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- PDB-4yj0: Crystal structure of the DM domain of human DMRT1 bound to 25mer ... -

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Basic information

Entry
Database: PDB / ID: 4yj0
TitleCrystal structure of the DM domain of human DMRT1 bound to 25mer target DNA
Components
  • (DNA (25-MER)) x 2
  • Doublesex- and mab-3-related transcription factor 1
KeywordsTRANSCRIPTION / Transcription factor / Protein-DNA Complex / double Zn-finger
Function / homology
Function and homology information


regulation of nodal signaling pathway / Sertoli cell differentiation / negative regulation of meiotic nuclear division / male sex differentiation / male germ cell proliferation / positive regulation of meiosis I / positive regulation of male gonad development / Sertoli cell development / chromatin => GO:0000785 / germ cell migration ...regulation of nodal signaling pathway / Sertoli cell differentiation / negative regulation of meiotic nuclear division / male sex differentiation / male germ cell proliferation / positive regulation of meiosis I / positive regulation of male gonad development / Sertoli cell development / chromatin => GO:0000785 / germ cell migration / male sex determination / oocyte development / cis-regulatory region sequence-specific DNA binding / positive regulation of mitotic nuclear division / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell morphogenesis / sequence-specific double-stranded DNA binding / spermatogenesis / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / identical protein binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Doublesex- and mab-3-related transcription factor 1-like / Double-sex mab3 related transcription factor 1 / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif
Similarity search - Domain/homology
DNA / DNA (> 10) / Doublesex- and mab-3-related transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.814 Å
AuthorsMurphy, M.W. / Lee, J.K. / Rojo, S. / Gearhart, M.D. / Kurahashi, K. / Banerjee, S. / Loeuille, G. / Bashamboo, A. / McElreavey, K. / Zarkower, D. ...Murphy, M.W. / Lee, J.K. / Rojo, S. / Gearhart, M.D. / Kurahashi, K. / Banerjee, S. / Loeuille, G. / Bashamboo, A. / McElreavey, K. / Zarkower, D. / Aihara, H. / Bardwell, V.J.
Funding support United States, France, 7items
OrganizationGrant numberCountry
National Institutes of HealthGM59152 United States
National Institutes of HealthGM50399 United States
National Institutes of HealthAI087098 United States
National Institutes of HealthGM095558 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)P41 GM103403 United States
COSAction DSDnet BM1303 France
Institut PasteurProgram Blanc Assistance Publique France
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: An ancient protein-DNA interaction underlying metazoan sex determination.
Authors: Murphy, M.W. / Lee, J.K. / Rojo, S. / Gearhart, M.D. / Kurahashi, K. / Banerjee, S. / Loeuille, G.A. / Bashamboo, A. / McElreavey, K. / Zarkower, D. / Aihara, H. / Bardwell, V.J.
History
DepositionMar 2, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 27, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Doublesex- and mab-3-related transcription factor 1
B: Doublesex- and mab-3-related transcription factor 1
C: Doublesex- and mab-3-related transcription factor 1
D: DNA (25-MER)
E: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,20811
Polymers39,8165
Non-polymers3926
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10030 Å2
ΔGint-93 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.185, 138.926, 141.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Doublesex- and mab-3-related transcription factor 1 / DM domain expressed in testis protein 1


Mass: 8153.620 Da / Num. of mol.: 3 / Fragment: residues 70-131
Source method: isolated from a genetically manipulated source
Details: SPRLPKCARCRNHGYASPLKGHKRFCMWRDCQCKKCNLIAERQRVMAAQVALRRQQAQEEEL
Source: (gene. exp.) Homo sapiens (human) / Gene: DMRT1, DMT1 / Plasmid: peSUMOPRO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y5R6
#2: DNA chain DNA (25-MER)


Mass: 7703.981 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (25-MER)


Mass: 7650.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 5.14 Å3/Da / Density % sol: 76.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M BitsTris pH 7.5, 10% MPD, 7-11% PEG 3350, 10uM zinc chloride
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.23 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 13, 2011
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23 Å / Relative weight: 1
ReflectionResolution: 3.814→49.897 Å / Num. all: 8170 / Num. obs: 8170 / % possible obs: 98.59 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 128.7 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 9.5
Reflection shellResolution: 3.81→4.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.94 / Mean I/σ(I) obs: 1.9 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIXdev_1801refinement
SCALAdata scaling
PDB_EXTRACT3.15data extraction
RESOLVEphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 3.814→34.731 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 3.87 / Phase error: 31.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 809 9.9 %Random selection
Rwork0.2289 ---
obs0.2323 8170 98.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.814→34.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1509 1019 6 0 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042675
X-RAY DIFFRACTIONf_angle_d0.8953803
X-RAY DIFFRACTIONf_dihedral_angle_d25.2891111
X-RAY DIFFRACTIONf_chiral_restr0.032403
X-RAY DIFFRACTIONf_plane_restr0.021348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8137-4.05230.39361240.3561135X-RAY DIFFRACTION94
4.0523-4.36470.32781340.30331224X-RAY DIFFRACTION100
4.3647-4.80290.28981350.26761223X-RAY DIFFRACTION100
4.8029-5.49550.29241360.26111250X-RAY DIFFRACTION100
5.4955-6.91480.28821410.23511247X-RAY DIFFRACTION100
6.9148-34.73290.18851390.15921282X-RAY DIFFRACTION97

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