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- PDB-8zeb: Crystal structure of BCL-XL bound by cp-B6X-4 -

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Basic information

Entry
Database: PDB / ID: 8zeb
TitleCrystal structure of BCL-XL bound by cp-B6X-4
Components
  • Bcl-2-like protein 1
  • THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)
KeywordsAPOPTOSIS / BCL-XL / CYCLIC PEPTIDE
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / apoptotic mitochondrial changes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / RAS processing / channel activity / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / spermatogenesis / nuclear membrane / defense response to virus / negative regulation of neuron apoptotic process / in utero embryonic development / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / 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)
Phage 203 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSun, X.N. / Liu, J.X. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800664 China
CitationJournal: Sci China Chem / Year: 2025
Title: Biphenyl-Dihydrothiazole-Cyclized Peptide Libraries for Peptide Lig-and and Drug Discovery
Authors: Liu, J.J. / Sun, X.N. / Zhuang, J. / Liu, Z.Y. / Xu, C.Y. / Wu, D.L. / Wu, C.L.
History
DepositionMay 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 29, 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: Bcl-2-like protein 1
B: Bcl-2-like protein 1
D: THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)
C: THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)


Theoretical massNumber of molelcules
Total (without water)35,9484
Polymers35,9484
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-50 kcal/mol
Surface area14560 Å2
MethodPISA
2
A: Bcl-2-like protein 1
C: THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)


Theoretical massNumber of molelcules
Total (without water)17,9742
Polymers17,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-9 kcal/mol
Surface area9500 Å2
MethodPISA
3
B: Bcl-2-like protein 1
D: THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)


Theoretical massNumber of molelcules
Total (without water)17,9742
Polymers17,9742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.022, 97.605, 93.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 16188.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07817
#2: Protein/peptide THR-PRO-GLU-TRP-ALA-SER-THR-LEU-ARG-PRO-GLU-(CCS)-(EDN)-(Z7Z)-(PRS)


Mass: 1786.014 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: TPEWASTLRPE(CCS)(EDN)(Z7Z)(PRS) / Source: (synth.) Phage 203 (virus)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 289.15 K / Method: evaporation
Details: 15% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97904 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 1.837→53.606 Å / Num. obs: 21539 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.96 Å2 / CC1/2: 0.996 / Net I/σ(I): 8
Reflection shellResolution: 1.837→2.036 Å / Num. unique obs: 3017 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YAA

7yaa


Resolution: 1.95→48.8 Å / SU ML: 0.1858 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4274 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2257 1069 4.96 %
Rwork0.1809 20463 -
obs0.1832 21532 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.83 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 0 154 2660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082582
X-RAY DIFFRACTIONf_angle_d0.86823509
X-RAY DIFFRACTIONf_chiral_restr0.0475359
X-RAY DIFFRACTIONf_plane_restr0.0057455
X-RAY DIFFRACTIONf_dihedral_angle_d7.0531773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.28951310.24752376X-RAY DIFFRACTION94.11
2.04-2.140.27141270.212543X-RAY DIFFRACTION99.66
2.14-2.280.28961320.1992532X-RAY DIFFRACTION99.89
2.28-2.450.2621230.18852587X-RAY DIFFRACTION100
2.45-2.70.21711390.18322539X-RAY DIFFRACTION100
2.7-3.090.22681460.18772575X-RAY DIFFRACTION100
3.09-3.90.21741340.16732603X-RAY DIFFRACTION100
3.9-48.80.19261370.16462708X-RAY DIFFRACTION99.93

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