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- PDB-9h5h: MITF in complex with 1-(phenylethynyl)cyclohexan-1-ol -

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Basic information

Entry
Database: PDB / ID: 9h5h
TitleMITF in complex with 1-(phenylethynyl)cyclohexan-1-ol
ComponentsIsoform M1 of Microphthalmia-associated transcription factor
KeywordsTRANSCRIPTION / transcription factor / regulator of melanocyte survival
Function / homology
Function and homology information


melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / regulation of RNA biosynthetic process / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of osteoclast differentiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / melanocyte differentiation ...melanocyte apoptotic process / Regulation of MITF-M dependent genes involved in invasion / Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy / positive regulation of DNA-templated transcription initiation / Regulation of MITF-M dependent genes involved in metabolism / regulation of RNA biosynthetic process / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / regulation of osteoclast differentiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / melanocyte differentiation / bone remodeling / camera-type eye development / Regulation of MITF-M-dependent genes involved in apoptosis / E-box binding / Regulation of MITF-M-dependent genes involved in pigmentation / SUMOylation of transcription factors / cell fate commitment / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / osteoclast differentiation / negative regulation of cell migration / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / regulation of cell population proliferation / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / lysosomal membrane / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / 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 / nucleoplasm / nucleus / cytoplasm / cytosol
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 / 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
Similarity search - Domain/homology
: / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsRenatus, M. / Wirth, E. / Gutmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: MITF in complex with 1-(phenylethynyl)cyclohexan-1-ol
Authors: Jahnke, W. / Renatus, M.
History
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform M1 of Microphthalmia-associated transcription factor
B: Isoform M1 of Microphthalmia-associated transcription factor
C: Isoform M1 of Microphthalmia-associated transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,40010
Polymers29,6413
Non-polymers7597
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.353, 90.353, 82.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

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Components

#1: Protein Isoform M1 of Microphthalmia-associated transcription factor / Class E basic helix-loop-helix protein 32 / bHLHe32


Mass: 9880.433 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MITF, BHLHE32 / Production host: Escherichia coli (E. coli) / References: UniProt: O75030
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-A1ISF / 1-(2-phenylethynyl)cyclohexan-1-ol


Mass: 200.276 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.2 M ammonium sulfate, 5 % (v/v) PEG 400, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0000096 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0000096 Å / Relative weight: 1
ReflectionResolution: 1.731→64.018 Å / Num. obs: 31365 / % possible obs: 95.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 37.86 Å2 / CC1/2: 1 / Rpim(I) all: 0.013 / Net I/σ(I): 23.2
Reflection shellResolution: 1.731→1.826 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1568 / CC1/2: 0.712 / Rpim(I) all: 0.451

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→50.51 Å / SU ML: 0.2214 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.6322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1420 5 %
Rwork0.2238 26991 -
obs0.2254 28411 79.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.6 Å2
Refinement stepCycle: LAST / Resolution: 1.74→50.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 44 89 1677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691669
X-RAY DIFFRACTIONf_angle_d0.74232235
X-RAY DIFFRACTIONf_chiral_restr0.0487231
X-RAY DIFFRACTIONf_plane_restr0.0062293
X-RAY DIFFRACTIONf_dihedral_angle_d14.2252696
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0923917248-2.02922676023-1.963472539931.255163205131.523682853261.50764595477-0.005950844107970.0510703358957-0.282519524319-0.0767844172812-0.1295980977340.222507157135-0.02583488538490.03833040251120.1689963960380.249359399552-0.01630321991740.04926119213630.248133096698-0.06540720275820.33434088545815.72322269697.046616708619.27041212414
25.23152588817-1.67089349605-4.51955908639-0.05146371489951.271415076123.308663675140.123456465704-0.09467355752640.312254686749-0.09539035997770.0907540073501-0.01452695054660.04759953827130.135146690693-0.2445279041680.311037476266-0.004312224040690.0870426684330.315397155746-0.005635206089810.3698177440815.10744680295.6826907420712.0899936001
33.736050021340.8602136649950.7587326595615.27658881731-0.8941705801354.07156202637-0.279831243962-0.771308365883-0.004554257030210.5757378150160.02846665062730.3008377055350.2486465101740.3004442013830.1431551745520.2903242466070.007394141687420.02336113068680.1932344524740.008228285183860.084539442621437.3460363524-5.312985159523.38360086208
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA219 - 2921 - 74
22chain BBB219 - 2931 - 75
33chain CCC262 - 2951 - 34

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