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Basic information

Entry
Database: PDB / ID: 9h5f
TitleMITF(217-296)
ComponentsIsoform M1 of Microphthalmia-associated transcription factor
KeywordsTRANSCRIPTION / Microphthalmia-associated transcription factor
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: 2.3 Å
AuthorsRenatus, M. / Wirth, E. / Gutmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of microphthalmia-associated transcription factor MTID(217-296)
Authors: Jahnke, W. / Renatus, M. / Wirth, E.
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)29,9296
Polymers29,6413
Non-polymers2883
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.640, 90.640, 82.773
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

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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.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.87 Å3/Da / Density % sol: 57.11 %
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: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.3→64.092 Å / Num. obs: 15627 / % possible obs: 98.5 % / Redundancy: 13 % / Biso Wilson estimate: 40.69 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 749 / CC1/2: 0.874 / Rpim(I) all: 0.244

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→64.09 Å / SU ML: 0.2886 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 749 4.8 %
Rwork0.2306 14871 -
obs0.2318 15620 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.83 Å2
Refinement stepCycle: LAST / Resolution: 2.3→64.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 15 51 1592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00111576
X-RAY DIFFRACTIONf_angle_d0.28882106
X-RAY DIFFRACTIONf_chiral_restr0.0301228
X-RAY DIFFRACTIONf_plane_restr0.0021278
X-RAY DIFFRACTIONf_dihedral_angle_d11.7384656
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.480.35271340.28342935X-RAY DIFFRACTION99.48
2.48-2.730.29761640.26612967X-RAY DIFFRACTION99.97
2.73-3.120.29911440.26892984X-RAY DIFFRACTION99.9
3.12-3.930.25441270.22252824X-RAY DIFFRACTION93.03
3.93-64.090.21951800.20383161X-RAY DIFFRACTION100
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)
13.10628688383-2.9425636077-2.159133807061.463175326011.402527400161.17815654976-0.07788738018930.182555290449-0.527140072105-0.0407415263963-0.1094468787470.3052248130350.08371258057250.0242616789880.1792347577230.311284656419-0.03577075486730.0694525743210.283104082633-0.09316858864180.41747205772714.9526972287.8636411373110.0312502142
24.95159019685-2.94442618964-4.606344490960.5797366455351.750104240283.073345402460.2295101523520.09416049203360.434042795213-0.14914027440.13591407181-0.114778757458-0.05696361024480.0171394076836-0.2702237329730.360612515141-0.05356415572360.08047264178470.417094547408-0.05657362980970.48263064095114.87519765885.9423260796512.0940589545
34.449316947540.16962429246-0.2044097473953.02644609057-0.19100576133.50956909866-0.107557281324-0.6487888417440.554479165930.394221697050.003955475911910.2090761605130.3505475423620.3711195569050.1067516663130.366743757697-0.01107607626910.05411289509450.261328405551-0.02586239769070.1884726647437.5383120239-5.333061451433.44355428579
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 BBB218 - 2931 - 76
33chain CCC263 - 2951 - 33

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