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- PDB-6fx5: MITF dimerization mutant -

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Basic information

Entry
Database: PDB / ID: 6fx5
TitleMITF dimerization mutant
ComponentsMicrophthalmia-associated transcription factor
KeywordsTRANSCRIPTION / melanocytes / bHLHZip / autophagy
Function / homology
Function and homology information


melanocyte apoptotic process / SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of DNA-templated transcription initiation / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation ...melanocyte apoptotic process / SUMOylation of transcription factors / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of DNA-templated transcription initiation / Transcriptional and post-translational regulation of MITF-M expression and activity / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / pigmentation / E-box binding / cell fate commitment / osteoclast differentiation / negative regulation of cell migration / Wnt signaling pathway / regulation of cell population proliferation / regulation of gene expression / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / cell differentiation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / lysosomal membrane / DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleus / cytoplasm
Similarity search - Function
MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain ...MiT/TFE transcription factors, C-terminal / MiT/TFE transcription factors, N-terminal / Domain of unknown function (DUF3371) / MITF/TFEB/TFEC/TFE3 N-terminus / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPogenberg, V. / Milewski, M. / Wilmanns, M.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mechanism of conditional partner selectivity in MITF/TFE family transcription factors with a conserved coiled coil stammer motif.
Authors: Pogenberg, V. / Ballesteros-Alvarez, J. / Schober, R. / Sigvaldadottir, I. / Obarska-Kosinska, A. / Milewski, M. / Schindl, R. / Ogmundsdottir, M.H. / Steingrimsson, E. / Wilmanns, M.
History
DepositionMar 8, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microphthalmia-associated transcription factor
B: Microphthalmia-associated transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0684
Polymers18,8762
Non-polymers1922
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-42 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.720, 92.830, 86.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-412-

HOH

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Components

#1: Protein Microphthalmia-associated transcription factor


Mass: 9437.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Mitf, Bw, Mi, Vit / Production host: Escherichia coli (E. coli) / References: UniProt: Q08874
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: Crystals grew in conditions between 2.0 M and 2.4 M Ammonium sulfate and 0.1 and 0.15 M Cadmium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.05→33.045 Å / Num. obs: 9762 / % possible obs: 96.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.6 Å2 / CC1/2: 0.99 / Rsym value: 0.108 / Net I/σ(I): 7.8
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 987 / CC1/2: 0.88 / Rsym value: 0.303 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ath

4ath


Resolution: 2.05→33.045 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.32
RfactorNum. reflection% reflection
Rfree0.2463 886 9.08 %
Rwork0.2236 --
obs0.2258 9762 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→33.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1181 0 10 33 1224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171202
X-RAY DIFFRACTIONf_angle_d1.3851614
X-RAY DIFFRACTIONf_dihedral_angle_d20.198475
X-RAY DIFFRACTIONf_chiral_restr0.105179
X-RAY DIFFRACTIONf_plane_restr0.009210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.17850.32261460.25261482X-RAY DIFFRACTION98
2.1785-2.34670.29911400.24021463X-RAY DIFFRACTION97
2.3467-2.58270.29811580.23441466X-RAY DIFFRACTION96
2.5827-2.95630.26351620.23711467X-RAY DIFFRACTION96
2.9563-3.72380.2241220.21491494X-RAY DIFFRACTION95
3.7238-33.04920.21341580.2131504X-RAY DIFFRACTION93

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