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- PDB-6g6j: The crystal structures of Human MYC:MAX bHLHZip complex -

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Basic information

Entry
Database: PDB / ID: 6g6j
TitleThe crystal structures of Human MYC:MAX bHLHZip complex
Components
  • Myc proto-oncogene protein
  • Protein max
KeywordsAPOPTOSIS / Myc/Max
Function / homology
Function and homology information


Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling ...Mad-Max complex / SCF ubiquitin ligase complex binding / positive regulation of metanephric cap mesenchymal cell proliferation / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / RNA polymerase II transcription repressor complex / regulation of cell cycle process / regulation of somatic stem cell population maintenance / Binding of TCF/LEF:CTNNB1 to target gene promoters / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / protein-DNA complex disassembly / transcription regulator activator activity / DNA methylation-dependent heterochromatin formation / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / negative regulation of stress-activated MAPK cascade / regulation of telomere maintenance / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / Transcriptional Regulation by E2F6 / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / MLL1 complex / chromosome organization / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of telomerase activity / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / protein-DNA complex / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / cellular response to UV / positive regulation of fibroblast proliferation / MAPK cascade / sequence-specific double-stranded DNA binding / cellular response to xenobiotic stimulus / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / chromatin remodeling / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / dendrite / DNA damage response / positive regulation of cell population proliferation / chromatin / protein-containing complex binding / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Helix-loop-helix DNA-binding domain / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain ...Leucine zipper, Myc / Myc leucine zipper domain / Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Helix-loop-helix DNA-binding domain / MYOD Basic-Helix-Loop-Helix Domain, subunit B / 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. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Myc proto-oncogene protein / Protein max
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsAllen, M.D. / Zinzalla, G.
CitationJournal: Biochemistry / Year: 2019
Title: Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA.
Authors: Sammak, S. / Hamdani, N. / Gorrec, F. / Allen, M.D. / Freund, S.M.V. / Bycroft, M. / Zinzalla, G.
History
DepositionApr 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Apr 5, 2023Group: Database references / Experimental preparation / Category: database_2 / exptl_crystal_grow
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myc proto-oncogene protein
B: Protein max
C: Myc proto-oncogene protein
D: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,39710
Polymers42,8214
Non-polymers5766
Water3,243180
1
A: Myc proto-oncogene protein
B: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7956
Polymers21,4102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-68 kcal/mol
Surface area10720 Å2
MethodPISA
2
C: Myc proto-oncogene protein
D: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6024
Polymers21,4102
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-47 kcal/mol
Surface area10440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.319, 145.180, 48.499
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Myc proto-oncogene protein / Class E basic helix-loop-helix protein 39 / bHLHe39 / Proto-oncogene c-Myc / Transcription factor p64


Mass: 11501.192 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MYC, BHLHE39 / Production host: Escherichia coli (E. coli) / References: UniProt: P01106
#2: Protein Protein max / Class D basic helix-loop-helix protein 4 / bHLHd4 / Myc-associated factor X


Mass: 9909.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAX, BHLHD4 / Production host: Escherichia coli (E. coli) / References: UniProt: P61244
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 3.06 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% (w/v) PEG 3350 0.2M sodium sulfate decahydrate, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→51.93 Å / Num. obs: 25627 / % possible obs: 99.7 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.048 / Rrim(I) all: 0.109 / Net I/σ(I): 8.9
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3679 / CC1/2: 0.875 / Rpim(I) all: 0.265 / Rrim(I) all: 0.608 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KNP

1knp


Resolution: 2.25→40.554 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.53
RfactorNum. reflection% reflection
Rfree0.2362 1239 4.85 %
Rwork0.2054 --
obs0.2069 25534 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.25→40.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2537 0 30 180 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062586
X-RAY DIFFRACTIONf_angle_d0.6773455
X-RAY DIFFRACTIONf_dihedral_angle_d2.4611655
X-RAY DIFFRACTIONf_chiral_restr0.037373
X-RAY DIFFRACTIONf_plane_restr0.003453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.34010.29451290.26052667X-RAY DIFFRACTION100
2.3401-2.44660.26441300.24512659X-RAY DIFFRACTION99
2.4466-2.57550.27271450.2242634X-RAY DIFFRACTION99
2.5755-2.73690.27861440.22622660X-RAY DIFFRACTION99
2.7369-2.94810.25731510.22192654X-RAY DIFFRACTION99
2.9481-3.24470.24871230.21642719X-RAY DIFFRACTION100
3.2447-3.71390.2391320.19552727X-RAY DIFFRACTION100
3.7139-4.67810.19611420.16052739X-RAY DIFFRACTION100
4.6781-40.56020.20921430.2112836X-RAY DIFFRACTION98

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