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- PDB-1nkp: Crystal structure of Myc-Max recognizing DNA -

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Basic information

Entry
Database: PDB / ID: 1nkp
TitleCrystal structure of Myc-Max recognizing DNA
Components
  • 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
  • Max protein
  • Myc proto-oncogene protein
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION / DNA / bHLHZ / oncogene / heterodimer / TRANSCRIPTION-DNA COMPLEX
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 / myotube differentiation / positive regulation of B cell apoptotic process / RUNX3 regulates WNT signaling / 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 / protein-DNA complex disassembly / Transcription of E2F targets under negative control by DREAM complex / 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 / middle ear morphogenesis / skeletal system morphogenesis / Signaling by ALK / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / pigmentation / rRNA metabolic process / Transcriptional Regulation by E2F6 / positive regulation of telomere maintenance / E-box binding / MLL1 complex / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / skeletal muscle cell differentiation / positive regulation of transcription initiation by RNA polymerase II / chromosome organization / 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 / MAPK6/MAPK4 signaling / protein processing / NOTCH1 Intracellular Domain Regulates Transcription / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / RNA polymerase II transcription regulator complex / spindle / cellular response to xenobiotic stimulus / Wnt signaling pathway / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / 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 / DNA-binding transcription factor binding / Estrogen-dependent gene expression / 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 / response to xenobiotic stimulus / DNA-binding transcription factor activity / axon / positive regulation of cell population proliferation / DNA damage response / dendrite / ubiquitin protein ligase binding / 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
DNA / DNA (> 10) / Myc proto-oncogene protein / Protein max
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phased translation search / Resolution: 1.8 Å
AuthorsNair, S.K. / Burley, S.K.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: X-ray structures of Myc-Max and Mad-Max recognizing DNA: Molecular bases of regulation by proto-oncogenic transcription factors
Authors: Nair, S.K. / Burley, S.K.
History
DepositionJan 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
H: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: Myc proto-oncogene protein
B: Max protein
D: Myc proto-oncogene protein
E: Max protein


Theoretical massNumber of molelcules
Total (without water)63,7498
Polymers63,7498
Non-polymers00
Water10,467581
1
F: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
G: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
A: Myc proto-oncogene protein
B: Max protein


Theoretical massNumber of molelcules
Total (without water)31,8754
Polymers31,8754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
J: 5'-D(*CP*GP*AP*GP*TP*AP*GP*CP*AP*CP*GP*TP*GP*CP*TP*AP*CP*TP*C)-3'
D: Myc proto-oncogene protein
E: Max protein


Theoretical massNumber of molelcules
Total (without water)31,8754
Polymers31,8754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.244, 45.128, 86.484
Angle α, β, γ (deg.)87.91, 84.61, 71.50
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 5805.760 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Protein Myc proto-oncogene protein / c-myc


Mass: 10468.156 Da / Num. of mol.: 2 / Fragment: bHLHZ region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Myc / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01106
#3: Protein Max protein


Mass: 9795.012 Da / Num. of mol.: 2 / Fragment: bHLHZ region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Max / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61244
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Components of the solutions
IDNameCrystal-IDSol-ID
13-7% PEG 400011
230% methyl pentane diol11
31MM cobalt hexamine chloride11
450MM sodium cacodylate pH 6.511
5PEG 400012
6methyl pentane diol12
7cobalt hexamine chloride12
8sodium cacodylate pH 6.512
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13-7 %PEG40001reservoir
230 %MPD1reservoir
31 mMcobalt hexammine chloride1reservoir
450 mMsodium cacodylate1reservoirpH6.5
510 mg/mlprotein1drop
61
71
81

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.91 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 49228 / % possible obs: 95.9 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.053
Reflection
*PLUS
Num. measured all: 276421
Reflection shell
*PLUS
% possible obs: 90.9 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: Phased translation search
Starting model: PDB ENTRY 1AN2

1an2


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.263 4123 Random
Rwork0.219 --
obs0.219 40874 -
all-49228 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.674 Å2-1.363 Å2-2.839 Å2
2--6.3 Å2-7.378 Å2
3----5.627 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 1540 0 581 4906
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0048
X-RAY DIFFRACTIONc_angle_d0.94736
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.95

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