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

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Basic information

Entry
Database: PDB / ID: 9tlv
TitleDe novo designed single-chain antiparallel coiled-coil hairpin with binding site for MCL-1, Sc-apCC-2-MCL-1-3 in complex with MCL-1
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • Sc-apCC-2-MCL-1-3
KeywordsDE NOVO PROTEIN / Protein Binder / Computational Design / Coiled-coil / complex
Function / homology
Function and homology information


positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / transmembrane protein transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand ...positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / cellular homeostasis / mitochondrial fusion / Bcl-2 family protein complex / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / transmembrane protein transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / response to cytokine / negative regulation of autophagy / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / Signaling by ALK fusions and activated point mutants / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of apoptotic process / DNA damage response / mitochondrion / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Apoptosis regulator, Mcl-1 / 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 ...Apoptosis regulator, Mcl-1 / 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
Induced myeloid leukemia cell differentiation protein Mcl-1
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMylemans, B. / Acevedo-Jake, A. / 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
A: Sc-apCC-2-MCL-1-3
B: Induced myeloid leukemia cell differentiation protein Mcl-1
C: Sc-apCC-2-MCL-1-3
D: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)52,4664
Polymers52,4664
Non-polymers00
Water2,558142
1
A: Sc-apCC-2-MCL-1-3
B: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)26,2332
Polymers26,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-17 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: Sc-apCC-2-MCL-1-3
D: Induced myeloid leukemia cell differentiation protein Mcl-1


Theoretical massNumber of molelcules
Total (without water)26,2332
Polymers26,2332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-15 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.194, 57.952, 63.079
Angle α, β, γ (deg.)90.000, 114.239, 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

#1: Protein Sc-apCC-2-MCL-1-3


Mass: 8467.871 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)
#2: Protein Induced myeloid leukemia cell differentiation protein Mcl-1


Mass: 17765.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MCL-1 from residue 172-327 / Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q07820
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 1.98 Å3/Da / Density % sol: 37.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.03 M Magnesium chloride hexahydrate, 0.03 M Calcium chloride dihydrate, 0.01 M Tris, 0.01M BICINE, 2.5% v/v MPD; 12.5% PEG1000; 12.5% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 10, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95374 Å / Relative weight: 1
ReflectionResolution: 2→57.52 Å / Num. obs: 27768 / % possible obs: 99.31 % / Redundancy: 13.7 % / Biso Wilson estimate: 31.36 Å2 / CC1/2: 1 / Net I/σ(I): 18.9
Reflection shellResolution: 2→2.07 Å / Num. unique obs: 2749 / 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→57.52 Å / SU ML: 0.2014 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1425
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2558 2594 4.81 %
Rwork0.2081 51291 -
obs0.2104 27658 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.62 Å2
Refinement stepCycle: LAST / Resolution: 2→57.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 0 142 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413342
X-RAY DIFFRACTIONf_angle_d1.13014523
X-RAY DIFFRACTIONf_chiral_restr0.0633539
X-RAY DIFFRACTIONf_plane_restr0.0125582
X-RAY DIFFRACTIONf_dihedral_angle_d14.09631207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.26731570.23722696X-RAY DIFFRACTION99.79
2.04-2.080.30391220.23722639X-RAY DIFFRACTION96.2
2.08-2.120.26071450.23862636X-RAY DIFFRACTION99.43
2.12-2.160.30621230.22962718X-RAY DIFFRACTION99.79
2.16-2.210.2821540.22582695X-RAY DIFFRACTION99.65
2.21-2.270.33251380.23992664X-RAY DIFFRACTION97.46
2.27-2.330.30481480.21922708X-RAY DIFFRACTION99.65
2.33-2.40.32011550.21922706X-RAY DIFFRACTION99.65
2.4-2.480.25991540.2232665X-RAY DIFFRACTION100
2.48-2.570.22111160.22112746X-RAY DIFFRACTION99.86
2.57-2.670.28781410.21832714X-RAY DIFFRACTION99.62
2.67-2.790.27791180.22692744X-RAY DIFFRACTION99.65
2.79-2.940.22641160.2172725X-RAY DIFFRACTION99.93
2.94-3.120.27911490.21672704X-RAY DIFFRACTION99.93
3.12-3.360.27711040.2052761X-RAY DIFFRACTION99.83
3.36-3.70.2321380.17842721X-RAY DIFFRACTION99.9
3.7-4.240.23651800.17832671X-RAY DIFFRACTION99.93
4.24-5.330.18741040.18612744X-RAY DIFFRACTION99.86
5.34-57.520.22011320.20712634X-RAY DIFFRACTION97.05
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)
13.39864514682-0.01936504528390.5763651483276.49993329631-0.2691490495272.39416758689-0.3929029382680.106503404711.203057661590.7133190903820.0546937208796-0.4510726274810.009067132687250.29917410120.2317470465280.130733500985-0.1179813415540.0219785618560.1749165340450.05397776588940.6283671167426.883924938910.85801005765.88483065212
22.71161429612-0.275257115489-0.6718522613479.24319157594-1.979571412832.029095547930.05325201519830.4709693514240.968502568754-0.28272596465-0.0423316092889-0.118286437505-0.0728673870713-0.0553529808640.05286861982060.153938527348-0.01802346104250.0283405968560.2255314997940.1329434208960.3413742380918.252551658910.97855946482.21518039573
32.24930151914-0.896157480312-0.5081084509942.850430573820.4013974238552.233087917760.1520584804930.863419103065-1.12747323993-0.189337034810.3289487843521.5147065250.132758464863-0.5048026374180.01461917280580.197465922701-0.00937695964123-0.1806485003780.398897670623-0.426710049583-0.09876176307187.26692003455-8.56067409469-5.25834601306
42.76170447704-0.7474354197061.378182023751.966195918231.166452495552.123640108840.2150530628491.40707016941-0.300849002785-0.655410329567-0.2967890289110.173616276437-0.134976954617-0.3765816338590.1135253256910.441302139450.0728319014726-0.01494881457120.623352090112-0.07305829282230.2064922212169.76662343834-2.54215032736-10.7231331343
53.720304749950.3602755268551.076841334544.29712202311.166259531195.78574481040.01999625666630.256531768583-1.10478397297-0.3293673325810.413118790308-0.4854955308440.6766928607390.666355614261-0.4129992911640.2263857749960.05494122672160.00427259819860.267736223784-0.06806069716520.45152204699627.3729363695-8.561568961361.16434186762
63.970658721710.2562768188970.4516091294836.779150244450.7755191509024.6434930598-0.07203531256720.295533872027-0.6641534483070.08788045302470.136624394161-0.4605999572290.60164051849-0.08537322007020.01399954186130.166356062825-0.04507540279260.03047956487440.178461857999-0.00932156000040.22641434925416.1791025364-5.747016684449.8148339416
74.2545585793-1.71328545768-1.281094560373.636697009571.675111284012.15914615061-0.04509912857340.442454975171-0.720251769682-0.0572402353089-0.08014736944330.1638342066930.15821647848-0.1418723067410.1281714777120.127613616892-0.0138840847459-0.01510578809910.19665941049-0.07238192346830.18217757557213.1586483405-7.804300581791.12412203507
83.466135597333.77557198776-0.03179303819894.208520041980.1621647028427.039440182420.1891924939470.8665476833390.948427028962-0.42867822382-0.437670025940.747339773212-0.655948778919-1.292196328940.1468684859810.2397305371980.161080661478-0.03019875895890.4289581725630.1401102081120.1912844943265.08752276286.17897603837-2.85042344811
93.966055309956.27581963823.620644018267.881611378783.0872859454.55990332259-0.121762806448-0.143446662540.177273469591-0.324675583999-0.1006886601390.208834269334-0.352890402537-0.06744656481680.1773242904080.1304927156120.1276038679850.0291307330910.239560711293-0.02580142830620.37681740507219.81969991514.6276183351-32.598597933
101.99279993536-0.715922220523-0.5635749637346.104516842231.382425488783.43190980046-0.0535033356323-0.05418719096960.3176048963350.207882410737-0.04235234883470.3181219933460.0882575386742-0.1266092159070.07619497810120.1099636863980.03170680344770.02065637992110.128211715028-0.01257422740240.13776375884324.00325513628.9263675517-30.9741041003
113.03213363926-0.307744787686-0.7031356226482.7170929412-1.177490457632.47599985033-0.0034620314441-0.697010750412-0.4124861611860.365887328611-0.129785172442-0.196627277383-0.02104778648170.2211512430980.1061079843670.203903680924-0.0365607940996-0.02278897756560.2326886394590.07239937469040.17892788636930.960211394-7.3825053591-22.7405037894
123.42295816118-0.9527734499850.1275623550224.167184490570.05974749034433.72996565597-0.173343931088-0.190728105434-0.625465348911-0.1112440306290.1192847442480.3238751735570.483025924555-0.03881012307130.08885005685290.182831678410.02223394548340.04608840578220.184848088520.005967877179690.21370741078427.8584197166-5.95285493132-38.7992127142
134.303890222612.46100721946-1.714425445453.38341400518-1.728937808551.90284448151-0.0473084286372-0.220521203699-0.60573296694-0.00477289040531-0.137063723191-0.3305357406080.1250582687960.1295225341080.1769229419460.1237129755440.00505365746544-0.0177276995790.1696853215610.03784128408110.14722142850930.8678924609-8.69734866675-30.0914031384
147.62860832994-1.65547320606-0.4823196825365.727410777581.169966938284.310714035230.128712512177-0.8060957271750.6252739966220.354206496237-0.0678317958624-0.707131526477-1.318856110950.871842456245-0.001719717843830.303290823659-0.101969559797-0.0457559825540.238644539932-0.006522777053990.12414317492838.77254004835.28422060238-25.1161667568
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 38 )AA4 - 384 - 38
22chain 'A' and (resid 39 through 69 )AA39 - 6939 - 69
33chain 'B' and (resid 0 through 19 )BB0 - 191 - 20
44chain 'B' and (resid 20 through 51 )BB20 - 5121 - 52
55chain 'B' and (resid 52 through 67 )BB52 - 6753 - 68
66chain 'B' and (resid 68 through 88 )BB68 - 8869 - 89
77chain 'B' and (resid 89 through 136 )BB89 - 13690 - 137
88chain 'B' and (resid 137 through 148 )BB137 - 148138 - 149
99chain 'C' and (resid 3 through 33 )CC3 - 331 - 31
1010chain 'C' and (resid 34 through 70 )CC34 - 7032 - 68
1111chain 'D' and (resid 0 through 67 )DD0 - 671 - 68
1212chain 'D' and (resid 68 through 88 )DD68 - 8869 - 89
1313chain 'D' and (resid 89 through 136 )DD89 - 13690 - 137
1414chain 'D' and (resid 137 through 149 )DD137 - 149138 - 150

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