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(-) Description

Title :  CRYSTAL STRUCTURE OF MBNL1 TANDEM ZINC FINGER 3 AND 4 DOMAIN IN COMPLEX WITH CGCUGU RNA
 
Authors :  M. Teplova, D. J. Patel
Date :  08 May 08  (Deposition) - 02 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A (1x),E (2x),F (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C (1x),G (2x),H (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Tandem Zinc Finger Domain, Rna, Metal-Binding, Nucleus, Rna-Binding, Zinc-Finger, Metal Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Teplova, D. J. Patel
Structural Insights Into Rna Recognition By The Alternative-Splicing Regulator Muscleblind-Like Mbnl1.
Nat. Struct. Mol. Biol. V. 15 1343 2008
PubMed-ID: 19043415  |  Reference-DOI: 10.1038/NSMB.1519

(-) Compounds

Molecule 1 - MUSCLEBLIND-LIKE PROTEIN 1
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28B
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTANDEM ZINC FINGER 3 AND 4 DOMAINS (UNP RESIDUES 178-246)
    GeneMBNL1, EXP, KIAA0428, MBNL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRIPLET-EXPANSION RNA-BINDING PROTEIN
 
Molecule 2 - 5'-R(*CP*GP*CP*UP*GP*U)-3'
    ChainsE, F, G, H
    EngineeredYES
    Other DetailsCHEMICALLY SYNTHESIZED RNA OLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (2x)A (1x)   E (2x)F (1x)  
Biological Unit 2 (1x) B   F  
Biological Unit 3 (2x)  C (1x)   G (2x)H (1x)
Biological Unit 4 (1x)   D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:185 , CYS A:193 , CYS A:200 , HIS A:204BINDING SITE FOR RESIDUE ZN A 303
2AC2SOFTWARECYS A:221 , CYS A:229 , CYS A:234 , HIS A:238BINDING SITE FOR RESIDUE ZN A 304
3AC3SOFTWARECYS B:185 , CYS B:193 , CYS B:200 , HIS B:204BINDING SITE FOR RESIDUE ZN B 303
4AC4SOFTWARECYS B:221 , CYS B:229 , CYS B:234 , HIS B:238BINDING SITE FOR RESIDUE ZN B 304
5AC5SOFTWARECYS C:185 , CYS C:193 , CYS C:200 , HIS C:204BINDING SITE FOR RESIDUE ZN C 303
6AC6SOFTWARECYS C:221 , CYS C:229 , CYS C:234 , HIS C:238BINDING SITE FOR RESIDUE ZN C 304
7AC7SOFTWARECYS D:185 , CYS D:193 , CYS D:200 , HIS D:204BINDING SITE FOR RESIDUE ZN D 303
8AC8SOFTWARECYS D:221 , CYS D:229 , CYS D:234 , HIS D:238BINDING SITE FOR RESIDUE ZN D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D2S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D2S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D2S)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.MBNL1_HUMAN13-41
47-73
179-207
 
 
 
215-241
 
 
 
  8-
-
A:179-207
B:179-207
C:179-207
D:179-207
A:215-241
B:215-241
C:215-241
D:215-241
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.MBNL1_HUMAN13-41
47-73
179-207
 
 
 
215-241
 
 
 
  2-
-
A:179-207
-
-
-
A:215-241
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.MBNL1_HUMAN13-41
47-73
179-207
 
 
 
215-241
 
 
 
  2-
-
-
B:179-207
-
-
-
B:215-241
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.MBNL1_HUMAN13-41
47-73
179-207
 
 
 
215-241
 
 
 
  2-
-
-
-
C:179-207
-
-
-
C:215-241
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_C3H1PS50103 Zinc finger C3H1-type profile.MBNL1_HUMAN13-41
47-73
179-207
 
 
 
215-241
 
 
 
  2-
-
-
-
-
D:179-207
-
-
-
D:215-241

(-) Exons   (0, 0)

(no "Exon" information available for 3D2S)

(-) 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:67
 aligned with MBNL1_HUMAN | Q9NR56 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:67
                                   188       198       208       218       228       238       
          MBNL1_HUMAN   179 TDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhh.....hhhhh..........ee....eee.hhhhhh.............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_C3H1  PDB: A:179-207      -------ZF_C3H1  PDB: A:215-241    ---- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 3d2s A 179 TDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
                                   188       198       208       218       228       238       

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with MBNL1_HUMAN | Q9NR56 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:68
                                   187       197       207       217       227       237        
          MBNL1_HUMAN   178 RTDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhh.........................eee.hhhhhhh............hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_C3H1  PDB: B:179-207      -------ZF_C3H1  PDB: B:215-241    ---- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 3d2s B 178 RTDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
                                   187       197       207       217       227       237        

Chain C from PDB  Type:PROTEIN  Length:67
 aligned with MBNL1_HUMAN | Q9NR56 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:67
                                   188       198       208       218       228       238       
          MBNL1_HUMAN   179 TDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
               SCOP domains ------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhh.....hhhhh................eee.hhhhhh.............hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_C3H1  PDB: C:179-207      -------ZF_C3H1  PDB: C:215-241    ---- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 3d2s C 179 TDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
                                   188       198       208       218       228       238       

Chain D from PDB  Type:PROTEIN  Length:68
 aligned with MBNL1_HUMAN | Q9NR56 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:68
                                   187       197       207       217       227       237        
          MBNL1_HUMAN   178 RTDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
               SCOP domains -------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhh..........................eee.hhhhhhh............hhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ZF_C3H1  PDB: D:179-207      -------ZF_C3H1  PDB: D:215-241    ---- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 3d2s D 178 RTDRLEVCREYQRGNCNRGENDCRFAHPADSTMIDTNDNTVTVCMDYIKGRCSREKCKYFHPPAHLQA 245
                                   187       197       207       217       227       237        

Chain E from PDB  Type:DNA/RNA  Length:6
                                      
                 3d2s E   1 CGCUGU   6

Chain F from PDB  Type:DNA/RNA  Length:5
                                     
                 3d2s F   1 CGCUG   5

Chain G from PDB  Type:DNA/RNA  Length:6
                                      
                 3d2s G   1 CGCUGU   6

Chain H from PDB  Type:DNA/RNA  Length:5
                                     
                 3d2s H   1 CGCUG   5

   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 3D2S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D2S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D2S)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MBNL1_HUMAN | Q9NR56)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    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:0001069    regulatory region RNA binding    Interacting selectively and non-covalently with a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair.
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:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    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:0045445    myoblast differentiation    The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0043484    regulation of RNA splicing    Any process that modulates the frequency, rate or extent of 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.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0010494    cytoplasmic stress granule    A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
    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)

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        MBNL1_HUMAN | Q9NR563d2n 3d2q

(-) Related Entries Specified in the PDB File

3d2n 3d2q