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Basic information

Entry
Database: PDB / ID: 6vgg
TitleCrystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), and mithramycin, in complex with 16mer DNA CAGAGGATGTGGCTTC
Components
  • Core-binding factor subunit beta
  • DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
  • DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')
  • Runt-related transcription factor 2
  • Transcriptional regulator ERG
KeywordsTRANSCRIPTION / Ewing sarcoma / enhancer / transcription factor / oncogenesis / prostate cancer / ETS-family / Runt-family
Function / homology
Function and homology information


ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / RUNX3 regulates RUNX1-mediated transcription / osteoblast fate commitment / RUNX1 regulates transcription of genes involved in BCR signaling / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex ...ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / RUNX3 regulates RUNX1-mediated transcription / osteoblast fate commitment / RUNX1 regulates transcription of genes involved in BCR signaling / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX1 regulates transcription of genes involved in interleukin signaling / RUNX2 regulates bone development / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / lymphocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / response to sodium phosphate / RUNX2 regulates genes involved in cell migration / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Transcriptional regulation by RUNX2 / RUNX2 regulates genes involved in differentiation of myeloid cells / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endochondral ossification / SMAD protein signal transduction / embryonic cranial skeleton morphogenesis / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / definitive hemopoiesis / embryonic forelimb morphogenesis / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / osteoblast development / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / smoothened signaling pathway / positive regulation of stem cell proliferation / bone mineralization / RUNX2 regulates osteoblast differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / odontogenesis of dentin-containing tooth / regulation of cell differentiation / hemopoiesis / RUNX3 regulates p14-ARF / T cell differentiation / regulation of ossification / chondrocyte differentiation / positive regulation of osteoblast differentiation / BMP signaling pathway / cell maturation / ossification / epithelial cell proliferation / positive regulation of epithelial cell proliferation / stem cell proliferation / negative regulation of smoothened signaling pathway / stem cell differentiation / Regulation of RUNX3 expression and activity / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / chromatin DNA binding / Transcriptional regulation of granulopoiesis / neuron differentiation / protein polyubiquitination / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / osteoblast differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / gene expression / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein phosphorylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ribonucleoprotein complex / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily ...Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Core-binding factor, beta subunit / Core-binding factor, beta subunit superfamily / Core binding factor beta subunit / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Sterile alpha motif/pointed domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
mithramycin / DNA / DNA (> 10) / Transcriptional regulator ERG / Runt-related transcription factor 2 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 Å
AuthorsHou, C. / Rohr, J. / Tsodikov, O.V.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)PC150300P1 United States
Department of Defense (DOD, United States)PC150300P2 United States
CitationJournal: Structure / Year: 2021
Title: Allosteric interference in oncogenic FLI1 and ERG transactions by mithramycins.
Authors: Hou, C. / Mandal, A. / Rohr, J. / Tsodikov, O.V.
History
DepositionJan 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Oct 11, 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
A: Transcriptional regulator ERG
B: DNA (5'-D(P*CP*AP*GP*AP*GP*GP*AP*TP*GP*TP*GP*GP*CP*TP*TP*C)-3')
C: DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')
D: Runt-related transcription factor 2
G: Core-binding factor subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7258
Polymers62,5315
Non-polymers2,1953
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-46 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.678, 104.678, 322.836
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

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Protein , 3 types, 3 molecules ADG

#1: Protein Transcriptional regulator ERG / Transforming protein ERG


Mass: 14927.827 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Details: The N-terminal GPHM sequence is left over from the affinity tag after its cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11308
#4: Protein Runt-related transcription factor 2 / Acute myeloid leukemia 3 protein / Core-binding factor subunit alpha-1 / CBF-alpha-1 / Oncogene AML- ...Acute myeloid leukemia 3 protein / Core-binding factor subunit alpha-1 / CBF-alpha-1 / Oncogene AML-3 / Osteoblast-specific transcription factor 2 / OSF-2 / Polyomavirus enhancer-binding protein 2 alpha A subunit / PEBP2-alpha A / SL3-3 enhancer factor 1 alpha A subunit / SL3/AKV core-binding factor alpha A subunit


Mass: 19542.148 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RUNX2, AML3, CBFA1, OSF2, PEBP2A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13950
#5: Protein Core-binding factor subunit beta / CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEBP2-beta / SL3-3 enhancer ...CBF-beta / Polyomavirus enhancer-binding protein 2 beta subunit / PEBP2-beta / SL3-3 enhancer factor 1 subunit beta / SL3/AKV core-binding factor beta subunit


Mass: 18263.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The N-terminal sequence AGSSHHHHHHSQDP is the affinity tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CBFB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13951

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DNA chain , 2 types, 2 molecules BC

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


Mass: 4954.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(P*GP*AP*AP*GP*CP*CP*AP*CP*AP*TP*CP*CP*TP*CP*TP*G)-3')


Mass: 4843.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA / Source: (synth.) Homo sapiens (human)

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Non-polymers , 3 types, 5 molecules

#6: Chemical ChemComp-QWP / mithramycin / (1S)-5-deoxy-1-C-[(2S,3S)-7-{[2,6-dideoxy-3-O-(2,6-dideoxy-beta-D-arabino-hexopyranosyl)-beta-D-arabino-hexopyranosyl]oxy}-3-{[2,6-dideoxy-3-C-methyl-beta-D-ribo-hexopyranosyl-(1->3)-2,6-dideoxy-beta-D-lyxo-hexopyranosyl-(1->3)-2,6-dideoxy-beta-D-arabino-hexopyranosyl]oxy}-5,10-dihydroxy-6-methyl-4-oxo-1,2,3,4-tetrahydroanthracen-2-yl]-1-O-methyl-D-xylulose


Mass: 1085.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C52H76O24 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 4.09 Å3/Da / Density % sol: 69.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.3 M K/Na Tartrate, 50 mM Hepes, pH 7.0, soaked in 1 mM mithramycin-Mg

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.3→50 Å / Num. obs: 7632 / % possible obs: 98.3 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 28.6
Reflection shellResolution: 4.3→4.37 Å / Rmerge(I) obs: 0.871 / Num. unique obs: 348 / CC1/2: 0.934 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VGE

6vge


Resolution: 4.31→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.925 / SU B: 163.205 / SU ML: 0.938 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.875
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2846 372 4.9 %RANDOM
Rwork0.2514 ---
obs0.2531 7214 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 471.04 Å2 / Biso mean: 287.314 Å2 / Biso min: 175.73 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å22.23 Å20 Å2
2--4.46 Å20 Å2
3----14.46 Å2
Refinement stepCycle: final / Resolution: 4.31→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 656 152 2 3515
Biso mean--268.15 201.86 -
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0133667
X-RAY DIFFRACTIONr_bond_other_d0.0050.0183023
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.6125104
X-RAY DIFFRACTIONr_angle_other_deg1.1221.8417032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2065330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0320.925173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89715474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.181529
X-RAY DIFFRACTIONr_chiral_restr0.0410.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023536
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
LS refinement shellResolution: 4.31→4.415 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.499 28 -
Rwork0.479 480 -
obs--94.07 %
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)
12.6882-1.87583.860610.5496-1.94556.31920.1836-0.19640.2678-0.208-0.23190.08130.0284-0.09970.04840.13770.09230.12381.2727-0.11050.2181-59.51347.227-9.502
20.6828-1.0022-1.56321.93031.96824.64281.36380.55080.38-0.4276-0.7435-0.4169-0.7659-0.447-0.62031.2230.0621-0.00181.8296-0.0860.5409-52.54645.047-23.257
37.8491-5.0258-0.59343.25440.52153.84032.14260.70880.2944-1.2405-0.5403-0.2557-0.104-0.1216-1.60241.03680.13860.06011.4290.13660.7159-52.5344.844-25.32
42.38861.0336-0.21627.6333.28445.070.10460.18230.12130.0043-0.34180.05720.84950.06690.23720.63710.2052-0.1451.26840.13420.1547-43.16225.908-38.302
50.34721.59260.37039.7282.33620.60270.5439-0.0956-0.4941.7894-0.5225-1.08990.58090.0965-0.02141.16770.9694-0.37151.70620.38851.3524-35.8578.776-29.741
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A305 - 402
2X-RAY DIFFRACTION2B1 - 16
3X-RAY DIFFRACTION3C2 - 17
4X-RAY DIFFRACTION4D111 - 227
5X-RAY DIFFRACTION5G2 - 139

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