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- PDB-9e6e: Yeast Fzf1 Zn-fingers 1-3 bound to YHB1 26 bp DNA -

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Basic information

Entry
Database: PDB / ID: 9e6e
TitleYeast Fzf1 Zn-fingers 1-3 bound to YHB1 26 bp DNA
Components
  • DNA 1
  • DNA 2
  • Zinc finger protein FZF1
KeywordsDNA BINDING PROTEIN/DNA / Yeast Zn-finger Transcriptional activator / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


cyanamide metabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
: / C2H2-type zinc finger / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger protein FZF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMoore, S.A. / Ma, C. / Xiao, W.
Funding support Canada, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2019-05604 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2011-262138 Canada
Canadian Institutes of Health Research (CIHR)MOP-126155 Canada
CitationJournal: To Be Published
Title: Zn-finger transcription factor Fzf1 binds to its target DNA in a non-canonical manner
Authors: Ma, C. / Xiao, W. / Moore, S.A.
History
DepositionOct 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Zinc finger protein FZF1
E: DNA 1
F: DNA 2
B: DNA 1
C: DNA 2
A: Zinc finger protein FZF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,67412
Polymers101,2826
Non-polymers3926
Water27015
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)61.905, 66.265, 174.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 11 through 19 or resid 21...
d_2ens_1(chain "D" and (resid 11 through 19 or resid 21...
d_1ens_2chain "B"
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ASNASNCYSCYSAF11 - 1911 - 19
d_12ens_1LYSLYSGLNGLNAF21 - 7821 - 78
d_13ens_1ARGARGLEULEUAF80 - 8780 - 87
d_14ens_1ARGARGHISHISAF89 - 9489 - 94
d_15ens_1LYSLYSALAALAAF99 - 10199 - 101
d_16ens_1ARGARGILEILEAF103 - 104103 - 104
d_17ens_1ZNZNZNZNAJ301
d_18ens_1ZNZNZNZNAK302
d_21ens_1ASNASNCYSCYSDA11 - 1911 - 19
d_22ens_1LYSLYSGLNGLNDA21 - 7821 - 78
d_23ens_1ARGARGLEULEUDA80 - 8780 - 87
d_24ens_1ARGARGLYSLYSDA89 - 9789 - 97
d_25ens_1LYSLYSLEULEUDA99 - 10099 - 100
d_26ens_1ZNZNZNZNDG301
d_27ens_1ZNZNZNZNDH302
d_11ens_2DADADADABD11
d_21ens_2DADADADAEB11
d_11ens_3DTDTDTDTCE11
d_21ens_3DTDTDTDTFC11

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.913125995567, -0.407550327047, 0.0101807241376), (-0.407457325807, -0.913168863865, -0.0100575202445), (0.013395665959, 0.00503557255429, -0.999897594328)0.313105285305, -12.0425128099, 1.21372919699
2given(0.885143005585, -0.465286104223, -0.00554083757574), (-0.465318512219, -0.885060306107, -0.0121217465642), (0.000736104834354, 0.013307733484, -0.999911177245)0.467886858953, -11.809984447, 0.498046062992
3given(0.898011887212, -0.439781830946, -0.0129070366381), (-0.439932782357, -0.897934654395, -0.0131340566944), (-0.0058135559821, 0.0174727675791, -0.999830438104)0.0485005892421, -11.8729952331, 0.346828922592

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Components

#1: Protein Zinc finger protein FZF1 / Sulfite resistance protein 1


Mass: 34048.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FZF1, SUL1, YGL254W, NCR299 / Plasmid: PGEX-6P-1 / Details (production host): BamH1/Sal1 site / Production host: Escherichia coli (E. coli) / References: UniProt: P32805
#2: DNA chain DNA 1


Mass: 8334.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-6P-1 / Details (production host): BamH1/Sal1 site / Production host: Escherichia coli (E. coli)
#3: DNA chain DNA 2


Mass: 8258.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: FZF1 / Plasmid: PGEX-6P-1 / Details (production host): BamH1/Sal1 site / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.1 Å3/Da / Density % sol: 46.99 % / Description: Elongated prisms
Crystal growTemperature: 100 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M bis-Tris pH 5.5, and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 7, 2002 / Details: Vertical Focusing Mirror
RadiationMonochromator: Axilon DCMM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.95→36.37 Å / Num. obs: 15710 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 67.68 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Net I/σ(I): 9.6
Reflection shellResolution: 2.95→3.14 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.932 / Mean I/σ(I) obs: 2 / Num. unique obs: 2485 / CC1/2: 0.909 / Rpim(I) all: 0.386 / Rrim(I) all: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→36.37 Å / SU ML: 0.3123 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3745
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2474 773 4.98 %
Rwork0.2184 14745 -
obs0.2198 15518 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.96 Å2
Refinement stepCycle: LAST / Resolution: 2.95→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 2202 6 15 3693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633987
X-RAY DIFFRACTIONf_angle_d0.86685852
X-RAY DIFFRACTIONf_chiral_restr0.0517637
X-RAY DIFFRACTIONf_plane_restr0.011379
X-RAY DIFFRACTIONf_dihedral_angle_d27.44621740
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FAX-RAY DIFFRACTIONTorsion NCS1.55596434319
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS1.35654802663
ens_3d_2ECX-RAY DIFFRACTIONTorsion NCS1.05546968278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.140.38471250.34742392X-RAY DIFFRACTION98.47
3.14-3.380.31481160.29032349X-RAY DIFFRACTION96.48
3.38-3.720.26741350.23032418X-RAY DIFFRACTION98.57
3.72-4.260.27251130.2192479X-RAY DIFFRACTION100
4.26-5.360.22781340.20772491X-RAY DIFFRACTION99.96
5.36-36.370.2011500.17392616X-RAY DIFFRACTION99.82
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)
11.641501837640.754819890042-0.9555124635612.840297307530.4317926637022.033019664370.254344340796-0.420218050579-0.331121177721-0.249376973609-0.0576570279553-0.08271108420650.02312122915650.3940254582120.000179599410170.596952581493-0.07419441773320.01850729436590.6573413540790.03606287422340.613199074559-10.1622380398-21.39569889914.82107228172
23.3075844228-0.7582645846960.7896747413113.50456474176-1.593320110080.8642800632090.286830751651-0.381847322855-0.1034086420260.1512449506680.151552732777-0.356061685932-0.3174979629640.7233710412410.006837310620150.711502466286-0.108164149275-0.007605213649490.825645480301-0.01817246216580.710651304075-5.56023568142-19.67374972598.13856105011
34.559589356870.492782813214-1.844228682923.295034004480.0737824795390.7663241272330.2143749963410.252463008758-0.0394939703099-0.2224495253880.289482971227-0.1134874017730.2557491580060.114674998050.01429918635130.553826321669-0.0178523975445-0.0638129767050.594667811618-0.009404906321190.665194955079-1.647109770919.73687533662-7.55890719078
43.507648843430.445110652122-0.8255475084042.03630118856-0.6868715380061.17326677047-0.009387186091520.3568485941850.119660300311-0.08325866349260.1061776478850.05764157903330.122127346962-0.1681003175970.000166680751090.4896825562590.0372643374505-0.05520367216270.420489583179-0.03233099586980.526810118176-4.6924741413712.6807423001-4.6106590378
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'D' and resid 11 through 100)DA11 - 1001 - 90
22(chain 'E' or chain 'F' and resid 1 through 27)E - FE - F1 - 27
33(chain 'B' or chain 'C' and resid 1 through 27)B - CG - H1 - 27
44(chain 'A' and resid 11 through 104)AJ11 - 1041 - 94

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