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- PDB-4yk9: Complex structure of BCL-XL and mutated BIM BH3 domain -

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Basic information

Entry
Database: PDB / ID: 4yk9
TitleComplex structure of BCL-XL and mutated BIM BH3 domain
Components
  • BH3BIM
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS / BCL-XL / BIM / BH3 / complex
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / synaptic vesicle recycling via endosome / RAS processing / positive regulation of synaptic vesicle clustering / BH domain binding / apoptotic process in bone marrow cell / positive regulation of synaptic vesicle endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of synaptic vesicle exocytosis / synaptic vesicle recycling via endosome / RAS processing / positive regulation of synaptic vesicle clustering / BH domain binding / apoptotic process in bone marrow cell / positive regulation of synaptic vesicle endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / regulation of mitochondrial membrane permeability / negative regulation of execution phase of apoptosis / fertilization / regulation of growth / Bcl-2 family protein complex / response to cycloheximide / clathrin binding / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / hepatocyte apoptotic process / germ cell development / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of ATP biosynthetic process / negative regulation of anoikis / BH3 domain binding / regulation of synaptic vesicle endocytosis / 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 / regulation of long-term synaptic depression / extrinsic apoptotic signaling pathway in absence of ligand / clathrin-coated pit / response to cytokine / MDM2/MDM4 family protein binding / release of cytochrome c from mitochondria / response to ischemia / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / mitochondrion organization / response to radiation / cellular response to gamma radiation / male gonad development / response to virus / mitochondrial membrane / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle / synaptic vesicle membrane / presynapse / channel activity / GTPase binding / neuron apoptotic process / regulation of apoptotic process / spermatogenesis / nuclear membrane / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / cell population proliferation / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / positive regulation of cell population proliferation / centrosome / protein kinase binding / negative regulation of apoptotic process / protein-containing complex binding / endoplasmic reticulum / mitochondrion / membrane / identical protein binding / cytoplasm / cytosol
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 / Blc2-like / Apoptosis Regulator Bcl-x ...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 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHa, N.C. / Kim, J.S.
Citation
Journal: To be published
Title: Complex structure of BCL-XL and mutated BIM BH3 domain
Authors: Ha, N.C. / Kim, J.S.
#1: Journal: Immunity / Year: 2003
Title: The structure of a Bcl-xL/Bim fragment complex: implications for Bim function.
Authors: Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: BH3BIM
F: Bcl-2-like protein 1
G: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47310
Polymers49,1904
Non-polymers2836
Water2,108117
1
A: Bcl-2-like protein 1
B: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7846
Polymers24,5952
Non-polymers1894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area8040 Å2
MethodPISA
2
F: Bcl-2-like protein 1
G: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6894
Polymers24,5952
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.738, 81.738, 42.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 21925.014 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Production host: Escherichia coli (E. coli) / References: UniProt: Q64373
#2: Protein/peptide BH3BIM


Mass: 2669.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6), 0.01 M calcium chloride and 15% v/v 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 37932 / % possible obs: 99.2 % / Redundancy: 6.4 % / Net I/σ(I): 2.08

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data processing
Cootmodel building
MOLREPphasing
RefinementResolution: 1.7→19.633 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1745 5.01 %
Rwork0.1923 --
obs0.1941 34825 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 15 117 2812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072767
X-RAY DIFFRACTIONf_angle_d1.1773747
X-RAY DIFFRACTIONf_dihedral_angle_d16.797998
X-RAY DIFFRACTIONf_chiral_restr0.072376
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.37891460.34672674X-RAY DIFFRACTION98
1.75-1.80640.33851350.3092806X-RAY DIFFRACTION99
1.8064-1.8710.29031370.28162743X-RAY DIFFRACTION99
1.871-1.94580.29331360.24152768X-RAY DIFFRACTION99
1.9458-2.03430.28231540.22142750X-RAY DIFFRACTION100
2.0343-2.14140.26741510.20322775X-RAY DIFFRACTION100
2.1414-2.27540.21161610.16622722X-RAY DIFFRACTION100
2.2754-2.45080.19851250.1712772X-RAY DIFFRACTION100
2.4508-2.69680.22641410.17362784X-RAY DIFFRACTION100
2.6968-3.08580.22871530.17032762X-RAY DIFFRACTION100
3.0858-3.88280.18311650.15762767X-RAY DIFFRACTION100
3.8828-19.63410.17741410.16432757X-RAY DIFFRACTION100

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