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- PDB-9foi: Structure of human KCTD1 -

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Basic information

Entry
Database: PDB / ID: 9foi
TitleStructure of human KCTD1
ComponentsBTB/POZ domain-containing protein KCTD1
KeywordsLIGASE / KCTD1 / Potassium channel tetramerization domain containing 1 / BTB
Function / homology
Function and homology information


Negative regulation of activity of TFAP2 (AP-2) family transcription factors / transcription factor binding / protein homooligomerization / transcription corepressor activity / negative regulation of DNA-templated transcription / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
: / : / BTB/POZ domain-containing protein KCTD1/15, C-terminal domain / Potassium channel tetramerisation-type BTB domain / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
IODIDE ION / SUCCINIC ACID / BTB/POZ domain-containing protein KCTD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsPinkas, D.M. / Richardson, W. / Bufton, J.C. / Hunt, A.E. / Manning, C.E. / Shrestha, L. / Borkowska, O. / Pike, A.C.W. / Burgess-Brown, N.A. / Bullock, A.N.
Funding support Switzerland, United Kingdom, 2items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 Switzerland
Wellcome Trust106169/ZZ14/Z United Kingdom
CitationJournal: Structure / Year: 2024
Title: A BTB extension and ion-binding domain contribute to the pentameric structure and TFAP2A binding of KCTD1.
Authors: Pinkas, D.M. / Bufton, J.C. / Hunt, A.E. / Manning, C.E. / Richardson, W. / Bullock, A.N.
History
DepositionJun 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB/POZ domain-containing protein KCTD1
B: BTB/POZ domain-containing protein KCTD1
C: BTB/POZ domain-containing protein KCTD1
D: BTB/POZ domain-containing protein KCTD1
E: BTB/POZ domain-containing protein KCTD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,61117
Polymers147,5735
Non-polymers1,03712
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25760 Å2
ΔGint-103 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.558, 96.634, 115.995
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
BTB/POZ domain-containing protein KCTD1 / Potassium channel tetramerization domain-containing protein 1


Mass: 29514.652 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: ; / Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD1, C18orf5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q719H9

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Non-polymers , 5 types, 75 molecules

#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 6
Details: 0.1 M SPG pH 6.0 (mix ratio 2:7:7 succinate/sodium dihydrogen phosphate/glycine) and 60.0% MPD. Cryoprotected with mother liquor supplemented with 25% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.71→114.84 Å / Num. obs: 40432 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 56.99 Å2 / CC1/2: 0.993 / Net I/σ(I): 7
Reflection shellResolution: 2.71→2.85 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5875 / CC1/2: 0.428

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→66.89 Å / SU ML: 0.3898 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.2948
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2472 1955 4.85 %
Rwork0.2068 38388 -
obs0.2087 40343 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.76 Å2
Refinement stepCycle: LAST / Resolution: 2.71→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8325 0 53 63 8441
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00468577
X-RAY DIFFRACTIONf_angle_d0.713811597
X-RAY DIFFRACTIONf_chiral_restr0.04951272
X-RAY DIFFRACTIONf_plane_restr0.00421516
X-RAY DIFFRACTIONf_dihedral_angle_d13.69613213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.36561290.30512690X-RAY DIFFRACTION98.43
2.77-2.850.3381390.3022719X-RAY DIFFRACTION99.76
2.85-2.930.32281370.292738X-RAY DIFFRACTION99.83
2.93-3.030.3381320.27332738X-RAY DIFFRACTION99.9
3.03-3.140.31581480.24962739X-RAY DIFFRACTION99.97
3.14-3.260.28021440.24392694X-RAY DIFFRACTION100
3.26-3.410.26821320.20652757X-RAY DIFFRACTION100
3.41-3.590.24091320.19922783X-RAY DIFFRACTION100
3.59-3.810.22311470.17942704X-RAY DIFFRACTION100
3.81-4.110.24011410.1782727X-RAY DIFFRACTION99.93
4.11-4.520.21291600.17352761X-RAY DIFFRACTION100
4.52-5.180.21561550.17832729X-RAY DIFFRACTION99.97
5.18-6.520.24291290.21492777X-RAY DIFFRACTION99.97
6.52-66.890.21371300.19552832X-RAY DIFFRACTION99.43

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