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- PDB-1j46: 3D Solution NMR Structure of the Wild Type HMG-BOX Domain of the ... -

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Entry
Database: PDB / ID: 1j46
Title3D Solution NMR Structure of the Wild Type HMG-BOX Domain of the Human Male Sex Determining Factor Sry Complexed to DNA
Components
  • 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3'
  • 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)-3'
  • SEX-DETERMINING REGION Y PROTEIN
KeywordsTRANSCRIPTION/DNA / MALE SEX DETERMINING FACTOR / SRY / SEX-REVERSAL MUTATION / DNA BENDING MUTANT / DIPOLAR COUPLINGS / MULTIDIMENSIONAL NMR / TRANSCRIPTION-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 / DNA (> 10) / Sex-determining region Y protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsClore, G.M. / Murphy, E.C.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation.
Authors: Murphy, E.C. / Zhurkin, V.B. / Louis, J.M. / Cornilescu, G. / Clore, G.M.
History
DepositionJul 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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
B: 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3'
C: 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)-3'
A: SEX-DETERMINING REGION Y PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,2163
Polymers19,2163
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)1 / 400RESTRAINED REGULARIZED MEAN STRUCTURE
Representative

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Components

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


Mass: 4178.747 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)-3'


Mass: 4382.835 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein SEX-DETERMINING REGION Y PROTEIN / SRY


Mass: 10654.570 Da / Num. of mol.: 1 / Fragment: HMG-BOX DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q05066

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) DOUBLE RESONANCE AND HETERONUCLEAR FILTERED FOR DNA; (3) QUANTITATIVE J CORRELATION FOR ...Text: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) DOUBLE RESONANCE AND HETERONUCLEAR FILTERED FOR DNA; (3) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (4) 2D, 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPERIMENTS; (4) 2D and 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS FOR DIPOLAR COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF 4.5-5% 3:1 DMPC:DHPC

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Sample preparation

Sample conditionsIonic strength: 50 mM SODIUM PHOSPHATE / pH: 7.2 / Temperature: 308.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DRX600BrukerDRX6006002
Bruker DRX750BrukerDRX7507503

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Processing

NMR softwareName: X-PLOR NIH VERSION (HTTP://NMR.CIT.NIH.GOV) / Version: (HTTP://NMR.CIT.NIH.GOV) / Developer: CLORE, KUSZEWSKI, SCHWIETERS / Classification: refinement
RefinementSoftware ordinal: 1
Details: THE STRUCTURE WAS CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. J. MAGN. RESON., IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR NOE RESTRAINTS, ...Details: THE STRUCTURE WAS CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. J. MAGN. RESON., IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL SHIFT RESTRAINTS (KUSZWESKI ET AL. J. MAGN. RESON. SERIES B 106, 92-96 (1995), J COUPLING RESTRAINTS (GARRETT ET AL. J. MAGN. RESON. SERIES B 104, 99, 103 (1994); DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998); J.MAGN.RESON. 133, 216-221(1998)), AND RADIUS OF GYRATION (KUSZEWSKI ET AL. JACS 121, 2337 (1999)). THE NON-BONDED CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-136); THE DELPHIC TORSION ANGLE DATABASE POTENTIAL (KUSZEWSKI & C J. MAGN. RESON. 146, 249 (2000)); AND THE DELPHIC BASE-BASE POSITIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. JACS 123, 3903 (2001)). IN THIS ENTRY THE SECOND TO LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES (400 FOR THE WILD TYPE COMPLEX) AND THE MEAN COORDINATE POSITIONS (OBTAINED BY BEST FITTING TO RESIDUES 4-81 OF THE PROTEIN AND 101-128 OF THE DNA). WILD TYPE M9I MUTANT PDB ID: 1J46 1J47 DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.003 A 0.003 A ANGLES 0.81 DEG 0.80 DEG IMPROPERS 0.79 DEG 0.79 DEG DEVIATIONS FROM EXPT RESTRAINTS NOES (1795/1693) 0.04 A 0.03 A TORSION ANGLES (433/429) 0.29 DEG 0.30 DEG 3JHNA COUPLINGS (70/66) 0.84 HZ 0.90 HZ 13C CHEMICAL SHIFTS (165/165) 0.99 PPM 0.95 PPM HETERONUCLEAR DIPOLAR COUPLING R-FACTORS (CLORE AND GARRETT J. AM. CHEM. SOC. 121, 9008-9012): PROTEIN 1DNH (71/66) 5.5% 7.6% PROTEIN 1DCH (67/67) 6.3% 10.0% PROTEIN 1DNC' (68/62) 18.9% 28.9% PROTEIN 2DHNC'(68/62) 18.8% 21.6% DNA 1DNH (9/10) 10.2% 16.1% DNA 1DCH (37/33) 11.2% 10.7% DNA 1H-1H DIPOLAR COUPLINGS (55/53) 0.56 HZ 0.75 HZ % RESIDUES IN MOST FAVORABLE REGION OF RAMACHADRAN MAP 94.7% 94.7%
NMR ensembleConformer selection criteria: RESTRAINED REGULARIZED MEAN STRUCTURE
Conformers calculated total number: 400 / Conformers submitted total number: 1

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