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

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Basic information

Entry
Database: PDB / ID: 9tlu
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for BCL-xL, Sc-apCC-2-BCL-xL-3 in complex with BCL-xL
Components
  • Bcl-2-like protein 1
  • Sc-apCC-2-BCL-xL-3
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil / complex
Function / homology
Function and homology information


The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / apoptotic mitochondrial changes / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes ...The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / apoptotic mitochondrial changes / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to cytokine / negative regulation of autophagy / regulation of mitochondrial membrane potential / regulation of cytokinesis / intrinsic apoptotic signaling pathway in response to DNA damage / endocytosis / RAS processing / synaptic vesicle membrane / nuclear membrane / channel activity / Interleukin-4 and Interleukin-13 signaling / defense response to virus / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / Apoptosis regulator, Bcl-2, BH1 motif, conserved site / Apoptosis regulator, Bcl-2 family BH1 motif signature. / Apoptosis regulator, Bcl-2, BH2 motif, conserved site / Apoptosis regulator, Bcl-2 family BH2 motif signature. / Bcl-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsMylemans, B. / Acevedo-Jake, A. / Caulton, S.G. / Edwards, T.A. / Lovering, A.L. / WIlson, A.J. / 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
B: Bcl-2-like protein 1
A: Bcl-2-like protein 1
C: Sc-apCC-2-BCL-xL-3
D: Sc-apCC-2-BCL-xL-3


Theoretical massNumber of molelcules
Total (without water)52,3394
Polymers52,3394
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.441, 85.441, 145.517
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 or (resid 3 and (name...
d_2ens_1(chain "B" and (resid 2 through 23 or (resid 24...
d_1ens_2(chain "C" and (resid 5 through 7 or (resid 8...
d_2ens_2(chain "D" and (resid 5 through 41 or (resid 42...

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_1SERSERALAALAAB2 - 1432 - 143
d_21ens_1SERSERTRPTRPBA2 - 242 - 24
d_22ens_1METMETALAALABA27 - 14327 - 143
d_11ens_2ALAALALEULEUCC5 - 698 - 72
d_21ens_2ALAALALEULEUDD5 - 698 - 72

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.0890676385259, -0.995504129757, -0.0322255086085), (-0.995996966422, -0.0892636913686, 0.00469428173756), (-0.00754974471061, 0.0316784002266, -0.999469599495)1.45466689672, 2.98557069983, -27.6789536185
2given(0.0936782680206, -0.994064999204, 0.0553096687522), (-0.99223795183, -0.0977808681324, -0.0768293484025), (0.0817815935853, -0.0476831121476, -0.995508961168)4.79806280299, -1.46790618024, -31.6143270821

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Components

#1: Protein Bcl-2-like protein 1


Mass: 17506.504 Da / Num. of mol.: 2 / Mutation: 27_80del
Source method: isolated from a genetically manipulated source
Details: Deletion of loop 27-80 / Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q07817
#2: Protein Sc-apCC-2-BCL-xL-3


Mass: 8662.958 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric acid, 10% v/v MPD / PH range: 4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.99→73.99 Å / Num. obs: 20106 / % possible obs: 99.9 % / Redundancy: 20.4 % / Biso Wilson estimate: 77.44 Å2 / CC1/2: 1 / Net I/σ(I): 15.49
Reflection shellResolution: 2.99→3.42 Å / Num. unique obs: 2546 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.99→73.99 Å / SU ML: 0.4496 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.9432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3216 544 4.46 %
Rwork0.2747 11646 -
obs0.2767 12190 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.19 Å2
Refinement stepCycle: LAST / Resolution: 2.99→73.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 0 0 3287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00543346
X-RAY DIFFRACTIONf_angle_d0.85444529
X-RAY DIFFRACTIONf_chiral_restr0.047498
X-RAY DIFFRACTIONf_plane_restr0.0064592
X-RAY DIFFRACTIONf_dihedral_angle_d16.50931191
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BAX-RAY DIFFRACTIONTorsion NCS1.61057671673
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.25209796779
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.290.38831560.38182899X-RAY DIFFRACTION99.97
3.29-3.770.35791080.29712908X-RAY DIFFRACTION99.93
3.77-4.750.3121430.2752908X-RAY DIFFRACTION99.97
4.75-73.990.29491370.23892931X-RAY DIFFRACTION99.77
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)
12.99012429108-0.167316796227-0.03715982546741.04766981057-3.573119921547.63930280976-0.2162670614160.197634987430.1669829501690.1036360524020.0982065771299-0.0704933463321-0.8877269409580.3531796428550.1203163972150.750814663501-0.177186321178-0.1262207488470.358634747058-0.06174922404070.65276329365421.8074653011-22.5688702091-1.02681885571
2-1.22061108511-0.213521790329-3.28883115512.78886078858-2.206176725864.823639657150.09919088734610.0478614311307-0.2169138435870.2274700954810.0003988204288220.2851816461330.699583494932-0.902753070855-0.09417916299580.653349625545-0.314764670316-0.2127605998990.920788488424-0.09705996412730.7741635015825.6887597381-16.4834162909-27.5543116183
36.302601014510.5075335134994.313117034645.171956840461.393153752229.06507113277-0.05327813364650.319974232442-0.012082727411-0.645506244030.226682634957-0.490122383766-0.8609721084470.155745444933-0.1757150312790.465599498482-0.03647564844710.001325323834120.478698917498-0.09056106763830.52174862960227.8546013617-13.35691248-47.5439047027
41.2178542088-0.6325795264860.9684742807746.403991486572.441087040398.501487135460.418647394799-0.7706273232040.2846569150770.86701120908-0.6505057200090.1557613855410.272380586547-0.9197717633050.3282225408940.651790477008-0.153204215317-0.04755330198330.60368211865-0.04555069622050.42922784477719.7092833347-23.644470228818.8251603727
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A'AB2 - 1431 - 140
22chain 'B'BA2 - 1451 - 144
33chain 'C'CC2 - 701 - 69
44chain 'D'DD5 - 691 - 65

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