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- PDB-9efw: Co-crystal structure of yeast Forkhead transcription factor Fkh1 ... -

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Basic information

Entry
Database: PDB / ID: 9efw
TitleCo-crystal structure of yeast Forkhead transcription factor Fkh1 bound to DNA
Components
  • (DNA) x 2
  • Fork head protein homolog 1
KeywordsDNA BINDING PROTEIN/DNA / DNA binding / Transcription factor / DNA shape readout / Forkhead proteins / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of silent mating-type cassette heterochromatin formation / negative regulation of pseudohyphal growth / donor selection / positive regulation of DNA replication initiation / SUMOylation of transcription factors / centromeric DNA binding / mRNA 3'-end processing / termination of RNA polymerase II transcription / positive regulation of DNA-templated DNA replication initiation / Estrogen-dependent gene expression ...positive regulation of silent mating-type cassette heterochromatin formation / negative regulation of pseudohyphal growth / donor selection / positive regulation of DNA replication initiation / SUMOylation of transcription factors / centromeric DNA binding / mRNA 3'-end processing / termination of RNA polymerase II transcription / positive regulation of DNA-templated DNA replication initiation / Estrogen-dependent gene expression / DNA replication origin binding / negative regulation of transcription elongation by RNA polymerase II / G1/S transition of mitotic cell cycle / DNA-binding transcription repressor activity, RNA polymerase II-specific / G2/M transition of mitotic cell cycle / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
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. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. ...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. / 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) / Fork head protein homolog 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, G.L. / Jiang, Y. / Sun, Y. / Nasertorabi, F. / Batyuk, A. / Aparicio, O.M. / Cherezov, V. / Rohs, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130376 United States
CitationJournal: To Be Published
Title: Crystal structure of yeast Fkh1 transcription factor bound to DNA
Authors: Wang, G.L. / Jiang, Y. / Sun, Y. / Nasertorabi, F. / Batyuk, A. / Aparicio, O.M. / Cherezov, V. / Rohs, R.
History
DepositionNov 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fork head protein homolog 1
B: Fork head protein homolog 1
D: DNA
C: DNA
F: DNA
E: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9068
Polymers51,8286
Non-polymers782
Water1,78399
1
A: Fork head protein homolog 1
F: DNA
E: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9534
Polymers25,9143
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-26 kcal/mol
Surface area12220 Å2
MethodPISA
2
B: Fork head protein homolog 1
D: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9534
Polymers25,9143
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-22 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.161, 50.245, 59.041
Angle α, β, γ (deg.)110.78, 100.37, 82.63
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Fork head protein homolog 1


Mass: 14265.338 Da / Num. of mol.: 2 / Fragment: residues 299-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FKH1, YIL131C / Production host: Escherichia coli (E. coli) / References: UniProt: P40466
#2: DNA chain DNA


Mass: 5841.780 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 5806.801 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 2.34 Å3/Da / Density % sol: 47.48 % / Description: Cubic crystals
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES pH 7.0, 37.5-40% PEG 5K-MME, and 200mM of ammonium phosphate monobasic
PH range: 6.8-7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2023 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→29.51 Å / Num. obs: 27067 / % possible obs: 90.47 % / Redundancy: 2.9 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.029 / Net I/σ(I): 10.3
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.9 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2687 / CC1/2: 0.649 / Rpim(I) all: 0.736 / % possible all: 90.59

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Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
Blu-Icedata collection
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.51 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 33.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2374 1168 5.01 %
Rwork0.1889 --
obs0.1914 23291 90.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 1546 2 99 3535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063664
X-RAY DIFFRACTIONf_angle_d0.5975265
X-RAY DIFFRACTIONf_dihedral_angle_d24.0961549
X-RAY DIFFRACTIONf_chiral_restr0.034572
X-RAY DIFFRACTIONf_plane_restr0.005405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.30.36541500.30182835X-RAY DIFFRACTION92
2.3-2.420.3231420.28242696X-RAY DIFFRACTION89
2.42-2.570.34421380.26882621X-RAY DIFFRACTION86
2.57-2.770.29641520.262873X-RAY DIFFRACTION94
2.77-3.050.32651500.26232845X-RAY DIFFRACTION93
3.05-3.490.26061410.21612657X-RAY DIFFRACTION87
3.49-4.40.19881450.16742766X-RAY DIFFRACTION90
4.4-29.510.19221500.14152830X-RAY DIFFRACTION93
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)
13.72840.3346-1.24211.20530.55862.61840.1505-0.5335-0.35350.47440.0203-0.11420.2306-0.113600.72670.0153-0.00770.69790.01120.6039-5.89423.564850.9805
23.46340.40571.60122.78330.55333.32610.08480.25710.0952-0.20310.02410.0544-0.23550.0202-00.5598-0.03220.05730.57980.01310.521821.993715.750922.431
32.18410.4554-1.09211.59220.50961.56430.250.2701-0.4757-0.26220.16491.2246-0.0953-0.054200.683-0.0868-0.11280.66910.03780.83056.81667.568421.5477
41.43180.3313-0.9863.01820.97141.54970.1730.3957-0.7506-0.38650.16181.48810.0836-0.26310.00550.64-0.0532-0.11460.72560.09410.9386.22467.44620.7365
52.50131.2937-0.28851.3318-0.32171.2983-0.04710.2579-0.11060.3406-0.0879-0.2934-0.09880.52050.00010.65750.04460.02050.6528-0.08510.6649.059327.825744.5037
61.83951.4229-0.09321.671-0.10531.42680.12050.4431-0.2210.3688-0.2316-0.5453-0.11820.5033-0.00010.72660.0918-0.01760.7018-0.05130.6979.525427.03743.7906
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 299 through 421)
2X-RAY DIFFRACTION2(chain 'B' and resid 299 through 421)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 19)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 19)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 19)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 19)

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