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- PDB-8y1z: Crystal structure of the Mcl-1 in complex with a Short BH3 peptid... -

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Basic information

Entry
Database: PDB / ID: 8y1z
TitleCrystal structure of the Mcl-1 in complex with a Short BH3 peptide of BAK
Components
  • Induced myeloid leukemia cell differentiation protein Mcl-1
  • Short BH3 peptide from Bcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / MCL-1 / BAK / BH3
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / BH domain binding / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / BH domain binding / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cell fate determination / B cell apoptotic process / cellular homeostasis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / porin activity / thymocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / BH3 domain binding / B cell homeostasis / positive regulation of proteolysis / negative regulation of anoikis / blood vessel remodeling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / protein transmembrane transporter activity / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Pyroptosis / cellular response to unfolded protein / animal organ regeneration / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / response to cytokine / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / response to gamma radiation / establishment of localization in cell / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / : / response to hydrogen peroxide / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / Signaling by ALK fusions and activated point mutants / positive regulation of neuron apoptotic process / protein-folding chaperone binding / channel activity / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / positive regulation of apoptotic process / protein heterodimerization activity / response to xenobiotic stimulus / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / DNA damage response / protein-containing complex binding / negative regulation of apoptotic process / endoplasmic reticulum / protein homodimerization activity / mitochondrion / nucleoplasm / metal ion binding / identical protein binding / nucleus / membrane / 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 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.914 Å
AuthorsWang, H. / Guo, M. / Wei, H. / Chen, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31900880 China
National Natural Science Foundation of China (NSFC)82273496 China
National Natural Science Foundation of China (NSFC)819740748 China
Citation
Journal: Cell Death Differ. / Year: 2025
Title: Deciphering molecular specificity in MCL-1/BAK interaction and its implications for designing potent MCL-1 inhibitors.
Authors: Wei, H. / Wang, H. / Xiang, S. / Wang, J. / Qu, L. / Chen, X. / Guo, M. / Lu, X. / Chen, Y.
#1: Journal: Res Sq / Year: 2024
Title: Deciphering Molecular Specificity in MCL-1/BAK Interaction and Its Implications for Designing Potent MCL-1 Inhibitors
Authors: Chen, Y. / Wei, H. / Wang, H. / Xiang, S. / Wang, J. / Qu, L. / Chen, X. / Guo, M. / Lu, X.
History
DepositionJan 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2025Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Induced myeloid leukemia cell differentiation protein Mcl-1
B: Short BH3 peptide from Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)19,6492
Polymers19,6492
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-9 kcal/mol
Surface area8400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.742, 48.298, 63.527
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

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Components

#1: Protein Induced myeloid leukemia cell differentiation protein Mcl-1 / Bcl-2-like protein 3 / Bcl2-L-3 / Bcl-2-related protein EAT/mcl1 / mcl1/EAT


Mass: 17922.344 Da / Num. of mol.: 1 / Fragment: UNP residues 171-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCL1, BCL2L3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07820
#2: Protein/peptide Short BH3 peptide from Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 1726.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16611
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2M Lithium Acetate, 18-25% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.914→22.57 Å / Num. obs: 11590 / % possible obs: 97.95 % / Redundancy: 12.1 % / Biso Wilson estimate: 23.32 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08474 / Rpim(I) all: 0.0248 / Rrim(I) all: 0.08841 / Net I/σ(I): 15.3
Reflection shellResolution: 1.914→1.983 Å / Redundancy: 9 % / Rmerge(I) obs: 0.3896 / Mean I/σ(I) obs: 3.96 / Num. unique obs: 1048 / CC1/2: 0.966 / CC star: 0.991 / Rpim(I) all: 0.1325 / Rrim(I) all: 0.4122 / % possible all: 90.67

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.914→22.57 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 1163 10.04 %
Rwork0.1913 --
obs0.1957 11581 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.914→22.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 0 124 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111382
X-RAY DIFFRACTIONf_angle_d1.0541857
X-RAY DIFFRACTIONf_dihedral_angle_d25.403523
X-RAY DIFFRACTIONf_chiral_restr0.052207
X-RAY DIFFRACTIONf_plane_restr0.005241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9144-2.00150.30991400.22681183X-RAY DIFFRACTION92
2.0015-2.1070.25951360.21291256X-RAY DIFFRACTION96
2.107-2.23890.24531380.20861287X-RAY DIFFRACTION99
2.2389-2.41160.24491450.20921316X-RAY DIFFRACTION99
2.4116-2.6540.26511470.21571310X-RAY DIFFRACTION99
2.654-3.03740.28541480.20511317X-RAY DIFFRACTION100
3.0374-3.82440.22971450.16631341X-RAY DIFFRACTION100
3.8244-22.570.18621640.17461408X-RAY DIFFRACTION99

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