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- PDB-5zmc: Structural Basis for Reactivation of -146C>T Mutant TERT Promoter... -

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Basic information

Entry
Database: PDB / ID: 5zmc
TitleStructural Basis for Reactivation of -146C>T Mutant TERT Promoter by cooperative binding of p52 and ETS1/2
Components
  • DNA (5'-D(P*CP*GP*GP*GP*GP*AP*CP*CP*CP*GP*GP*AP*AP*GP*GP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*CP*TP*TP*CP*CP*GP*GP*GP*TP*CP*CP*CP*C)-3')
  • Nuclear factor NF-kappa-B p100 subunit
  • Protein C-ets-1
KeywordsTRANSCRIPTION/DNA / ETS1 / p52 / transcription factor / TRANSCRIPTION / -146c>T mutant TERT promoter activation / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / PML body organization / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / SUMOylation of immune response proteins / positive regulation of leukocyte adhesion to vascular endothelial cell ...follicular dendritic cell differentiation / Bcl3/NF-kappaB2 complex / PML body organization / DEx/H-box helicases activate type I IFN and inflammatory cytokines production / IkBA variant leads to EDA-ID / germinal center formation / RIP-mediated NFkB activation via ZBP1 / Interleukin-1 processing / SUMOylation of immune response proteins / positive regulation of leukocyte adhesion to vascular endothelial cell / non-canonical NF-kappaB signal transduction / TRAF6 mediated NF-kB activation / The NLRP3 inflammasome / negative regulation of cell cycle / positive regulation of blood vessel endothelial cell migration / regulation of angiogenesis / Purinergic signaling in leishmaniasis infection / canonical NF-kappaB signal transduction / spleen development / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / extracellular matrix organization / transcription corepressor binding / response to cytokine / nuclear receptor coactivator activity / NIK-->noncanonical NF-kB signaling / cell motility / Dectin-1 mediated noncanonical NF-kB signaling / TAK1-dependent IKK and NF-kappa-B activation / Oncogene Induced Senescence / PKMTs methylate histone lysines / positive regulation of miRNA transcription / positive regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / rhythmic process / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / response to lipopolysaccharide / transcription by RNA polymerase II / nucleic acid binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / immune response / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / innate immune response / response to antibiotic / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor NF-kappa-B, p100 subunit / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. ...Nuclear factor NF-kappa-B, p100 subunit / Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / NF-kappa-B/Dorsal / Rel homology domain, conserved site / NFkappaB IPT domain / NF-kappa-B/Rel/dorsal domain signature. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / Death-like domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein C-ets-1 / Nuclear factor NF-kappa-B p100 subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsXu, X. / Bharath, S.R. / Song, H.
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis for reactivating the mutant TERT promoter by cooperative binding of p52 and ETS1.
Authors: Xu, X. / Li, Y. / Bharath, S.R. / Ozturk, M.B. / Bowler, M.W. / Loo, B.Z.L. / Tergaonkar, V. / Song, H.
History
DepositionApr 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.title / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.2Nov 22, 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
C: DNA (5'-D(P*CP*GP*GP*GP*GP*AP*CP*CP*CP*GP*GP*AP*AP*GP*GP*G)-3')
D: DNA (5'-D(P*GP*CP*CP*CP*TP*TP*CP*CP*GP*GP*GP*TP*CP*CP*CP*C)-3')
B: Protein C-ets-1
A: Nuclear factor NF-kappa-B p100 subunit


Theoretical massNumber of molelcules
Total (without water)56,0824
Polymers56,0824
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.414, 71.414, 262.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

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


Mass: 5014.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*GP*CP*CP*CP*TP*TP*CP*CP*GP*GP*GP*TP*CP*CP*CP*C)-3')


Mass: 4787.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Protein C-ets-1 / p54


Mass: 13114.947 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETS1, EWSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P14921
#4: Protein Nuclear factor NF-kappa-B p100 subunit / DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 protein / Nuclear factor ...DNA-binding factor KBF2 / H2TF1 / Lymphocyte translocation chromosome 10 protein / Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 / Oncogene Lyt-10 / Lyt10


Mass: 33165.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFKB2, LYT10 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00653

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0 and 2.0 M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→71.41 Å / Num. obs: 15992 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.3
Reflection shellResolution: 2.99→3.22 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.8 / Num. unique obs: 2514 / CC1/2: 0.82 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0216refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A3Q, 1K78

1a3q

1k78


Resolution: 2.99→71.41 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.875 / SU B: 38.236 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 0.755 / ESU R Free: 0.4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28826 664 5.1 %RANDOM
Rwork0.25897 ---
obs0.26043 12379 89.39 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 101.287 Å2
Baniso -1Baniso -2Baniso -3
1-2.52 Å2-0 Å2-0 Å2
2--2.52 Å2-0 Å2
3----5.05 Å2
Refinement stepCycle: 1 / Resolution: 2.99→71.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 656 0 0 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0172516
X-RAY DIFFRACTIONr_bond_other_d0.0020.022004
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.7063528
X-RAY DIFFRACTIONr_angle_other_deg0.91834671
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1125207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.50523.25889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52115325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3341514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212343
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6964.977834
X-RAY DIFFRACTIONr_mcbond_other0.6964.976833
X-RAY DIFFRACTIONr_mcangle_it1.2217.4581039
X-RAY DIFFRACTIONr_mcangle_other1.2217.4581040
X-RAY DIFFRACTIONr_scbond_it0.7934.9461680
X-RAY DIFFRACTIONr_scbond_other0.7934.9471681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3557.4112489
X-RAY DIFFRACTIONr_long_range_B_refined3.61890.14410161
X-RAY DIFFRACTIONr_long_range_B_other3.61890.14310162
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.99→3.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 51 -
Rwork0.306 861 -
obs--88.72 %
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)
16.69761.5898-0.31457.2473-0.09532.9942-0.0685-0.00340.0655-0.2413-0.4341-0.60450.17310.54720.50260.3405-0.37840.07430.68960.03480.758955.808-51.825-34.552
28.35413.6774-1.21478.7985-0.19182.7262-0.31780.4720.2665-0.70080.1532-0.61210.07260.4190.16470.2763-0.27560.02060.47150.03720.506952.776-51.549-34.147
33.7055-2.22790.02843.875-1.33673.0642-0.4334-0.2030.22970.58210.2753-0.3808-0.39750.04530.15810.3951-0.2619-0.08910.3509-0.08050.412839.199-46.201-23.161
42.2097-0.7901-0.21294.3705-2.18525.1726-0.3710.2026-0.5918-0.22130.53580.63830.293-0.9047-0.16480.5541-0.15520.0430.6293-0.02770.568126.257-62.449-9.353
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C-5 - 10
2X-RAY DIFFRACTION2D107 - 122
3X-RAY DIFFRACTION3B332 - 437
4X-RAY DIFFRACTION4A226 - 328

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