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- PDB-7d8t: MITF bHLHLZ complex with M-box DNA -

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Basic information

Entry
Database: PDB / ID: 7d8t
TitleMITF bHLHLZ complex with M-box DNA
Components
  • DNA (5'-D(*TP*GP*TP*AP*AP*CP*AP*TP*GP*TP*GP*TP*CP*CP*CP*C)-3')
  • DNA (5'-D(P*GP*GP*GP*AP*CP*AP*CP*AP*TP*GP*TP*TP*AP*CP*AP*G)-3')
  • Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION FACTOR / TRANSCRIPTION / TRANSCRIPTION-DNA complex
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 / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition ...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 / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / 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 / tRNA binding / 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 / ATP binding / 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 / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / MYOD Basic-Helix-Loop-Helix Domain, subunit B / tRNA-binding domain / Putative tRNA binding 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 / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / MYOD Basic-Helix-Loop-Helix Domain, subunit B / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / 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 / Nucleic acid-binding proteins / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Methionine--tRNA ligase / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsGuo, M. / Fang, P. / Wang, J.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21778064 China
National Natural Science Foundation of China (NSFC)21778067 China
National Natural Science Foundation of China (NSFC)21977108 China
National Natural Science Foundation of China (NSFC)21977107 China
CitationJournal: Cell Res. / Year: 2023
Title: A unique hyperdynamic dimer interface permits small molecule perturbation of the melanoma oncoprotein MITF for melanoma therapy.
Authors: Liu, Z. / Chen, K. / Dai, J. / Xu, P. / Sun, W. / Liu, W. / Zhao, Z. / Bennett, S.P. / Li, P. / Ma, T. / Lin, Y. / Kawakami, A. / Yu, J. / Wang, F. / Wang, C. / Li, M. / Chase, P. / Hodder, ...Authors: Liu, Z. / Chen, K. / Dai, J. / Xu, P. / Sun, W. / Liu, W. / Zhao, Z. / Bennett, S.P. / Li, P. / Ma, T. / Lin, Y. / Kawakami, A. / Yu, J. / Wang, F. / Wang, C. / Li, M. / Chase, P. / Hodder, P. / Spicer, T.P. / Scampavia, L. / Cao, C. / Pan, L. / Dong, J. / Chen, Y. / Yu, B. / Guo, M. / Fang, P. / Fisher, D.E. / Wang, J.
History
DepositionOct 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(P*GP*GP*GP*AP*CP*AP*CP*AP*TP*GP*TP*TP*AP*CP*AP*G)-3')
D: DNA (5'-D(*TP*GP*TP*AP*AP*CP*AP*TP*GP*TP*GP*TP*CP*CP*CP*C)-3')
A: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
B: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Theoretical massNumber of molelcules
Total (without water)55,3394
Polymers55,3394
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-46 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.260, 207.260, 163.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: DNA chain DNA (5'-D(P*GP*GP*GP*AP*CP*AP*CP*AP*TP*GP*TP*TP*AP*CP*AP*G)-3')


Mass: 4947.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized M box DNA / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(*TP*GP*TP*AP*AP*CP*AP*TP*GP*TP*GP*TP*CP*CP*CP*C)-3')


Mass: 4849.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized M box DNA / Source: (synth.) Homo sapiens (human)
#3: Protein Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Mass: 22771.480 Da / Num. of mol.: 2 / Mutation: N385C
Source method: isolated from a genetically manipulated source
Details: Fusion protein of Microphthalmia-associated transcription factor and Methionyl-tRNA synthetase beta subunit
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Aquifex aeolicus VF5 (bacteria)
Gene: MITF, BHLHE32, metG', aq_422 / Strain: VF5 / Production host: Escherichia coli (E. coli) / References: UniProt: O75030, UniProt: O66738
Has protein modificationY

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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: 6.09 Å3/Da / Density % sol: 79.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Tris-Cl pH8.5, sodium citrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.2→120.734 Å / Num. all: 22309 / Num. obs: 22309 / % possible obs: 100 % / Redundancy: 11.3 % / Biso Wilson estimate: 88.47 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.14 / Rsym value: 0.133 / Net I/av σ(I): 3.3 / Net I/σ(I): 10.6 / Num. measured all: 251159
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.2-3.3711.40.9010.83659832230.2810.9440.9012.6100
3.37-3.5811.40.70213458430440.2180.7360.7023.6100
3.58-3.8211.40.4481.63274028790.1390.4690.4485.2100
3.82-4.1311.30.2452.93058926970.0760.2570.2458.1100
4.13-4.5311.30.1434.52810624800.0440.150.14312.4100
4.53-5.0611.30.1244.82545222490.0390.130.12415.7100
5.06-5.8411.30.12352225119710.0380.1290.12316100
5.84-7.1611.20.0877.31893616890.0270.0910.08717.9100
7.16-10.12110.0559.21465413310.0170.0580.05524.4100
10.12-48.1589.70.0767.272497460.0260.0810.07626.699.1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SCALA3.3.20data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D8S

7d8s


Resolution: 3.201→19.791 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 26.26
RfactorNum. reflection% reflection
Rfree0.2341 1007 5.08 %
Rwork0.204 --
obs0.2057 19815 89.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 217.31 Å2 / Biso min: 31.95 Å2
Refinement stepCycle: final / Resolution: 3.201→19.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2949 650 0 0 3599
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053704
X-RAY DIFFRACTIONf_angle_d0.6485139
X-RAY DIFFRACTIONf_dihedral_angle_d17.4772152
X-RAY DIFFRACTIONf_chiral_restr0.044613
X-RAY DIFFRACTIONf_plane_restr0.004557
LS refinement shellResolution: 3.2012→3.3692 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3818 65 -
Rwork0.2843 1247 -
obs--42 %
Refinement TLS params.Method: refined / Origin x: -58.4469 Å / Origin y: -35.8374 Å / Origin z: 33.4926 Å
111213212223313233
T0.2571 Å20.3359 Å2-0.0395 Å2-0.8595 Å2-0.3048 Å2--0.6924 Å2
L0.9253 °20.6834 °20.5925 °2-0.4848 °20.3621 °2--0.3636 °2
S0.2797 Å °0.1438 Å °-0.2233 Å °0.1901 Å °0.1571 Å °-0.5226 Å °-0.2833 Å °0.2792 Å °-0.0446 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC1 - 16
2X-RAY DIFFRACTION1allD1 - 16
3X-RAY DIFFRACTION1allA305 - 503
4X-RAY DIFFRACTION1allB305 - 503

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