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- PDB-9tlt: De novo designed single-chain antiparallel coiled-coil hairpin wi... -

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Basic information

Entry
Database: PDB / ID: 9tlt
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for KLHL20, Sc-apCC-2-KLHL20-4
ComponentsSc-apCC-2-KLHL20-4
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMylemans, B. / Woolfson, D.N.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006703/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V008412/2 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: De Novo-Designed Bifunctional
Authors: Mylemans, B. / Korona, B. / Acevedo-Jake, A.M. / MacRae, A. / Edwards, T.A. / Huang, D.T. / Wilson, A.J. / Itzhaki, L.S. / Woolfson, D.N.
History
DepositionDec 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sc-apCC-2-KLHL20-4
B: Sc-apCC-2-KLHL20-4
C: Sc-apCC-2-KLHL20-4
D: Sc-apCC-2-KLHL20-4
E: Sc-apCC-2-KLHL20-4
F: Sc-apCC-2-KLHL20-4
G: Sc-apCC-2-KLHL20-4
H: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)74,6788
Polymers74,6788
Non-polymers00
Water11,764653
1
A: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Sc-apCC-2-KLHL20-4


Theoretical massNumber of molelcules
Total (without water)9,3351
Polymers9,3351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.834, 53.711, 73.656
Angle α, β, γ (deg.)74.218, 72.058, 65.315
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
Sc-apCC-2-KLHL20-4


Mass: 9334.713 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES, 15 % w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.62 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 1.95→36.74 Å / Num. obs: 45552 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 16.16 Å2 / CC1/2: 1 / Net I/σ(I): 18.28
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 4529 / CC1/2: 0.986

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→36.74 Å / SU ML: 0.1931 / Cross valid method: FREE R-VALUE / σ(F): 2.23 / Phase error: 22.2378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 2197 4.83 %
Rwork0.1755 43302 -
obs0.1779 45499 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.45 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5070 0 0 653 5723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00825172
X-RAY DIFFRACTIONf_angle_d0.92166987
X-RAY DIFFRACTIONf_chiral_restr0.0442844
X-RAY DIFFRACTIONf_plane_restr0.0089926
X-RAY DIFFRACTIONf_dihedral_angle_d16.21742033
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.27341430.19392730X-RAY DIFFRACTION100
1.99-2.040.23711310.18022686X-RAY DIFFRACTION100
2.04-2.090.23591310.16922716X-RAY DIFFRACTION100
2.09-2.150.20871310.16452700X-RAY DIFFRACTION100
2.15-2.210.24421230.16082731X-RAY DIFFRACTION100
2.21-2.280.23231320.1712725X-RAY DIFFRACTION99.97
2.28-2.360.23471420.17582691X-RAY DIFFRACTION100
2.36-2.460.24371040.17992735X-RAY DIFFRACTION100
2.46-2.570.24991120.17772730X-RAY DIFFRACTION99.93
2.57-2.70.22851230.1812750X-RAY DIFFRACTION100
2.7-2.870.21761710.1882660X-RAY DIFFRACTION100
2.87-3.090.21981720.18262680X-RAY DIFFRACTION100
3.1-3.410.20741720.18452711X-RAY DIFFRACTION100
3.41-3.90.20941410.16362678X-RAY DIFFRACTION100
3.9-4.910.22071440.15482701X-RAY DIFFRACTION99.86
4.91-36.740.19571250.19852678X-RAY DIFFRACTION98.63

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