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- PDB-5i4z: Structure of apo OmoMYC -

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Basic information

Entry
Database: PDB / ID: 5i4z
TitleStructure of apo OmoMYC
ComponentsMyc proto-oncogene protein
KeywordsTRANSCRIPTION / leucine zipper / transcription factor / tumor suppressor / E-box
Function / homology
Function and homology information


positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors ...positive regulation of metanephric cap mesenchymal cell proliferation / SCF ubiquitin ligase complex binding / negative regulation of transcription initiation by RNA polymerase II / Myc-Max complex / regulation of somatic stem cell population maintenance / regulation of cell cycle process / Binding of TCF/LEF:CTNNB1 to target gene promoters / RNA polymerase II transcription repressor complex / RUNX3 regulates WNT signaling / TFAP2 (AP-2) family regulates transcription of cell cycle factors / negative regulation of cell division / negative regulation of monocyte differentiation / response to growth factor / transcription regulator activator activity / 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 / regulation of telomere maintenance / positive regulation of mesenchymal cell proliferation / protein-DNA complex disassembly / branching involved in ureteric bud morphogenesis / negative regulation of gene expression via chromosomal CpG island methylation / Signaling by ALK / : / E-box binding / : / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / ERK1 and ERK2 cascade / positive regulation of epithelial cell proliferation / transcription coregulator binding / response to gamma radiation / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / MAPK6/MAPK4 signaling / NOTCH1 Intracellular Domain Regulates Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / cellular response to UV / positive regulation of fibroblast proliferation / MAPK cascade / 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 / 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 / positive regulation of gene expression / protein-containing complex binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / nucleolus / 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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,53310
Polymers28,0722
Non-polymers4618
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-65 kcal/mol
Surface area10390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.700, 65.700, 149.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-244-

HOH

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Components

#1: Protein Myc proto-oncogene protein / OmoMYC / 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 348-439
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: MES, potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.064 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.064 Å / Relative weight: 1
ReflectionResolution: 1.95→49.35 Å / Num. obs: 24551 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.1
Reflection shellResolution: 1.95→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.818 / Mean I/σ(I) obs: 1.7 / % possible all: 92.9

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NKP

1nkp


Resolution: 1.95→49.348 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.2
RfactorNum. reflection% reflection
Rfree0.1941 1234 5.04 %
Rwork0.1731 --
obs0.1742 24506 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.348 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 23 114 1359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111285
X-RAY DIFFRACTIONf_angle_d1.1351723
X-RAY DIFFRACTIONf_dihedral_angle_d14.944538
X-RAY DIFFRACTIONf_chiral_restr0.053198
X-RAY DIFFRACTIONf_plane_restr0.005223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.02810.27781070.25062414X-RAY DIFFRACTION94
2.0281-2.12040.23741420.20872561X-RAY DIFFRACTION100
2.1204-2.23220.20591210.17522538X-RAY DIFFRACTION100
2.2322-2.3720.18191540.17222555X-RAY DIFFRACTION100
2.372-2.55520.1761440.17032564X-RAY DIFFRACTION100
2.5552-2.81230.21231530.1732556X-RAY DIFFRACTION100
2.8123-3.21920.19861280.17782620X-RAY DIFFRACTION100
3.2192-4.05550.1791330.15932661X-RAY DIFFRACTION100
4.0555-49.36380.191520.17012803X-RAY DIFFRACTION99
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)
14.75010.8038-0.72846.187-0.19174.93180.09450.65460.6812-0.2402-0.1486-0.3108-0.84190.0832-0.23670.3672-0.0465-0.00350.27530.08080.283439.860141.48625.1324
26.20544.1772-0.48092.6477-0.3088-0.17540.05430.0502-0.38520.20030.01730.016-0.0315-0.0747-0.09640.3107-0.04850.04490.38510.01470.40214.377422.10314.9527
35.7979-0.4289-1.81754.50581.09016.1898-0.05860.0607-0.28480.1807-0.1652-0.59340.20320.45910.18190.2043-0.01270.01260.26320.06870.351345.431926.488811.8503
43.1061.3866-1.65390.4725-0.8050.5737-0.01020.6650.02980.0330.1670.17710.0409-0.2149-0.08610.2482-0.01910.06050.39450.02140.36212.689525.50688.4054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 92 )
3X-RAY DIFFRACTION3chain 'B' and (resid 19 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 92 )

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