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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION
 
Authors :  R. T. Nolte, R. M. Conlin, S. C. Harrison, R. S. Brown
Date :  02 Mar 98  (Deposition) - 10 Jul 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Complex (Transcription Regulation/Dna), Rna Polymerase Iii, Transcription Initiation, Zinc Finger Protein, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Nolte, R. M. Conlin, S. C. Harrison, R. S. Brown
Differing Roles For Zinc Fingers In Dna Recognition: Structure Of A Six-Finger Transcription Factor Iiia Complex.
Proc. Natl. Acad. Sci. Usa V. 95 2938 1998
PubMed-ID: 9501194  |  Reference-DOI: 10.1073/PNAS.95.6.2938
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*CP*GP*GP*GP*CP*CP*TP*GP*GP*TP*TP*AP*GP*TP*AP*C P*CP*TP*GP*GP*AP* TP*GP*GP*GP*AP*GP*AP*CP*C)-3')
    Chains: B, E
    Engineered: YES
    Fragment: INTERNAL PROMOTER REGION
    Synonym: 5S RIBOSOMAL RNA GENE
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*GP*GP*TP*CP*TP*CP*CP*CP*AP*TP*CP*CP*AP*GP*GP*T P*AP*CP*TP*AP*AP* CP*CP*AP*GP*GP*CP*CP*CP*G)-3')
    Chains: C, F
    Engineered: YES
    Fragment: INTERNAL PROMOTER REGION
    Synonym: 5S RIBOSOMAL RNA GENE
    Synthetic: YES
 
Molecule 3 - PROTEIN (TRANSCRIPTION FACTOR IIIA)
    Cell: OOCYTE
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Cellular Location: INCLUSION BODY
    Expression System Plasmid: PRSET B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: NH2-TERMINAL SIX FINGERS, RESIDUE 1-190
    Organ: OVARY
    Organelle: NUCLEUS
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: CDNA
    Synonym: TRANSCRIPTION FACTOR IIIA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/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

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:15 , CYS A:20 , HIS A:33 , HIS A:37BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWARECYS A:45 , CYS A:50 , HIS A:63 , HIS A:67BINDING SITE FOR RESIDUE ZN A 202
03AC3SOFTWARECYS A:75 , SER A:77 , CYS A:80 , HIS A:93 , HIS A:98BINDING SITE FOR RESIDUE ZN A 203
04AC4SOFTWARECYS A:107 , CYS A:112 , HIS A:125 , HIS A:129BINDING SITE FOR RESIDUE ZN A 204
05AC5SOFTWARECYS A:137 , CYS A:142 , HIS A:155 , HIS A:159BINDING SITE FOR RESIDUE ZN A 205
06AC6SOFTWARECYS A:164 , CYS A:170 , HIS A:183 , HIS A:188BINDING SITE FOR RESIDUE ZN A 206
07AC7SOFTWARECYS D:15 , CYS D:20 , HIS D:33 , HIS D:37BINDING SITE FOR RESIDUE ZN D 201
08AC8SOFTWARECYS D:45 , CYS D:50 , HIS D:63 , HIS D:67BINDING SITE FOR RESIDUE ZN D 202
09AC9SOFTWARECYS D:75 , SER D:77 , CYS D:80 , HIS D:93 , HIS D:98BINDING SITE FOR RESIDUE ZN D 203
10AN1UNKNOWNCYS A:15 , CYS A:20 , HIS A:33 , HIS A:37ZN-BINDING SITE.
11AN2UNKNOWNCYS A:45 , CYS A:50 , HIS A:63 , HIS A:67ZN-BINDING SITE.
12AN3UNKNOWNCYS A:75 , CYS A:80 , HIS A:93 , HIS A:98ZN-BINDING SITE.
13AN4UNKNOWNCYS A:107 , CYS A:112 , HIS A:125 , HIS A:129ZN-BINDING SITE.
14AN5UNKNOWNCYS A:137 , CYS A:142 , HIS A:155 , HIS A:159ZN-BINDING SITE.
15AN6UNKNOWNCYS A:164 , CYS A:170 , HIS A:183 , HIS A:188ZN-BINDING SITE.
16BC1SOFTWARECYS D:107 , CYS D:112 , HIS D:125 , HIS D:129BINDING SITE FOR RESIDUE ZN D 204
17BC2SOFTWARECYS D:137 , CYS D:142 , HIS D:155 , HIS D:159BINDING SITE FOR RESIDUE ZN D 205
18BC3SOFTWARECYS D:164 , CYS D:170 , HIS D:183 , HIS D:188BINDING SITE FOR RESIDUE ZN D 206
19DN1UNKNOWNCYS D:15 , CYS D:20 , HIS D:33 , HIS D:37ZN-BINDING SITE.
20DN2UNKNOWNCYS D:45 , CYS D:50 , HIS D:63 , HIS D:67ZN-BINDING SITE.
21DN3UNKNOWNCYS D:75 , CYS D:80 , HIS D:93 , HIS D:98ZN-BINDING SITE.
22DN4UNKNOWNCYS D:107 , CYS D:112 , HIS D:125 , HIS D:129ZN-BINDING SITE.
23DN5UNKNOWNCYS D:137 , CYS D:142 , HIS D:155 , HIS D:159ZN-BINDING SITE.
24DN6UNKNOWNCYS D:164 , CYS D:170 , HIS D:183 , HIS D:188'ZN-BINDING

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TF6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TF6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TF3A_XENLA_001 *T96KTF3A_XENLA  ---  ---A/DT74K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TF3A_XENLA_001 *T96KTF3A_XENLA  ---  ---AT74K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TF3A_XENLA_001 *T96KTF3A_XENLA  ---  ---DT74K
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 10)

Asymmetric Unit (1, 10)
 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		  10A:15-37
D:15-37
A:45-67
D:45-67
A:75-98
D:75-98
A:107-129
D:107-129
A:137-159
D:137-159
-
-
-
Biological Unit 1 (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		  5A:15-37
-
A:45-67
-
A:75-98
-
A:107-129
-
A:137-159
-
-
-
-
Biological Unit 2 (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-
D:15-37
-
D:45-67
-
D:75-98
-
D:107-129
-
D:137-159
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 1TF6)

(-) 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:179
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:179
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
           TF3A_XENLA    32 YKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH 210
               SCOP domains d1tf6a1 A:10-40                d1tf6a2 A:41-70               d1tf6a3 A:71-100              d1tf6a4 A:101-131              d1tf6a5 A:132-160            d1tf6a6 A:161-188            SCOP domains
               CATH domains 1tf6A01 A:10-39               1tf6A02 A:40-68              1tf6A03 A:69-102                  1tf6A04 A:103-132             1tf6A05 A:133-161            1tf6A06 A:162-188           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhh..................hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh.......ee......ee...hhhhhhhhhhhh..................hhhhhhhhhhhh................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1      --------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ----------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf6 A  10 YKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH 188
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179         


Chain B from PDB  Type:DNA  Length:31
                                                               
                 1tf6 B   1 ACGGGCCTGGTTAGTACCTGGATGGGAGACC  31
                                    10        20        30 


Chain C from PDB  Type:DNA  Length:31
                                                               
                 1tf6 C  33 TGGTCTCCCATCCAGGTACTAACCAGGCCCG  63
                                    42        52        62 


Chain D from PDB  Type:PROTEIN  Length:182
 aligned with TF3A_XENLA | P03001 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:182
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
           TF3A_XENLA    29 PVVYKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH 210
               SCOP domains d1tf6d1 D:7-40                    d1tf6d2 D:41-70               d1tf6d3 D:71-100              d1tf6d4 D:101-131              d1tf6d5 D:132-160            d1tf6d6 D:161-188            SCOP domains
               CATH domains 1tf6D01 D:7-39                   1tf6D02 D:40-68              1tf6D03 D:69-102                  1tf6D04 D:103-132             1tf6D05 D:133-161            1tf6D06 D:162-188           CATH domains
           Pfam domains (1) ----------------------------------------------------zf-H2C2_2-1tf6D05 D:59-86   ------------------------------------------------zf-C2H2-1tf6D01 D:135-159----------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------zf-H2C2_2-1tf6D06 D:59-86   ------------------------------------------------zf-C2H2-1tf6D02 D:135-159----------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------zf-H2C2_2-1tf6D07 D:59-86   ------------------------------------------------zf-C2H2-1tf6D03 D:135-159----------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------zf-H2C2_2-1tf6D08 D:59-86   ------------------------------------------------zf-C2H2-1tf6D04 D:135-159----------------------------- Pfam domains (4)
         Sec.struct. author ....................hhhhhhhhhhhh..................hhhhhhhhhhhh....ee........ee..hhhhhhhhhhhh....................hhhhhhhhhhhh..................hhhhhhhhhhhh................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1      --------ZINC_FINGER_C2H2_1     -------ZINC_FINGER_C2H2_1     ----------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tf6 D   7 PVVYKRYICSFADCGAAYNKNWKLQAHLCKHTGEKPFPCKEEGCEKGFTSLHHLTRHSLTHTGEKNFTCDSDGCDLRFTTKANMKKHFNRFHNIKICVYVCHFENCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKVHAGYPCKKDDSCSFVGKTWTLYLKHVAECH 188
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186  


Chain E from PDB  Type:DNA  Length:31
                                                               
                 1tf6 E   1 ACGGGCCTGGTTAGTACCTGGATGGGAGACC  31
                                    10        20        30 


Chain F from PDB  Type:DNA  Length:31
                                                               
                 1tf6 F  33 TGGTCTCCCATCCAGGTACTAACCAGGCCCG  63
                                    42        52        62
   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, 12)

Asymmetric Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 12)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 2-Layer Sandwich (8480)
(-)
Topology: Double Stranded RNA Binding Domain (204)
(-)
Homologous Superfamily: Classic Zinc Finger (45)
(-)
[unclassified] (29)
1a1tf6A05A:133-161
1b1tf6D05D:133-161
1c1tf6D01D:7-39
1d1tf6A01A:10-39
1e1tf6A03A:69-102
1f1tf6D03D:69-102
1g1tf6A06A:162-188
1h1tf6D06D:162-188
1i1tf6A04A:103-132
1j1tf6D04D:103-132
1k1tf6A02A:40-68
1l1tf6D02D:40-68

(-) Pfam Domains  (2, 8)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,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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  1tf6
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  TF3A_XENLA | P03001
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 Related Entries

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

UniProtKB/Swiss-Prot
        TF3A_XENLA | P03001: 1tf3 1un6 2hgh 2j7j

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TF6)