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- PDB-5znf: ALTERNATING ZINC FINGERS IN THE HUMAN MALE ASSOCIATED PROTEIN ZFY... -

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Basic information

Entry
Database: PDB / ID: 5znf
TitleALTERNATING ZINC FINGERS IN THE HUMAN MALE ASSOCIATED PROTEIN ZFY: 2D NMR STRUCTURE OF AN EVEN FINGER AND IMPLICATIONS FOR "JUMPING-LINKER" DNA RECOGNITION
ComponentsZINC FINGER
KeywordsZINC FINGER DNA BINDING DOMAIN
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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsKochoyan, M. / Keutmann, H.T. / Weiss, M.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition.
Authors: Kochoyan, M. / Havel, T.F. / Nguyen, D.T. / Dahl, C.E. / Keutmann, H.T. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 1991
Title: Alternating Zinc Fingers in the Human Male Associated Protein Zfy: Refinement of the NMR Structure of an Even Finger by Selective Deuterium Labeling and Implications for DNA Recognition
Authors: Kochoyan, M. / Keutmann, H.T. / Weiss, M.A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Architectural Rules of the Zinc-Finger Motif: Comparative Two-Dimensional NMR Studies of Native and "Aromatic-Swap" Domains Define a "Weakly Polar Switch"
Authors: Kochoyan, M. / Keutmann, H.T. / Weiss, M.A.
History
DepositionAug 22, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: 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

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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)3,6802
Polymers3,6151
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)13 / -
Representative

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Components

#1: Protein/peptide ZINC FINGER /


Mass: 3615.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) 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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
DGIIHAVELrefinement
X-PLORBRUNGERrefinement
NMR ensembleConformers submitted total number: 13

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