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- PDB-1fu9: SOLUTION STRUCTURE OF THE NINTH ZINC-FINGER DOMAIN OF THE U-SHAPE... -

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Basic information

Entry
Database: PDB / ID: 1fu9
TitleSOLUTION STRUCTURE OF THE NINTH ZINC-FINGER DOMAIN OF THE U-SHAPED TRANSCRIPTION FACTOR
ComponentsU-SHAPED TRANSCRIPTIONAL COFACTOR
KeywordsTRANSCRIPTION / zinc-finger / beta-hairpin + alpha-helix
Function / homology
Function and homology information


lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / germ-band shortening / Factors involved in megakaryocyte development and platelet production / larval lymph gland hemopoiesis / lymph gland development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function ...lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / germ-band shortening / Factors involved in megakaryocyte development and platelet production / larval lymph gland hemopoiesis / lymph gland development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / compound eye development / chaeta development / DNA-binding transcription repressor activity / negative regulation of insulin receptor signaling pathway / heart development / RNA polymerase II-specific DNA-binding transcription factor binding / cell differentiation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / metal ion binding / nucleus
Similarity search - Function
Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Zinc-finger of C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein ush
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / molecular dynamics simulated annealing torsion angle dynamics
AuthorsLiew, C.K. / Kowalski, K. / Fox, A.H. / Newton, A. / Sharpe, B.K. / Crossley, M. / Mackay, J.P.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein-protein interactions.
Authors: Liew, C.K. / Kowalski, K. / Fox, A.H. / Newton, A. / Sharpe, B.K. / Crossley, M. / Mackay, J.P.
History
DepositionSep 14, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U-SHAPED TRANSCRIPTIONAL COFACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2402
Polymers4,1751
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide U-SHAPED TRANSCRIPTIONAL COFACTOR


Mass: 4174.862 Da / Num. of mol.: 1 / Fragment: NINTH ZINC-FINGER DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / References: UniProt: Q9VPQ6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
222HNHA
232HNHB
NMR detailsText: This structure was determined using a combination of 2D homonuclear and 3D 15N-heteronuclear techniques

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4mM U-shaped Finger 9; 0.6mM ZnSO4; 0.6mM TCEP; 95% H2O, 5% D2O95% H2O/5% D2O
20.2mM U-shaped Finger 9 U-15N; 0.3mM ZnSO4; 0.3mM TCEP; 95% D2O, 5% H2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.6mM ZnSO4 5.0 ambient 293 K
20.3mM ZnSO4 5.0 ambient 293 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alstructure solution
CNS0.5Brunger et alrefinement
RefinementMethod: molecular dynamics simulated annealing torsion angle dynamics
Software ordinal: 1
Details: The structures are based on a total of 535 restraints, 506 are NOE-derived distance constraints, 29 are dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20

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