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- PDB-9fq1: Structure of the disease-causing mutant P20S of human KCTD1 -

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Basic information

Entry
Database: PDB / ID: 9fq1
TitleStructure of the disease-causing mutant P20S of human KCTD1
ComponentsBTB/POZ domain-containing protein KCTD1
KeywordsSIGNALING PROTEIN / KCTD PROTEINS / SEN SYNDROME / HUMAN DISEASES / DOMAIN SWAPPING
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
: / PHOSPHATE ION / BTB/POZ domain-containing protein KCTD1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsBalasco, N. / Ruggiero, A. / Smaldone, G. / Esposito, L. / Berisio, R. / Vitagliano, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationCN00000013 Italy
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural studies of KCTD1 and its disease-causing mutant P20S provide insights into the protein function and misfunction.
Authors: Balasco, N. / Ruggiero, A. / Smaldone, G. / Pecoraro, G. / Coppola, L. / Pirone, L. / Pedone, E.M. / Esposito, L. / Berisio, R. / Vitagliano, L.
History
DepositionJun 14, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 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)147,3878
Polymers147,1585
Non-polymers2293
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21230 Å2
ΔGint-89 kcal/mol
Surface area45250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.053, 96.003, 116.805
Angle α, β, γ (deg.)90.00, 98.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29431.566 Da / Num. of mol.: 5 / Mutation: P20S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCTD1, C18orf5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q719H9
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.57 Å3/Da / Density % sol: 52.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.8 M sodium chloride, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M Potassium phosphate monobasic, 0.1 M Mes monohydrate (pH 6.5).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 30, 2018
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→15 Å / Num. obs: 52034 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.995 / Net I/σ(I): 6.8
Reflection shellResolution: 2.6→2.66 Å / Num. unique obs: 2616 / CC1/2: 0.379

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→14.992 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 2186 4.81 %
Rwork0.1936 --
obs0.196 45428 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→14.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8457 0 11 82 8550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068735
X-RAY DIFFRACTIONf_angle_d0.94411814
X-RAY DIFFRACTIONf_dihedral_angle_d16.2055265
X-RAY DIFFRACTIONf_chiral_restr0.0561295
X-RAY DIFFRACTIONf_plane_restr0.0061536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.6560.37231670.33822616X-RAY DIFFRACTION98
2.656-2.71740.35781390.31052701X-RAY DIFFRACTION100
2.7174-2.78490.31711100.28962715X-RAY DIFFRACTION100
2.7849-2.85970.37031450.27312704X-RAY DIFFRACTION100
2.8597-2.94330.32861510.28022677X-RAY DIFFRACTION100
2.9433-3.03750.2951410.26042670X-RAY DIFFRACTION100
3.0375-3.14510.32021400.24832718X-RAY DIFFRACTION100
3.1451-3.26980.3121150.23142725X-RAY DIFFRACTION100
3.2698-3.41690.30841320.2212708X-RAY DIFFRACTION100
3.4169-3.59470.25381210.20192706X-RAY DIFFRACTION100
3.5947-3.81650.22341370.17252709X-RAY DIFFRACTION100
3.8165-4.10550.19811320.17122709X-RAY DIFFRACTION100
4.1055-4.50840.1911280.15122747X-RAY DIFFRACTION99
4.5084-5.13770.1981350.14912694X-RAY DIFFRACTION100
5.1377-6.38850.2471480.18252722X-RAY DIFFRACTION99
6.3885-100.19611450.1622721X-RAY DIFFRACTION98

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