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- PDB-1bbo: HIGH-RESOLUTION SOLUTION STRUCTURE OF THE DOUBLE CYS2*HIS2 ZINC F... -

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Entry
Database: PDB / ID: 1bbo
TitleHIGH-RESOLUTION SOLUTION STRUCTURE OF THE DOUBLE CYS2*HIS2 ZINC FINGER FROM THE HUMAN ENHANCER BINDING PROTEIN MBP-1
ComponentsHUMAN ENHANCER-BINDING PROTEIN MBP-1
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN
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. / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type ...Zinc finger CCHC HIVEP-type / Zinc finger CCHC HIVEP-type profile. / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein 40
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Omichinski, J.G. / Gronenborn, A.M.
CitationJournal: Biochemistry / Year: 1992
Title: High-resolution solution structure of the double Cys2His2 zinc finger from the human enhancer binding protein MBP-1.
Authors: Omichinski, J.G. / Clore, G.M. / Robien, M. / Sakaguchi, K. / Appella, E. / Gronenborn, A.M.
History
DepositionMay 1, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
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_keywords / 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.pdbx_leaving_atom_flag / _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_keywords.text / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id

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Structure visualization

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Assembly

Deposited unit
A: HUMAN ENHANCER-BINDING PROTEIN MBP-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9053
Polymers6,7741
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)60 / -
Representative

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Components

#1: Protein HUMAN ENHANCER-BINDING PROTEIN MBP-1


Mass: 6774.106 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.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other

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Processing

RefinementSoftware ordinal: 1
Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE JRNL REFERENCE ABOVE. THE STRUCTURES ARE BASED ON 1135 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE ...Details: DETAILS OF THE STRUCTURE DETERMINATION AND ALL STRUCTURAL STATISTICS ARE GIVEN IN THE JRNL REFERENCE ABOVE. THE STRUCTURES ARE BASED ON 1135 INTERPROTON DISTANCE RESTRAINTS DERIVED FROM NOE MEASUREMENTS; AND 55 PHI, 44 PSI AND 45 CHI1 TORSION ANGLE RESTRAINTS DERIVED FROM COUPLING CONSTANTS AND NOE DATA, USING THE CONFORMATIONAL GRID SEARCH PROGRAM STEREOSEARCH (M. NILGES, G. M. CLORE, AND A. M. GRONENBORN, (1990) BIOPOLYMERS 29, 813. THE METHOD USED TO DETERMINE THE STRUCTURES IS THE HYBRID METRIC MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (M. NILGES, G. M. CLORE, AND A. M. GRONENBORN, FEBS LETT. 229, 317-324 (1988)). A TOTAL OF 30 STRUCTURES WERE CALCULATED. AS THERE IS SOME UNCERTAINTY IN THE EXACT ORIENTATION OF THE N- AND C- TERMINAL FINGERS RELATIVE TO EACH OTHER, THE COORDINATES ARE PRESENTED TWICE. IN MODELS 1 THROUGH 30, THE COORDINATES ARE BEST FITTED TO THE N-TERMINAL DOMAIN (RESIDUES 2 - 28). IN MODELS 31 THROUGH 60, THE COORDINATES ARE BEST FITTED TO THE C-TERMINAL DOMAIN (RESIDUES 27 - 55). THE ANGLE BETWEEN THE LONG AXES OF THE HELICES (RESIDUES 13 - 25 AND 41 - 55 FROM THE N- AND C- TERMINAL FINGERS, RESPECTIVELY) ADOPT A RANGE OF VALUES CENTERED AROUND A MEAN OF 47 DEGREES WITH A STANDARD DEVIATION OF +/- 5 DEGREES. CONSEQUENTLY, NO AVERAGE STRUCTURE IS GIVEN. THE NUMBERS IN LAST COLUMN IN THE COORDINATE FILES HAVE NO MEANING. ALL THE INTERPROTON DISTANCE AND TORSION ANGLE RESTRAINTS ARE INCLUDED HERE AS A SEPARATE FILE: MBP_EXPT_DATA.DAT
NMR ensembleConformers submitted total number: 60

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