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- PDB-3znf: HIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF A SINGLE ZINC FING... -

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Entry
Database: PDB / ID: 3znf
TitleHIGH-RESOLUTION THREE-DIMENSIONAL STRUCTURE OF A SINGLE ZINC FINGER FROM A HUMAN ENHANCER BINDING PROTEIN IN SOLUTION
ComponentsZINC FINGER
KeywordsZINC FINGER DNA BINDING DOMAIN
Function / homology
Function and homology information


BMP signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion ...BMP signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Zinc finger CCHC HIVEP-type / Zinc finger CCHC HIVEP-type profile. / 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 protein 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsGronenborn, A.M. / Clore, G.M. / Omichinski, J.G.
CitationJournal: Biochemistry / Year: 1990
Title: High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution.
Authors: Omichinski, J.G. / Clore, G.M. / Appella, E. / Sakaguchi, K. / Gronenborn, A.M.
History
DepositionJul 9, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_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_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
A: ZINC FINGER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6352
Polymers3,5691
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Atom site foot note1: THE C-TERMINAL TWO RESIDUES, LYS 29 AND LYS 30, ARE ILL-DEFINED.
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein/peptide ZINC FINGER


Mass: 3569.212 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P15822
#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

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Processing

RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF THE ZINC FINGER IN SOLUTION BY NMR IS BASED ON 487 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS AND 63 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT ...Details: THE 3D STRUCTURE OF THE ZINC FINGER IN SOLUTION BY NMR IS BASED ON 487 APPROXIMATE INTERPROTON DISTANCE RESTRAINTS AND 63 TORSION ANGLE RESTRAINTS DERIVED FROM NOE AND COUPLING CONSTANT MEASUREMENTS. THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD DESCRIBED BY M. NILGES, G. M. CLORE, AND A. M. GRONENBORN (1988) FEBS LETT 229, 317. THIS ENTRY REPRESENTS THE RESTRAINED MINIMIZED AVERAGE STRUCTURE (SA)$R DERIVED BY RESTRAINED LEAST SQUARE REFINEMENT OF THE MEAN STRUCTURE OBTAINED BY AVERAGING THE COORDINATES OF THE FINAL 41 SA STRUCTURES BEST FITTED TO EACH OTHER. THE ENTIRE SET OF 41 MODELS CAN BE FOUND IN PDB ENTRY 4ZNF. THE FIELD IN THIS ENTRY THAT OCCUPIES COLUMNS 61 - 66 (RESERVED FOR B-VALUES IN X-RAY CRYSTALLOGRAPHIC ENTRIES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE.
NMR ensembleConformers submitted total number: 1

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