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- PDB-7eod: MITF HLHLZ Delta AKE -

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Basic information

Entry
Database: PDB / ID: 7eod
TitleMITF HLHLZ Delta AKE
ComponentsIsoform M1 of Microphthalmia-associated transcription factor
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR
Function / homology
Function and homology information


canonical Wnt signaling pathway involved in negative regulation of apoptotic process / positive regulation of DNA-templated transcription initiation / regulation of RNA biosynthetic process / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / E-box binding / SUMOylation of transcription factors / cell fate commitment ...canonical Wnt signaling pathway involved in negative regulation of apoptotic process / positive regulation of DNA-templated transcription initiation / regulation of RNA biosynthetic process / regulation of osteoclast differentiation / melanocyte differentiation / bone remodeling / camera-type eye development / E-box binding / SUMOylation of transcription factors / cell fate commitment / negative regulation of cell migration / osteoclast differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of cell population proliferation / protein-containing complex assembly / DNA-binding transcription activator activity, RNA polymerase II-specific / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / chromatin / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
Similarity search - Function
Microphthalmia-associated transcription factor / 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 DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile.
Similarity search - Domain/homology
Microphthalmia-associated transcription factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, P. / Liu, Z. / 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
DepositionApr 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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

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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
D: Isoform M1 of Microphthalmia-associated transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,96115
Polymers34,9484
Non-polymers1,01311
Water5,657314
1
A: Isoform M1 of Microphthalmia-associated transcription factor
B: Isoform M1 of Microphthalmia-associated transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8436
Polymers17,4742
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-27 kcal/mol
Surface area9510 Å2
MethodPISA
2
C: Isoform M1 of Microphthalmia-associated transcription factor
D: Isoform M1 of Microphthalmia-associated transcription factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1199
Polymers17,4742
Non-polymers6457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-24 kcal/mol
Surface area9460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.020, 52.880, 55.470
Angle α, β, γ (deg.)82.640, 85.490, 71.850
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 8737.100 Da / Num. of mol.: 4 / Mutation: AKE deletion
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: O75030-9
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 49812 / % possible obs: 93.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.045 / Rrim(I) all: 0.087 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.9-1.943.50.68417050.8170.4190.80493.7
9.11-403.60.0212350.9990.0120.02492.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D8R

7d8r


Resolution: 1.9→39.16 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 2379 4.78 %
Rwork0.1883 47433 -
obs0.1907 49812 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.12 Å2 / Biso mean: 31.8999 Å2 / Biso min: 12.36 Å2
Refinement stepCycle: final / Resolution: 1.9→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 66 314 2623
Biso mean--60.04 47.05 -
Num. residues----271
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.93880.41191480.3341274888
1.9388-1.9810.34021450.2797278790
1.981-2.0270.30851340.2277282690
2.027-2.07770.281420.2397268786
2.0777-2.13390.2641520.2066288793
2.1339-2.19670.281490.1994285892
2.1967-2.26760.23841500.2084274790
2.2676-2.34860.26291340.1945287291
2.3486-2.44260.24541560.1958273889
2.4426-2.55380.2451330.1766277487
2.5538-2.68840.24341550.1801279591
2.6884-2.85680.26051380.1758287692
2.8568-3.07730.20661350.1684286290
3.0773-3.38680.2566960.1604271788
3.3868-3.87650.15791040.15289291
3.8765-4.88250.20371800.154255684
4.8825-400.23491280.2312281189
Refinement TLS params.Method: refined / Origin x: -4.1259 Å / Origin y: -6.3997 Å / Origin z: 9.6299 Å
111213212223313233
T0.1358 Å20.0054 Å20.0008 Å2-0.145 Å20.006 Å2--0.1741 Å2
L0.0394 °20.0778 °20.0221 °2-0.3083 °20.1714 °2--0.1559 °2
S-0.0013 Å °0.01 Å °-0.0139 Å °-0.0157 Å °0.0076 Å °0.0226 Å °-0.017 Å °0.013 Å °-0.0021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA218 - 287
2X-RAY DIFFRACTION1allA401 - 501
3X-RAY DIFFRACTION1allB218 - 287
4X-RAY DIFFRACTION1allB301 - 401
5X-RAY DIFFRACTION1allC218 - 287
6X-RAY DIFFRACTION1allC301 - 801
7X-RAY DIFFRACTION1allD219 - 287
8X-RAY DIFFRACTION1allD801
9X-RAY DIFFRACTION1allW3 - 549

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