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- PDB-1klr: NMR Structure of the ZFY-6T[Y10F] Zinc Finger -

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Basic information

Entry
Database: PDB / ID: 1klr
TitleNMR Structure of the ZFY-6T[Y10F] Zinc Finger
ComponentsZINC FINGER Y-CHROMOSOMAL PROTEIN
KeywordsTRANSCRIPTION / Zinc Finger
Function / homology
Function and homology information


DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Transcriptional activator, Zfx / Zfy domain / Zfx / Zfy transcription activation region / C2H2-type zinc-finger domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger Y-chromosomal protein
Similarity search - Component
MethodSOLUTION NMR / Distance geometry, Simulated annealing, , restrained molecular dynamics.
AuthorsLachenmann, M.J. / Ladbury, J.E. / Phillips, N.B. / Narayana, N. / Qian, X. / Weiss, M.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: The hidden thermodynamics of a zinc finger.
Authors: Lachenmann, M.J. / Ladbury, J.E. / Phillips, N.B. / Narayana, N. / Qian, X. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 1992
Title: Two-dimensional NMR studies of the zinc finger motif: solution structures and dynamics of mutant ZFY domains containing aromatic substitutions in the hydrophobic core
Authors: Qian, X. / Weiss, M.A.
History
DepositionDec 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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
Remark 999sequence The mutation Y10F was created for structural studies. In addition, the P2T mutation and C- ...sequence The mutation Y10F was created for structural studies. In addition, the P2T mutation and C-terminal K, originally introduced in ZFY-6T (PDB entry 5ZNF) improve sample behavior without affecting structure.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ZINC FINGER Y-CHROMOSOMAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6642
Polymers3,5991
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 52structures with the least restraint violations
RepresentativeModel #14fewest violations

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Components

#1: Protein/peptide ZINC FINGER Y-CHROMOSOMAL PROTEIN


Mass: 3599.080 Da / Num. of mol.: 1 / Mutation: P2T, Y10F / Source method: obtained synthetically
Details: This peptide was synthesized by solid-phase synthesis. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: P08048
#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
1222D NOESY
131DQF-COSY
142DQF-COSY
2533D-TOCSY-NOESY
2632D-ROESY
2742D-ROESY
NMR detailsText: This structure was determined using 2D and 3D homonuclear techniques. This structure represents a refinement of the structure originally published in secondary citation #1 (Qian, X. and Weiss, ...Text: This structure was determined using 2D and 3D homonuclear techniques. This structure represents a refinement of the structure originally published in secondary citation #1 (Qian, X. and Weiss, M.A.). Additional constraints were determined using higher-concentration samples and by homonuclear 3D-NMR methods.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM ZFY-6T[Y10F]90% H2O/10% D2O
22mM ZFY-6T[Y10F]99.98% D2O.
35mM ZFY-6T[Y10F]90% H2O/10% D2O
45mM ZFY-6T[Y10F]99.98% D2O.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150mM d11-Tris-HCl, 2.2mM ZnCl2 6.0 ambient 298 K
250mM d11-Tris-HCl, 5.5mM ZnCl2 6.0 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VXRSVarianVXRS5001
Varian UNITYPLUSVarianUNITYPLUS5002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4.3-5.3Varian, Inc.collection
NHFITRedfield, C.data analysis
DGIIStandaloneHavel, T.F.structure solution
X-PLOR3.1Brunger, A.T.refinement
VNMR4.3-5.3Varian, Inc.processing
RefinementMethod: Distance geometry, Simulated annealing, , restrained molecular dynamics.
Software ordinal: 1
Details: Structures are based on 229 interresidue NOE-derived distance constraints, 24 dihedral angle restraints, and 10 hydrogen bond restraints.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 52 / Conformers submitted total number: 25

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