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- PDB-8bzm: FOXK1-ELF1-heterodimer bound to DNA -

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Basic information

Entry
Database: PDB / ID: 8bzm
TitleFOXK1-ELF1-heterodimer bound to DNA
Components
  • (DNA) x 2
  • ETS-related transcription factor Elf-1
  • Forkhead box protein K1
KeywordsTRANSCRIPTION / transcription factor / DNA-binding protein / protein-DNA complex
Function / homology
Function and homology information


RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / canonical glycolysis / negative regulation of T cell receptor signaling pathway / muscle organ development / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / 14-3-3 protein binding / negative regulation of autophagy ...RUNX1 regulates transcription of genes involved in BCR signaling / RUNX1 regulates transcription of genes involved in interleukin signaling / canonical glycolysis / negative regulation of T cell receptor signaling pathway / muscle organ development / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / 14-3-3 protein binding / negative regulation of autophagy / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Transcription factor Elf, N-terminal / Transcription factor protein N terminal / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 ...Transcription factor Elf, N-terminal / Transcription factor protein N terminal / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / ETS-related transcription factor Elf-1 / Forkhead box protein K1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsMorgunova, E. / Popov, A. / Yin, Y. / Taipale, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2025
Title: DNA-guided transcription factor interactions extend human gene regulatory code.
Authors: Xie, Z. / Sokolov, I. / Osmala, M. / Yue, X. / Bower, G. / Pett, J.P. / Chen, Y. / Wang, K. / Cavga, A.D. / Popov, A. / Teichmann, S.A. / Morgunova, E. / Kvon, E.Z. / Yin, Y. / Taipale, J.
History
DepositionDec 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: DNA
A: Forkhead box protein K1
E: Forkhead box protein K1
F: DNA
C: DNA
D: DNA
I: Forkhead box protein K1
J: Forkhead box protein K1
B: ETS-related transcription factor Elf-1
H: ETS-related transcription factor Elf-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,50811
Polymers87,41610
Non-polymers921
Water61334
1
G: DNA
E: Forkhead box protein K1
F: DNA
H: ETS-related transcription factor Elf-1
hetero molecules

I: Forkhead box protein K1


Theoretical massNumber of molelcules
Total (without water)43,8006
Polymers43,7085
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area6670 Å2
ΔGint-44 kcal/mol
Surface area19350 Å2
2
A: Forkhead box protein K1
C: DNA
D: DNA
B: ETS-related transcription factor Elf-1

J: Forkhead box protein K1


Theoretical massNumber of molelcules
Total (without water)43,7085
Polymers43,7085
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area6360 Å2
ΔGint-46 kcal/mol
Surface area19380 Å2
Unit cell
Length a, b, c (Å)66.181, 105.868, 68.194
Angle α, β, γ (deg.)90.00, 112.94, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

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DNA chain , 2 types, 4 molecules GDFC

#1: DNA chain DNA


Mass: 5134.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: chain G (A) contains a sequence TTACTTCCTGTTTACGT / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA


Mass: 5590.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 2 types, 6 molecules AEIJBH

#2: Protein
Forkhead box protein K1 / Myocyte nuclear factor / MNF


Mass: 11114.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXK1, MNF / Plasmid: pETG20A-SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P85037
#4: Protein ETS-related transcription factor Elf-1 / E74-like factor 1


Mass: 10753.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELF1 / Plasmid: pETG20A-SBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P32519

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Non-polymers , 2 types, 35 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: PEG MME 3350, PEG 200, magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.6199 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6199 Å / Relative weight: 1
ReflectionResolution: 2.69→49.49 Å / Num. obs: 23997 / % possible obs: 99.8 % / Redundancy: 3.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.116 / Rrim(I) all: 0.232 / Net I/σ(I): 3.9 / Num. measured all: 92854
Reflection shellResolution: 2.69→2.84 Å / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 1.999 / Num. measured all: 13710 / Num. unique obs: 3493 / CC1/2: 0.399 / Rpim(I) all: 1.147 / Rrim(I) all: 2.31 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.889 / SU B: 46.509 / SU ML: 0.786 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3236 1218 5.3 %RANDOM
Rwork0.27053 ---
obs0.27352 21947 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.019 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å20 Å211.15 Å2
2---13.65 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.69→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 1408 6 34 6048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126469
X-RAY DIFFRACTIONr_bond_other_d0.0020.0155378
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.6798926
X-RAY DIFFRACTIONr_angle_other_deg1.1151.58112413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2915.441916
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8920.069288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.98315858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.971549
X-RAY DIFFRACTIONr_chiral_restr0.1610.22924
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026189
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021492
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_it8.8812.4422223
X-RAY DIFFRACTIONr_mcbond_other8.87412.4422222
X-RAY DIFFRACTIONr_mcangle_it13.95618.6312774
X-RAY DIFFRACTIONr_mcangle_other13.95418.6322775
X-RAY DIFFRACTIONr_scbond_it7.75511.3024246
X-RAY DIFFRACTIONr_scbond_other7.75511.3014247
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other12.43316.8236152
X-RAY DIFFRACTIONr_long_range_B_refined16.99118545
X-RAY DIFFRACTIONr_long_range_B_other16.99118545
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G13990.08
12D13990.08
21A30620.1
22E30620.1
31A28920.13
32I28920.13
41A29780.13
42J29780.13
51E29500.12
52I29500.12
61E30230.12
62J30230.12
71F13980.08
72C13980.08
81I31180.09
82J31180.09
91B29980.06
92H29980.06
LS refinement shellResolution: 2.695→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 78 -
Rwork0.503 1355 -
obs--80.91 %

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