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- PDB-6vgd: Crystal structure of the DNA binding domain (DBD) of human FLI1 a... -

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Basic information

Entry
Database: PDB / ID: 6vgd
TitleCrystal structure of the DNA binding domain (DBD) of human FLI1 and the complex of the DBD of human Runx2 with 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')
  • Friend leukemia integration 1 transcription factor
  • Runt-related transcription factor 2
KeywordsTRANSCRIPTION / Ewing sarcoma / enhancer / transcription factor / oncogenesis / prostate cancer / ETS-family / Runt-family
Function / homology
Function and homology information


ligamentous ossification / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / RUNX2 regulates bone development / positive regulation of CD8-positive, alpha-beta T cell differentiation / RUNX2 regulates chondrocyte maturation / negative regulation of CD4-positive, alpha-beta T cell differentiation ...ligamentous ossification / RUNX3 regulates RUNX1-mediated transcription / RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / RUNX2 regulates bone development / 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 / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / response to sodium phosphate / RUNX2 regulates genes involved in cell migration / hemostasis / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Transcriptional regulation by RUNX2 / SMAD protein signal transduction / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / RUNX2 regulates genes involved in differentiation of myeloid cells / RUNX3 Regulates Immune Response and Cell Migration / chondrocyte differentiation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / RUNX2 regulates osteoblast differentiation / hemopoiesis / positive regulation of osteoblast differentiation / regulation of cell differentiation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / BMP signaling pathway / RUNX3 regulates p14-ARF / ossification / animal organ morphogenesis / chromatin DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Regulation of RUNX3 expression and activity / transcription by RNA polymerase II / cell population proliferation / osteoblast differentiation / Transcriptional regulation of granulopoiesis / protein polyubiquitination / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / neuron differentiation / transcription regulator complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / sequence-specific DNA binding / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of DNA-templated transcription / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / DNA-templated transcription / nucleoplasm / ATP binding / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Friend leukemia integration 1 transcription factor, pointed domain / 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 ...Friend leukemia integration 1 transcription factor, pointed domain / 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) / Friend leukemia integration 1 transcription factor / Runt-related transcription factor 2 / Core-binding factor subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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: Friend leukemia integration 1 transcription factor
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)59,7025
Polymers59,7025
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6980 Å2
ΔGint-39 kcal/mol
Surface area22410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.513, 104.513, 322.040
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 Friend leukemia integration 1 transcription factor / Proto-oncogene Fli-1 / Transcription factor ERGB


Mass: 12098.655 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Details: The N-terminal GPHM is left from the affinity tag after its cleavage.
Source: (gene. exp.) Homo sapiens (human) / Gene: FLI1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q01543
#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
Source method: isolated from a genetically manipulated source
Details: The N-terminal region AGSSHHHHHHSQDP is a cloned affinity tag.
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: 4.26 Å3/Da / Density % sol: 71.1 %
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: 3.25→50 Å / Num. obs: 17612 / % possible obs: 99.3 % / Redundancy: 12.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9
Reflection shellResolution: 3.25→3.31 Å / Rmerge(I) obs: 0.954 / Num. unique obs: 825

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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: 6VG8

6vg8


Resolution: 4.2→35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.949 / SU B: 187.362 / SU ML: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.823
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2932 419 5.1 %RANDOM
Rwork0.2948 ---
obs0.2947 7806 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 466.18 Å2 / Biso mean: 285.539 Å2 / Biso min: 167.33 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å21.27 Å20 Å2
2--2.54 Å20 Å2
3----8.23 Å2
Refinement stepCycle: final / Resolution: 4.2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2703 656 0 0 3359
Num. residues----368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123494
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182893
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.5444848
X-RAY DIFFRACTIONr_angle_other_deg1.1721.7636712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.13820.925173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8415472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1061529
X-RAY DIFFRACTIONr_chiral_restr0.0510.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023488
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02805
LS refinement shellResolution: 4.2→4.307 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 23 -
Rwork0.495 543 -
all-566 -
obs--100 %
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)
14.6204-2.4539-0.73016.7537-5.29629.9152-0.14330.0013-0.1532-0.19370.1187-0.17570.29170.0950.02460.9563-0.49770.04490.3056-0.13620.3432-40.965915.5076-44.327
22.1082-1.31770.17792.33271.74922.5465-0.04670.4895-0.14480.83130.8045-0.45960.84471.1124-0.75781.4356-0.0921-0.10091.3741-0.34260.4625-39.330622.5731-30.5684
30.5134-0.106-1.628710.528-0.19655.74490.01750.1228-0.00640.39780.4361-0.3863-0.1373-0.5162-0.45360.9129-0.4682-0.12540.49650.04980.4374-39.486122.6252-28.509
48.113-2.0424-5.13574.45513.85256.2216-0.20470.3150.2860.0953-0.16170.3369-0.3172-1.16470.36651.2626-0.16-0.10290.98660.05430.4891-51.431139.9666-15.2561
54.9658-1.3046-2.32860.9980.36631.96240.08611.34250.3949-0.035-0.13870.8933-0.7475-0.54440.05272.35230.0723-0.20212.02370.23362.0736-62.936854.932-23.5378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A275 - 372
2X-RAY DIFFRACTION2B1 - 16
3X-RAY DIFFRACTION3C2 - 17
4X-RAY DIFFRACTION4D60 - 176
5X-RAY DIFFRACTION5G2 - 139

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