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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A ZINC FINGER - RNA COMPLEX REVEALS TWO MODES OF MOLECULAR RECOGNITION
 
Authors :  D. Lu, M. A. Searles, A. Klug
Date :  04 Sep 03  (Deposition) - 20 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  B,C,D,E,F
Biol. Unit 1:  C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Rna-Binding Protein/Rna, Complex(Zinc Finger/Rna), Tfiiia, 5S Ribosomal Rna, Zinc Finger, Rna-Protein Complex, X. Laevis, Transcription Regulation, Rna-Binding, Dna- Binding, Nuclear Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Lu, M. A. Searles, A. Klug
Crystal Structure Of A Zinc-Finger-Rna Complex Reveals Two Modes Of Molecular Recognition
Nature V. 426 96 2003
PubMed-ID: 14603324  |  Reference-DOI: 10.1038/NATURE02088
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR IIIA
    CellOOCYTE
    ChainsB, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET13A3F
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentFINGERS 4,5 AND 6, RESIDUES 127 - 212 UNDER SWISSPROT NUMBERING FOR SOMATIC TFIIIA
    OrganOVARY
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
    SynonymTFIIIA, FACTOR A, S-TFIIIA/O-TFIIIA
 
Molecule 2 - 5S RIBOSOMAL RNA
    CellOOCYTE
    ChainsE, F
    FragmentCENTRAL REGION, NUCLEOTIDES 4 - 15,64 -82,94-115, PLUS TWO TETRALOOPS JOINING 15 - 64 AND 82 - 94 RESPECTIVELY
    OrganOVARY
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
    Other DetailsUACG TETRALOOP LINKING NUCLEOTIDES 15 AND 64, GAAA TETRALOOP LINKING NUCLEOTIDES 82 AND 94
    Other Details - SourceIN VITRO TRANSCRIPTION TO PRODUCE THE RNA

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit BCDEF
Biological Unit 1 (1x) C E 
Biological Unit 2 (1x)B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1MG13Ligand/IonMAGNESIUM ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS B:107 , CYS B:112 , HIS B:125 , HIS B:129BINDING SITE FOR RESIDUE ZN B 204
02AC2SOFTWARECYS B:137 , CYS B:142 , HIS B:155 , HIS B:159BINDING SITE FOR RESIDUE ZN B 205
03AC3SOFTWARECYS B:164 , CYS B:170 , HIS B:183 , HIS B:188BINDING SITE FOR RESIDUE ZN B 206
04AC4SOFTWARECYS B:164 , ASP B:168 , CYS B:170BINDING SITE FOR RESIDUE MG B 306
05AC5SOFTWAREPRO B:163 , LYS B:165BINDING SITE FOR RESIDUE MG B 307
06AC6SOFTWARECYS B:137 , HIS B:139 , CYS B:142BINDING SITE FOR RESIDUE MG B 308
07AC7SOFTWARECYS C:107 , CYS C:112 , HIS C:125 , HIS C:129BINDING SITE FOR RESIDUE ZN C 204
08AC8SOFTWARECYS C:137 , CYS C:142 , HIS C:155 , HIS C:159BINDING SITE FOR RESIDUE ZN C 205
09AC9SOFTWARECYS C:164 , CYS C:170 , HIS C:183 , HIS C:188BINDING SITE FOR RESIDUE ZN C 206
10BC1SOFTWAREG E:7BINDING SITE FOR RESIDUE MG C 342
11BC2SOFTWARECYS C:137 , HIS C:139 , CYS C:142BINDING SITE FOR RESIDUE MG C 344
12BC3SOFTWARECYS D:137 , CYS D:142 , HIS D:155 , HIS D:159BINDING SITE FOR RESIDUE ZN D 205
13BC4SOFTWARECYS D:164 , CYS D:170 , HIS D:183 , HIS D:188BINDING SITE FOR RESIDUE ZN D 206
14BC5SOFTWAREG E:113BINDING SITE FOR RESIDUE MG E 341
15BC6SOFTWAREG E:97 , G E:98BINDING SITE FOR RESIDUE MG E 343
16BC7SOFTWAREG F:98BINDING SITE FOR RESIDUE MG F 302
17BC8SOFTWAREG F:114BINDING SITE FOR RESIDUE MG F 303
18BC9SOFTWAREG F:110BINDING SITE FOR RESIDUE MG F 304
19CC1SOFTWAREG F:70 , G F:71BINDING SITE FOR RESIDUE MG F 305
20CC2SOFTWAREG F:66 , C F:67 , G F:108 , U F:109BINDING SITE FOR RESIDUE MG F 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1UN6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UN6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UN6)

(-) PROSITE Motifs  (1, 5)

Asymmetric Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TF3A_XENLA37-59
67-89
97-120
129-151
 
159-181
 
 
216-236
245-268
276-298
  5-
-
-
B:107-129
C:107-129
B:137-159
C:137-159
D:137-159
-
-
-
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TF3A_XENLA37-59
67-89
97-120
129-151
 
159-181
 
 
216-236
245-268
276-298
  2-
-
-
-
C:107-129
-
C:137-159
-
-
-
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_FINGER_C2H2_1PS00028 Zinc finger C2H2 type domain signature.TF3A_XENLA37-59
67-89
97-120
129-151
 
159-181
 
 
216-236
245-268
276-298
  3-
-
-
B:107-129
-
B:137-159
-
D:137-159
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1UN6)

(-) 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 B from PDB  Type:PROTEIN  Length:87
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:87
                                   135       145       155       165       175       185       195       205       
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6b1 B:104-131           d1un6b2 B:132-160            d1un6b3 B:161-190              SCOP domains
               CATH domains 1un6B01 B:104-132            1un6B02 B:133-161            1un6B03 B:162-190             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1un6 B 104 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   113       123       133       143       153       163       173       183       

Chain C from PDB  Type:PROTEIN  Length:87
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:87
                                   135       145       155       165       175       185       195       205       
           TF3A_XENLA   126 VYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6c1 C:104-131           d1un6c2 C:132-160            d1un6c3 C:161-190              SCOP domains
               CATH domains 1un6C01 C:104-132            1un6C02 C:133-161            1un6C03 C:162-190             CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........ee..hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 1un6 C 104 MYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   113       123       133       143       153       163       173       183       

Chain D from PDB  Type:PROTEIN  Length:58
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:58
                                   164       174       184       194       204        
           TF3A_XENLA   155 LPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 212
               SCOP domains d1un6d1 D:133-160           d1un6d2 D:161-190              SCOP domains
               CATH domains 1un6D01 D:133-159          1un6D02 D:160-190               CATH domains
           Pfam domains (1) --zf-C2H2-1un6D01 D:135-159------------------------------- Pfam domains (1)
           Pfam domains (2) --zf-C2H2-1un6D02 D:135-159------------------------------- Pfam domains (2)
           Pfam domains (3) --zf-C2H2-1un6D03 D:135-159------------------------------- Pfam domains (3)
           Pfam domains (4) --zf-C2H2-1un6D04 D:135-159------------------------------- Pfam domains (4)
           Pfam domains (5) --zf-C2H2-1un6D05 D:135-159------------------------------- Pfam domains (5)
         Sec.struct. author ..ee........ee..hhhhhhhhhhhh.ee.........ee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ZINC_FINGER_C2H2_1     ------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 1un6 D 133 LPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECHQD 190
                                   142       152       162       172       182        

Chain E from PDB  Type:RNA  Length:61
                                                                                             
                 1un6 E   4 GCCGGCCACACCUACGGGGCCUGGUUAGUACCUGGGAAACCUGGGAAUACCAGGUGCCGGC 115
                                    13     || 67        77        94       104       114 
                                          19|                    86|                     
                                           64                     94                     

Chain F from PDB  Type:RNA  Length:61
                                                                                             
                 1un6 F   4 GCCGGCCACACCUACGGGGCCUGGUUAGUACCUGGGAAACCUGGGAAUACCAGGUGCCGGC 115
                                    13     || 67        77        94       104       114 
                                          19|                    86|                     
                                           64                     94                     

   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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: C2H2-zf (71)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain B,C,D   (TF3A_XENLA | P03001)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    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: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
        TF3A_XENLA | P030011tf3 1tf6 2hgh 2j7j

(-) Related Entries Specified in the PDB File

1tf3 TFIIIA FINGER 1-3 BOUND TO DEOXYRIBONUCLEIC ACID, NMR, 22 STRUCTURES
1tf6 CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RIBONUCLEIC ACID GENE INTERNAL CONTROL REGION