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- PDB-1n0z: Solution structure of the first zinc-finger domain from ZNF265 -

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Basic information

Entry
Database: PDB / ID: 1n0z
TitleSolution structure of the first zinc-finger domain from ZNF265
ComponentsZNF265
KeywordsTRANSCRIPTION / zinc finger / RNA splicing
Function / homology
Function and homology information


RNA splicing / lipopolysaccharide binding / mRNA processing / RNA binding / nucleoplasm / metal ion binding
Similarity search - Function
Zinc finger, RanBP2-type / Zinc finger Ran-binding domain-containing protein 2 / ZNF265 like / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Zinc finger Ran-binding domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsPlambeck, C.A. / Fairley, K. / Kwan, A.H.Y. / Westman, B.J. / Adams, D. / Morris, B. / Mackay, J.P.
CitationJournal: J.BIOL.CHEM. / Year: 2003
Title: The structure of the zinc finger domain from human splicing factor ZNF265 fold
Authors: Plambeck, C.A. / Kwan, A.H.Y. / Adams, D.J. / Westman, B.J. / van der Weyden, L. / Medcalf, R.L. / Morris, B.J. / Mackay, J.P.
History
DepositionOct 15, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ZNF265
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0702
Polymers5,0051
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide ZNF265 / Zinc finger protein 265


Mass: 5004.670 Da / Num. of mol.: 1 / Fragment: ZNF265-F1 / Mutation: N34D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF265 / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: O95218
#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
1212D TOCSY
131DQF-COSY
141Short mixing time NOESY
151Short mixing time TOCSY
NMR detailsText: The structure was determined using standard 2D NMR homonuclear techniques.

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Sample preparation

DetailsContents: 1mM ZNF265-F1, 2mM TCEP, 1.7mM ZnZO4 / Solvent system: 95% H2O/5% D2O
Sample conditionspH: 5.8 / Pressure: ambient / Temperature: 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 spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.2Linge et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: Structure calculations were performed using the package ARIA1.2 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 709 unambiguous NOE-derived distance ...Details: Structure calculations were performed using the package ARIA1.2 (Ambiguous Restraints in Iterative Assignment). Final structures are based on 709 unambiguous NOE-derived distance constraints, 14 sets of ambiguous NOE-derived distance constraints and 22 additional dihedral angle restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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