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- PDB-1tf3: TFIIIA FINGER 1-3 BOUND TO DNA, NMR, 22 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1tf3
TitleTFIIIA FINGER 1-3 BOUND TO DNA, NMR, 22 STRUCTURES
Components
  • (5S RNA GENE) x 2
  • TRANSCRIPTION FACTOR IIIA
KeywordsTRANSCRIPTION/DNA / TFIIIA / PROTEIN / DNA / TRANSCRIPTION FACTOR / 5S RNA GENE / DNA BINDING PROTEIN / ZINC FINGER / COMPLEX (TRANSCRIPTION REGULATION-DNA) / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


ribosomal large subunit biogenesis / DNA binding / RNA binding / zinc ion binding / nucleus
Similarity search - Function
: / TFIIIA, beta-beta-alpha zinc finger / : / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / TFIIIA, beta-beta-alpha zinc finger / : / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcription factor IIIA
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodSOLUTION NMR / simulated annealing
AuthorsFoster, M.P. / Wuttke, D.S. / Radhakrishnan, I. / Case, D.A. / Gottesfeld, J.M. / Wright, P.E.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Domain packing and dynamics in the DNA complex of the N-terminal zinc fingers of TFIIIA.
Authors: Foster, M.P. / Wuttke, D.S. / Radhakrishnan, I. / Case, D.A. / Gottesfeld, J.M. / Wright, P.E.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity
Authors: Wuttke, D.S. / Foster, M.P. / Case, D.A. / Gottesfeld, J.M. / Wright, P.E.
History
DepositionJul 1, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 5S RNA GENE
F: 5S RNA GENE
A: TRANSCRIPTION FACTOR IIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0626
Polymers19,8663
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 64RESTRAINT ENERGIES < 11 KCAL, NO DISTANCE VIOLATIONS > 0.3 A
Representative

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Components

#1: DNA chain 5S RNA GENE / 5S GENE


Mass: 4690.045 Da / Num. of mol.: 1
Fragment: C-BLOCK, NT 79-93 OF 5S RNA GENE, NON-CODING AND CODING STRANDS
Source method: obtained synthetically
Details: GENE FRAGMENT ENCODING FINGERS 1-3 OF TFIIIA WAS SUBCLONED INTO PET21A PLASMID AND EXPRESSED IN ESCHERICHIA COLI BL21 (DE3) CELLS. DNA OLIGONUCLEOTIDE WAS OBTAINED BY SOLID-PHASE SYNTHESIS
#2: DNA chain 5S RNA GENE / 5S GENE


Mass: 4489.926 Da / Num. of mol.: 1
Fragment: C-BLOCK, NT 79-93 OF 5S RNA GENE, NON-CODING AND CODING STRANDS
Source method: obtained synthetically
Details: GENE FRAGMENT ENCODING FINGERS 1-3 OF TFIIIA WAS SUBCLONED INTO PET21A PLASMID AND EXPRESSED IN ESCHERICHIA COLI BL21 (DE3) CELLS. DNA OLIGONUCLEOTIDE WAS OBTAINED BY SOLID-PHASE SYNTHESIS
#3: Protein TRANSCRIPTION FACTOR IIIA / TFIIIA


Mass: 10686.225 Da / Num. of mol.: 1 / Fragment: FINGERS 1-3 OF TFIIIA, RESIDUES 1, 11 - 101 / Mutation: C35S
Source method: isolated from a genetically manipulated source
Details: MINIMAL DNA BINDING, ZF1-3 CONTAINS THREE ZINC ATOMS, TETRAHEDRALLY COORDINATED BY TWO CYSTEINE AND TWO HISTIDINE SIDE CHAINS
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Cell: OOCYTES / Cell line: BL21 / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03001
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: NO

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Sample preparation

Sample conditionspH: 6.7 / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX7503

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Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
Amberstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: RESTRAINT ENERGIES < 11 KCAL, NO DISTANCE VIOLATIONS > 0.3 A
Conformers calculated total number: 64 / Conformers submitted total number: 22

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