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- PDB-1hrz: THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTI-DIM... -

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Basic information

Entry
Database: PDB / ID: 1hrz
TitleTHE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND-FILTERED NMR
Components
  • DNA (5'-D(*GP*CP*AP*CP*AP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*TP*GP*TP*GP*C)-3')
  • HUMAN SRY
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / male sex determination / anatomical structure morphogenesis / Deactivation of the beta-catenin transactivating complex / DNA-binding transcription factor binding / cell differentiation / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific ...positive regulation of male gonad development / Transcriptional regulation of testis differentiation / sex differentiation / male sex determination / anatomical structure morphogenesis / Deactivation of the beta-catenin transactivating complex / DNA-binding transcription factor binding / cell differentiation / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / positive regulation of gene expression / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor SRY / High mobility group box domain / DNA Binding (I), subunit A / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Sex-determining region Y protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Werner, M.H. / Huth, J.R. / Gronenborn, A.M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1995
Title: Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex.
Authors: Werner, M.H. / Huth, J.R. / Gronenborn, A.M. / Clore, G.M.
History
DepositionMay 9, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*GP*CP*AP*CP*AP*AP*AP*C)-3')
C: DNA (5'-D(*GP*TP*TP*TP*GP*TP*GP*C)-3')
A: HUMAN SRY


Theoretical massNumber of molelcules
Total (without water)14,3613
Polymers14,3613
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / -
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*CP*AP*CP*AP*AP*AP*C)-3')


Mass: 2404.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*GP*TP*TP*TP*GP*TP*GP*C)-3')


Mass: 2448.613 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein HUMAN SRY


Mass: 9508.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q05066

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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 / Details: NMR

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementSoftware ordinal: 1
Details: THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 1805 EXPERIMENTAL RESTRAINTS: (A) INTRA-PROTEIN: 290 SEQUENTIAL ...Details: THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON 1805 EXPERIMENTAL RESTRAINTS: (A) INTRA-PROTEIN: 290 SEQUENTIAL (|I-J|=1), 221 MEDIUM RANGE (1 < |I-J| >=5) AND 107 LONG RANGE (|I-J| >5) INTERRESIDUES. 238 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; 70 DISTANCE RESTRAINTS FOR 35 HYDROGEN BONDS; 153 TORSION ANGLE (71 PHI, 10 PSI, 56 CHI1 AND 16 CHI2) RESTRAINTS; 56 THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; 145 (73 CALPHA AND 72 CBETA) 13C SHIFT RESTRAINTS. (B) INTRA-DNA: 206 INTRARESIDUE, 96 SEQUENTIAL INTRASTRAND, 36 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 40 H-BOND RESTRAINTS; 72 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA, GAMMA, EPSILON AND ZETA BACKBONE TORSION ANGLES. (C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS THE STRUCTURES IN THIS ENTRY REPRESENT 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES. THE RESTRAINED REGULARIZED MEAN STRUCTURE CAN BE FOUND IN PDB ENTRY 1HRY. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING.
NMR ensembleConformers submitted total number: 35

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