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- PDB-6vg8: Crystal structure of the DNA binding domains of human FLI1 and Ru... -

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Basic information

Entry
Database: PDB / ID: 6vg8
TitleCrystal structure of the DNA binding domains of human FLI1 and Runx2 in complex with 16-mer DNA CAGAGGATGTGGCTTC
Components
  • 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 / Oncogenesis / Ewing sarcoma / Enhancer / Bone cancer / Leukemia / ETS-family / Runt-family
Function / homology
Function and homology information


ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / osteoblast fate commitment / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX2 regulates bone development / RUNX2 regulates chondrocyte maturation / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / response to sodium phosphate ...ligamentous ossification / regulation of fibroblast growth factor receptor signaling pathway / osteoblast fate commitment / regulation of odontogenesis of dentin-containing tooth / chondrocyte development / RUNX2 regulates bone development / RUNX2 regulates chondrocyte maturation / bHLH transcription factor binding / positive regulation of chondrocyte differentiation / response to sodium phosphate / hemostasis / YAP1- and WWTR1 (TAZ)-stimulated gene expression / RUNX2 regulates genes involved in cell migration / RUNX2 regulates genes involved in differentiation of myeloid cells / Transcriptional regulation by RUNX2 / endochondral ossification / SMAD protein signal transduction / embryonic cranial skeleton morphogenesis / embryonic forelimb morphogenesis / blood circulation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / osteoblast development / megakaryocyte development / smoothened signaling pathway / positive regulation of stem cell proliferation / bone mineralization / regulation of cell differentiation / odontogenesis of dentin-containing tooth / RUNX2 regulates osteoblast differentiation / hemopoiesis / T cell differentiation / regulation of ossification / positive regulation of osteoblast differentiation / chondrocyte differentiation / BMP signaling pathway / negative regulation of smoothened signaling pathway / cell maturation / ossification / epithelial cell proliferation / stem cell proliferation / positive regulation of epithelial cell proliferation / stem cell differentiation / animal organ morphogenesis / neuron differentiation / chromatin DNA binding / osteoblast differentiation / Transcriptional regulation of granulopoiesis / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / nuclear body / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / 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. / SAM / Pointed domain ...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. / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.31 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


Theoretical massNumber of molelcules
Total (without water)35,5984
Polymers35,5984
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-31 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.427, 104.427, 326.382
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 sequence is the remainder of an affinity tag after its cleavage and removal.
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 oligomer / 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 oligomer / 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: 13701.669 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

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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: 7.22 Å3/Da / Density % sol: 82.95 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 7% w/v PEG 4000, 50 mM Na Citrate, pH 5.6, 4% v/v isopropanol

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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: Mar 10, 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: 16635 / % possible obs: 93.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 12.9
Reflection shellResolution: 3.25→3.31 Å / Rmerge(I) obs: 0.433 / Num. unique obs: 696

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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: 5JVT

5jvt


Resolution: 4.31→34.21 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.962 / SU B: 74.824 / SU ML: 0.835 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.709
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 409 5.3 %RANDOM
Rwork0.273 ---
obs0.2736 7298 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 410.55 Å2 / Biso mean: 246.997 Å2 / Biso min: 165.91 Å2
Baniso -1Baniso -2Baniso -3
1-6.15 Å23.08 Å20 Å2
2--6.15 Å20 Å2
3----19.97 Å2
Refinement stepCycle: final / Resolution: 4.31→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1720 656 0 0 2376
Num. residues----248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122494
X-RAY DIFFRACTIONr_bond_other_d0.0030.0181984
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.53509
X-RAY DIFFRACTIONr_angle_other_deg1.1771.8444608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9285214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04320.594101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3315297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5651517
X-RAY DIFFRACTIONr_chiral_restr0.0530.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02568
LS refinement shellResolution: 4.31→4.418 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.621 31 -
Rwork0.513 498 -
obs--99.81 %

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