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- PDB-7d8s: MITF bHLHLZ apo structure -

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Basic information

Entry
Database: PDB / ID: 7d8s
TitleMITF bHLHLZ apo structure
ComponentsMicrophthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
KeywordsTRANSCRIPTION / 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 / methionine-tRNA ligase activity / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / methionyl-tRNA aminoacylation / regulation of osteoclast 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 / methionine-tRNA ligase activity / Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition / methionyl-tRNA aminoacylation / regulation of osteoclast differentiation / melanocyte differentiation / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / bone remodeling / Regulation of MITF-M-dependent genes involved in apoptosis / camera-type eye development / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / protein-containing complex assembly / tRNA binding / 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 / ATP binding / nucleus / cytosol / 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 / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Helix-loop-helix DNA-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 / : / Methionyl-tRNA synthetase, beta subunit, C-terminal / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Methionyl-tRNA synthetase beta subunit / Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
Aquifex aeolicus VF5 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
B: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
C: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
D: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3747
Polymers91,0864
Non-polymers2883
Water5,621312
1
A: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
B: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6393
Polymers45,5432
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-33 kcal/mol
Surface area23690 Å2
MethodPISA
2
C: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
D: Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7354
Polymers45,5432
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-41 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.005, 62.306, 65.307
Angle α, β, γ (deg.)90.120, 72.740, 86.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Microphthalmia-associated transcription factor,Methionyl-tRNA synthetase beta subunit


Mass: 22771.480 Da / Num. of mol.: 4 / 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
#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.: 312 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.38 Å3/Da / Density % sol: 48.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Sodium acetate pH 4.5, Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.28→50 Å / Num. obs: 34574 / % possible obs: 96.5 % / Redundancy: 4 % / Biso Wilson estimate: 26.73 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 37
Reflection shellResolution: 2.28→2.36 Å / Rmerge(I) obs: 0.305 / Num. unique obs: 3686

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KTD

6ktd
PDB Unreleased entry


Resolution: 2.28→38.942 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.97
RfactorNum. reflection% reflection
Rfree0.2705 1728 5 %
Rwork0.2313 --
obs0.2334 34574 90.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.87 Å2 / Biso mean: 55.07 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.28→38.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5435 0 15 312 5762
Biso mean--75.88 56.87 -
Num. residues----724
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065496
X-RAY DIFFRACTIONf_angle_d1.0487415
X-RAY DIFFRACTIONf_chiral_restr0.079902
X-RAY DIFFRACTIONf_plane_restr0.004942
X-RAY DIFFRACTIONf_dihedral_angle_d16.3832050
LS refinement shellResolution: 2.28→2.36 Å / Rfactor Rfree error: 0 /
Num. reflection% reflection
Rfree171 -
obs-97.6 %
Refinement TLS params.Method: refined / Origin x: -0.9343 Å / Origin y: 0.1744 Å / Origin z: -0.8 Å
111213212223313233
T0.264 Å20.0149 Å2-0.0232 Å2-0.3099 Å2-0 Å2--0.2844 Å2
L0.2533 °2-0.0435 °2-0.2223 °2-0.3727 °20.0129 °2--0.4834 °2
S0.006 Å °0.0578 Å °0.0084 Å °0.0301 Å °0.0398 Å °-0.0043 Å °-0.033 Å °-0.0511 Å °-0.0421 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA316 - 503
2X-RAY DIFFRACTION1allB324 - 503
3X-RAY DIFFRACTION1allC314 - 503
4X-RAY DIFFRACTION1allD324 - 503
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allE3
7X-RAY DIFFRACTION1allS1 - 409

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