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- PDB-8t5e: De novo design of high-affinity protein binders to bioactive heli... -

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Basic information

Entry
Database: PDB / ID: 8t5e
TitleDe novo design of high-affinity protein binders to bioactive helical peptides
Components
  • Bcl-2-like protein 11
  • Bim_fulldiff
KeywordsDE NOVO PROTEIN / Alpha-helical peptides / protein design / diffusion / deep learning
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / developmental pigmentation / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / microtubule binding / spermatogenesis / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / cytosol
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain
Similarity search - Domain/homology
Bcl-2-like protein 11
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsTorres, S.V. / Leung, P.J.Y. / Bera, A.K. / Baker, D. / Kang, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2024
Title: De novo design of high-affinity binders of bioactive helical peptides.
Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. ...Authors: Vazquez Torres, S. / Leung, P.J.Y. / Venkatesh, P. / Lutz, I.D. / Hink, F. / Huynh, H.H. / Becker, J. / Yeh, A.H. / Juergens, D. / Bennett, N.R. / Hoofnagle, A.N. / Huang, E. / MacCoss, M.J. / Exposit, M. / Lee, G.R. / Bera, A.K. / Kang, A. / De La Cruz, J. / Levine, P.M. / Li, X. / Lamb, M. / Gerben, S.R. / Murray, A. / Heine, P. / Korkmaz, E.N. / Nivala, J. / Stewart, L. / Watson, J.L. / Rogers, J.M. / Baker, D.
History
DepositionJun 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bim_fulldiff
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)19,5012
Polymers19,5012
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-17 kcal/mol
Surface area8080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.790, 66.667, 74.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Bim_fulldiff


Mass: 16226.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3274.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521

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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: 1.7 Å3/Da / Density % sol: 28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M Citric acid pH 2.5, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 3→74.3 Å / Num. obs: 2861 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 75.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.8
Reflection shellResolution: 3→3.18 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 8.8 / Num. unique obs: 445 / CC1/2: 0.985 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_4761refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→49.62 Å / SU ML: 0.3211 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.1774
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2644 159 5.64 %
Rwork0.2392 2661 -
obs0.2408 2820 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 77.56 Å2
Refinement stepCycle: LAST / Resolution: 3→49.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 0 0 1244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00291253
X-RAY DIFFRACTIONf_angle_d0.49581675
X-RAY DIFFRACTIONf_chiral_restr0.0319189
X-RAY DIFFRACTIONf_plane_restr0.0044219
X-RAY DIFFRACTIONf_dihedral_angle_d4.0288176
LS refinement shellResolution: 3→49.62 Å
RfactorNum. reflection% reflection
Rfree0.2644 159 -
Rwork0.2392 2661 -
obs--99.3 %

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