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- PDB-6g6k: The crystal structures of Human MYC:MAX bHLHZip complex -

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Basic information

Entry
Database: PDB / ID: 6g6k
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 / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process ...Mad-Max complex / positive regulation of metanephric cap mesenchymal cell proliferation / positive regulation of acinar cell proliferation / acinar cell proliferation / negative regulation of transcription initiation by RNA polymerase II / SCF ubiquitin ligase complex binding / NK T cell proliferation / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / cellular response to interferon-alpha / RNA polymerase II transcription repressor complex / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / myotube differentiation / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / detection of mechanical stimulus involved in sensory perception of sound / response to growth factor / response to alkaloid / B cell apoptotic process / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / protein-DNA complex disassembly / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / positive regulation of mesenchymal cell proliferation / regulation of telomere maintenance / skeletal system morphogenesis / Signaling by ALK / middle ear morphogenesis / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / rRNA metabolic process / Transcriptional Regulation by E2F6 / pigmentation / E-box binding / positive regulation of telomere maintenance / MLL1 complex / skeletal muscle cell differentiation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / chromosome organization / positive regulation of transcription initiation by RNA polymerase II / negative regulation of fibroblast proliferation / core promoter sequence-specific DNA binding / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / G1/S transition of mitotic cell cycle / euchromatin / protein-DNA complex / protein processing / MAPK6/MAPK4 signaling / positive regulation of miRNA transcription / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / cellular response to xenobiotic stimulus / spindle / positive regulation of fibroblast proliferation / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / cellular response to UV / MAPK cascade / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / cellular response to hypoxia / Estrogen-dependent gene expression / DNA-binding transcription factor binding / intracellular iron ion homeostasis / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / Ub-specific processing proteases / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / response to xenobiotic stimulus / axon / positive regulation of cell population proliferation / DNA damage response / ubiquitin protein ligase binding / dendrite / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription
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 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 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 / 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: 1.35 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)42,8926
Polymers42,8214
Non-polymers712
Water6,467359
1
A: Myc proto-oncogene protein
B: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4463
Polymers21,4102
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-35 kcal/mol
Surface area11600 Å2
MethodPISA
2
C: Myc proto-oncogene protein
D: Protein max
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4463
Polymers21,4102
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-34 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.399, 52.310, 73.089
Angle α, β, γ (deg.)93.89, 101.92, 106.79
Int Tables number1
Space group name H-MP1

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.075 %(w/v) of each Additive, 5 %(v/v) EtOH, 0.1 M MOPS/HEPES-Na, pH 7.5, Additive: 0.75 %(w/v) menthol, 0.75 %(w/v) caffeic acid, 0.75 %(w/v) D- ...Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.075 %(w/v) of each Additive, 5 %(v/v) EtOH, 0.1 M MOPS/HEPES-Na, pH 7.5, Additive: 0.75 %(w/v) menthol, 0.75 %(w/v) caffeic acid, 0.75 %(w/v) D-quinic acid, 0.75 %(w/v) shikimic acid, 0.75 %(w/v) gallic acid monohydrate, 0.75 %(w/v) N-vanillylnonanamide.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→38.27 Å / Num. obs: 80704 / % possible obs: 87.9 % / Redundancy: 2.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.049 / Rrim(I) all: 0.079 / Net I/σ(I): 8.7
Reflection shellResolution: 1.35→1.42 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.1 / CC1/2: 0.748 / Rpim(I) all: 0.345 / Rrim(I) all: 0.559 / % possible all: 81.3

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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: 1.35→38.266 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0.91 / Phase error: 19.99
RfactorNum. reflection% reflection
Rfree0.2026 7247 4.89 %
Rwork0.1728 --
obs0.1743 80678 80.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→38.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 2 359 3145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052896
X-RAY DIFFRACTIONf_angle_d0.7563884
X-RAY DIFFRACTIONf_dihedral_angle_d2.0081953
X-RAY DIFFRACTIONf_chiral_restr0.057415
X-RAY DIFFRACTIONf_plane_restr0.004521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.36530.33431860.32663792X-RAY DIFFRACTION66
1.3653-1.38140.33362200.29843812X-RAY DIFFRACTION63
1.3814-1.39830.31181970.26654194X-RAY DIFFRACTION75
1.3983-1.4160.26052400.25644882X-RAY DIFFRACTION83
1.416-1.43460.28392430.22924887X-RAY DIFFRACTION84
1.4346-1.45420.25762480.21644997X-RAY DIFFRACTION84
1.4542-1.4750.21562280.19274834X-RAY DIFFRACTION85
1.475-1.4970.20051980.17254928X-RAY DIFFRACTION83
1.497-1.52040.16872250.15774783X-RAY DIFFRACTION82
1.5204-1.54540.2052590.16564904X-RAY DIFFRACTION85
1.5454-1.5720.20732500.15014747X-RAY DIFFRACTION82
1.572-1.60060.18792110.14784776X-RAY DIFFRACTION81
1.6006-1.63140.19392900.13874854X-RAY DIFFRACTION85
1.6314-1.66470.17322380.13464726X-RAY DIFFRACTION81
1.6647-1.70090.18132520.13554714X-RAY DIFFRACTION80
1.7009-1.74040.16862190.13234619X-RAY DIFFRACTION79
1.7404-1.7840.20582280.15714258X-RAY DIFFRACTION73
1.784-1.83220.22232280.15883724X-RAY DIFFRACTION66
1.8322-1.88610.19742240.15143942X-RAY DIFFRACTION67
1.8861-1.9470.20372690.15154885X-RAY DIFFRACTION86
1.947-2.01660.2252320.14265151X-RAY DIFFRACTION87
2.0166-2.09730.1642760.13475105X-RAY DIFFRACTION89
2.0973-2.19280.14552760.13715016X-RAY DIFFRACTION86
2.1928-2.30830.18893060.14895026X-RAY DIFFRACTION88
2.3083-2.45290.22212590.15774924X-RAY DIFFRACTION85
2.4529-2.64230.19942490.1624924X-RAY DIFFRACTION84
2.6423-2.90810.20892490.17644826X-RAY DIFFRACTION82
2.9081-3.32870.20151750.17864093X-RAY DIFFRACTION70
3.3287-4.1930.18143110.1724959X-RAY DIFFRACTION86
4.193-38.28110.242610.22075749X-RAY DIFFRACTION98

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