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- PDB-5i50: Structure of OmoMYC bound to double-stranded DNA -

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Basic information

Entry
Database: PDB / ID: 5i50
TitleStructure of OmoMYC bound to double-stranded DNA
Components
  • DNA (5'-D(P*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*CP*TP*AP*CP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*CP*GP*GP*GP*TP*G)-3')
  • Myc proto-oncogene protein
KeywordsTRANSCRIPTION / leucine zipper / transcription factor / tumor suppressor / E-box
Function / homology
Function and homology information


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 ...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 / transcription regulator activator activity / Transcription of E2F targets under negative control by DREAM complex / response to growth factor / regulation of telomere maintenance / negative regulation of stress-activated MAPK cascade / fibroblast apoptotic process / Regulation of NFE2L2 gene expression / protein-DNA complex disassembly / positive regulation of mesenchymal cell proliferation / negative regulation of gene expression via chromosomal CpG island methylation / branching involved in ureteric bud morphogenesis / Signaling by ALK / E-box binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / chromosome organization / Cyclin E associated events during G1/S transition / core promoter sequence-specific DNA binding / Cyclin A:Cdk2-associated events at S phase entry / negative regulation of fibroblast proliferation / positive regulation of telomerase activity / ERK1 and ERK2 cascade / transcription coregulator binding / positive regulation of epithelial cell proliferation / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / 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 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / cellular response to UV / MAPK cascade / positive regulation of fibroblast proliferation / cellular response to xenobiotic stimulus / cellular response to hypoxia / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Interleukin-4 and Interleukin-13 signaling / intracellular iron ion homeostasis / Estrogen-dependent gene expression / 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 damage response / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of gene expression / chromatin / 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 / cytoplasm
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
DNA / DNA (> 10) / Myc proto-oncogene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsKoelmel, W. / Jung, L.A. / Kuper, J. / Eilers, M. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation2341 Germany
CitationJournal: Oncogene / Year: 2017
Title: OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors.
Authors: Jung, L.A. / Gebhardt, A. / Koelmel, W. / Ade, C.P. / Walz, S. / Kuper, J. / von Eyss, B. / Letschert, S. / Redel, C. / d'Artista, L. / Biankin, A. / Zender, L. / Sauer, M. / Wolf, E. / ...Authors: Jung, L.A. / Gebhardt, A. / Koelmel, W. / Ade, C.P. / Walz, S. / Kuper, J. / von Eyss, B. / Letschert, S. / Redel, C. / d'Artista, L. / Biankin, A. / Zender, L. / Sauer, M. / Wolf, E. / Evan, G. / Kisker, C. / Eilers, M.
History
DepositionFeb 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Source and taxonomy
Category: pdbx_audit_support / pdbx_entity_src_syn ...pdbx_audit_support / pdbx_entity_src_syn / pdbx_seq_map_depositor_info / struct_conn
Item: _pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_audit_support.funding_organization / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 10, 2024Group: 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
A: Myc proto-oncogene protein
B: Myc proto-oncogene protein
C: DNA (5'-D(P*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*CP*TP*AP*CP*AP*C)-3')
D: DNA (5'-D(P*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*CP*GP*GP*GP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)41,5804
Polymers41,5804
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-66 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.538, 95.545, 64.944
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number4
Space group name H-MP1211

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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: 14036.048 Da / Num. of mol.: 2 / Fragment: OmoMYC, UNP Residues 350-439
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: DNA chain DNA (5'-D(P*CP*AP*CP*CP*CP*GP*GP*TP*CP*AP*CP*GP*TP*GP*GP*CP*CP*TP*AP*CP*AP*C)-3')


Mass: 6658.294 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*TP*AP*GP*GP*CP*CP*AP*CP*GP*TP*GP*AP*CP*CP*GP*GP*GP*TP*G)-3')


Mass: 6849.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.62 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MES, magnesium sulfate, potassium chloride, PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.7→47.77 Å / Num. obs: 11787 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 68.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Net I/σ(I): 11.9
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.845 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.593 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5I4Z

5i4z


Resolution: 2.701→37.945 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2794 555 4.73 %
Rwork0.2265 --
obs0.229 11726 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.701→37.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1557 902 0 0 2459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062585
X-RAY DIFFRACTIONf_angle_d0.7763661
X-RAY DIFFRACTIONf_dihedral_angle_d23.7031080
X-RAY DIFFRACTIONf_chiral_restr0.034416
X-RAY DIFFRACTIONf_plane_restr0.004321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7006-2.97230.39571600.3362787X-RAY DIFFRACTION100
2.9723-3.40210.35881250.26822747X-RAY DIFFRACTION98
3.4021-4.28540.27391220.21912790X-RAY DIFFRACTION99
4.2854-37.94920.22981480.19012847X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0526-3.0557-1.1623.07141.0492.7289-0.15270.2321-0.7105-0.02340.361-0.45740.04420.2942-0.33590.14530.0380.13370.296-0.12330.68143.7945-17.3269-15.8928
21.36460.38080.92562.428-0.21.1129-0.13130.12290.7320.02660.00690.1555-0.70740.1306-0.44140.7374-0.08850.63350.3584-0.06090.7533-5.438324.0246-13.0704
34.58414.1406-0.82793.8283-1.15962.2555-0.45680.3603-0.6031-0.06480.12960.15760.5077-0.4991-0.05530.1704-0.08110.27190.2754-0.0080.6343-16.9909-17.2137-18.1095
41.7768-0.10830.79971.8242-0.70820.6114-0.2622-0.16780.50570.4369-0.0014-0.2282-0.67640.2492-0.45650.9525-0.03930.69110.25240.04460.6376-0.261623.2715-13.4169
51.5788-0.9762-1.71990.61051.02572.0837-0.0297-0.0648-0.00170.01650.1741-0.07660.13340.31960.11421.42580.33760.81381.2343-0.08721.191111.6678-21.6605-36.0861
63.646-1.00550.86070.48120.29982.31050.1701-0.80070.27330.6870.02520.41780.0279-0.4804-0.21680.7940.02710.45750.7591-0.08271.039-13.3831-18.2441-10.9543
75.04540.84720.02192.1635-1.17520.7016-0.3804-0.3513-0.25030.82020.26710.54351.0518-1.51740.08440.8595-0.1120.49680.90790.02390.8913-13.2928-20.7413-10.9284
84.6599-4.3957-2.71927.91393.57941.8607-0.3544-0.89780.0183-0.00490.9902-0.91110.35552.1896-0.71491.43270.30030.77271.7671-0.12281.335412.6923-15.6143-36.1093
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 92 )
3X-RAY DIFFRACTION3chain 'B' and (resid -3 through 33 )
4X-RAY DIFFRACTION4chain 'B' and (resid 34 through 92 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 6 )
6X-RAY DIFFRACTION6chain 'C' and (resid 7 through 22 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 16 )
8X-RAY DIFFRACTION8chain 'D' and (resid 17 through 22 )

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