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- PDB-6g1l: MITF/CLEARbox structure -

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Basic information

Entry
Database: PDB / ID: 6g1l
TitleMITF/CLEARbox structure
Components
  • CLEAR-box
  • Microphthalmia-associated transcription factor
KeywordsTRANSCRIPTION / melanocyte / autophagy / transcription factor / DNA binding
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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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 / nucleoplasm / 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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...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 domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
DNA / DNA (> 10) / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPogenberg, V. / Wilmanns, M.
CitationJournal: Sci Rep / Year: 2019
Title: MITF has a central role in regulating starvation-induced autophagy in melanoma.
Authors: Moller, K. / Sigurbjornsdottir, S. / Arnthorsson, A.O. / Pogenberg, V. / Dilshat, R. / Fock, V. / Brynjolfsdottir, S.H. / Bindesboll, C. / Bessadottir, M. / Ogmundsdottir, H.M. / Simonsen, A. ...Authors: Moller, K. / Sigurbjornsdottir, S. / Arnthorsson, A.O. / Pogenberg, V. / Dilshat, R. / Fock, V. / Brynjolfsdottir, S.H. / Bindesboll, C. / Bessadottir, M. / Ogmundsdottir, H.M. / Simonsen, A. / Larue, L. / Wilmanns, M. / Thorsson, V. / Steingrimsson, E. / Ogmundsdottir, M.H.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Microphthalmia-associated transcription factor
B: CLEAR-box


Theoretical massNumber of molelcules
Total (without water)19,2502
Polymers19,2502
Non-polymers00
Water30617
1
A: Microphthalmia-associated transcription factor
B: CLEAR-box

A: Microphthalmia-associated transcription factor
B: CLEAR-box


Theoretical massNumber of molelcules
Total (without water)38,5004
Polymers38,5004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-y+1/2,z1
Buried area7140 Å2
ΔGint-45 kcal/mol
Surface area14930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.091, 103.858, 112.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein Microphthalmia-associated transcription factor


Mass: 14352.553 Da / Num. of mol.: 1
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: DNA chain CLEAR-box


Mass: 4897.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.36 Å3/Da / Density % sol: 63.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.9 M Sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.4→41.07 Å / Num. obs: 10459 / % possible obs: 99.5 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1087 / CC1/2: 0.604 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ati

4ati


Resolution: 2.4→40.585 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.81
RfactorNum. reflection% reflection
Rfree0.2529 460 4.4 %
Rwork0.2148 --
obs0.2164 10448 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms663 325 0 17 1005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081034
X-RAY DIFFRACTIONf_angle_d0.8561454
X-RAY DIFFRACTIONf_dihedral_angle_d29.478433
X-RAY DIFFRACTIONf_chiral_restr0.043156
X-RAY DIFFRACTIONf_plane_restr0.005137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.74720.32631600.29563277X-RAY DIFFRACTION99
2.7472-3.4610.26721360.24563305X-RAY DIFFRACTION100
3.461-40.59090.23481640.19013406X-RAY DIFFRACTION99

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