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- PDB-6vge: Crystal structure of the DNA binding domains of human transcripti... -

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Basic information

Entry
Database: PDB / ID: 6vge
TitleCrystal structure of the DNA binding domains of human transcription factor ERG, human Runx2 bound to core binding factor beta (Cbfb), 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 / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endochondral ossification / SMAD protein signal transduction / myeloid cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / embryonic cranial skeleton morphogenesis / 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 / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / RUNX2 regulates osteoblast differentiation / odontogenesis of dentin-containing tooth / hemopoiesis / regulation of cell differentiation / RUNX3 regulates p14-ARF / T cell differentiation / regulation of ossification / chondrocyte differentiation / BMP signaling pathway / positive regulation of osteoblast differentiation / cell maturation / ossification / positive regulation of epithelial cell proliferation / 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 / osteoblast differentiation / sequence-specific double-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / transcription regulator complex / Estrogen-dependent gene expression / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein phosphorylation / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / ribonucleoprotein complex / 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 / cytosol / cytoplasm
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
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: 4.25 Å
AuthorsHou, C. / 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 7, 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


Theoretical massNumber of molelcules
Total (without water)62,5315
Polymers62,5315
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.917, 103.917, 322.912
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#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 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
#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)
#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 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Details: The N-terminal AGSSHHHHHHSQDP is the affinity tag. The gaps correspond to disorder in the crystal.
Source: (gene. exp.) Homo sapiens (human) / Gene: CBFB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13951

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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: 4.03 Å3/Da / Density % sol: 69.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.6 M K/Na Tartrate, 0.1 M Hepes, pH7.0

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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: RAYONIX MX300-HS / Detector: CCD / Date: Oct 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.25→50 Å / Num. obs: 7550 / % possible obs: 94.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.9
Reflection shellResolution: 4.25→4.32 Å / Rmerge(I) obs: 1.382 / Num. unique obs: 367 / CC1/2: 0.785 / CC star: 0.938

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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: 6VGD

6vgd


Resolution: 4.25→35 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.907 / SU B: 240.05 / SU ML: 1.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.96
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3172 408 5.4 %RANDOM
Rwork0.3125 ---
obs0.3128 7120 95.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 438.53 Å2 / Biso mean: 282.708 Å2 / Biso min: 189.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å21.54 Å20 Å2
2--3.08 Å20 Å2
3----10.01 Å2
Refinement stepCycle: final / Resolution: 4.25→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2705 656 0 0 3361
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123496
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182891
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.5444850
X-RAY DIFFRACTIONr_angle_other_deg1.1081.7636710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37120.925173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.72415474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8041529
X-RAY DIFFRACTIONr_chiral_restr0.0440.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023488
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
LS refinement shellResolution: 4.25→4.359 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.585 34 -
Rwork0.521 498 -
all-532 -
obs--93.5 %
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)
14.7967-2.9543-1.04258.5329-5.188511.049-0.00730.0192-0.13010.0797-0.07390.10360.1102-0.12040.08121.052-0.59390.04210.3913-0.13920.2425-40.71815.396-44.442
23.6478-3.9148-0.8455.23612.33012.2698-0.2313-0.03290.10040.84290.8085-0.49290.73520.8483-0.57721.6519-0.4613-0.08151.1406-0.20620.2738-39.10122.424-30.639
30.6715-2.73-0.553611.59761.0283.4988-0.3677-0.30910.18482.00681.5933-0.3068-0.2405-0.5704-1.22561.7191-0.5734-0.00751.01020.29220.5638-39.26222.512-28.568
45.0021-1.4887-1.99275.11362.23161.8207-0.21290.41940.53610.14-0.02390.5335-0.0791-0.67850.23681.3479-0.2408-0.01391.0571-0.0210.4596-51.11539.798-15.329
54.2613-1.7241-2.29040.98360.89051.26070.28681.3686-0.20280.1088-0.42920.8663-0.3849-0.80540.14232.8022-0.0191-0.19672.27350.14462.3602-62.57754.608-23.647
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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