transcript 1 (1) Exon 1.3 UniProt: 37-73  ---------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.4  PDB: A:73-95  Transcript 1 (2)
                  2k1p A 63 GS--------------SANDWQCKTCSNVNWARRSECNMCNTPKYAK 95
                             |       -      | 68        78        88       
                             |             65                              
                            64
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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 2K1P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2K1P)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Zn_Beta_Ribbon (109)

(-) Gene Ontology  (10, 10)

NMR Structure(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 3g9y

(-) Related Entries Specified in the PDB File

1qu6 ZINC FINGER 1 FROM ZNF265 / ZRANB2
2c6b ZINC FINGER FROM HDM2
2cr8 ZINC FINGER FROM MDM4
2gqe ZINC FINGER FROM NUP153
inj3 ZINC FINGER FROM NPL4