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Yorodumi- PDB-1hry: THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTID-DI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hry | ||||||
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Title | THE 3D STRUCTURE OF THE HUMAN SRY-DNA COMPLEX SOLVED BY MULTID-DIMENSIONAL HETERONUCLEAR-EDITED AND-FILTERED NMR | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / DNA / SRY / DNA-BINDING PROTEIN / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Clore, G.M. / Werner, M.H. / Huth, J.R. / Gronenborn, A.M. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hry.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hry.ent.gz | 37.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/1hry ftp://data.pdbj.org/pub/pdb/validation_reports/hr/1hry | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 2404.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Keywords: DEOXYRIBONUCLEIC ACID |
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#2: DNA chain | Mass: 2448.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized / Keywords: DEOXYRIBONUCLEIC ACID |
#3: Protein | Mass: 9508.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Keywords: POLYPEPTIDE / References: UniProt: Q05066 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: 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- ...Text: 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 |
-Sample preparation
Crystal grow | *PLUS Method: other / Details: NMR |
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-Processing
Software |
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NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | ||||||||||||
Refinement | Method: simulated annealing / Software ordinal: 1 Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 644 NUMBER OF NUCLEIC ACID ATOMS 322 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WERE CALCULATED USING ...Details: NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 644 NUMBER OF NUCLEIC ACID ATOMS 322 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99 - 103) AND CARBON CHEMICAL SHIFT RESTRAINTS (KUSZEWSKI ET AL. (1995) MAGN. RESON. SERIES B 106, 92 - 96). 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 STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE. THE LAST COLUMN REPRESENTS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE 35 INDIVIDUAL STRUCTURES CAN BE FOUND IN PDB ENTRY 1HRZ. THE LAST COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. | ||||||||||||
NMR constraints | NA other-angle constraints total count: 72 / NOE constraints total: 1805 / NOE intraresidue total count: 444 / NOE long range total count: 107 / NOE medium range total count: 221 / NOE sequential total count: 386 / Hydrogen bond constraints total count: 40 / Protein chi angle constraints total count: 72 / Protein other angle constraints total count: 271 / Protein phi angle constraints total count: 71 / Protein psi angle constraints total count: 10 | ||||||||||||
NMR ensemble | Conformers submitted total number: 1 |