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- PDB-2yq7: Structure of Bcl-xL bound to BimLOCK -

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Basic information

Entry
Database: PDB / ID: 2yq7
TitleStructure of Bcl-xL bound to BimLOCK
Components
  • BCL-2-LIKE PROTEIN 11
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / CONSTRAINED PEPTIDE / BCL-2 FAMILY
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 / apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell apoptotic process / ear development / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of T cell apoptotic process / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / tube formation / regulation of organ growth / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / NFE2L2 regulating tumorigenic genes / response to cycloheximide / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / thymocyte apoptotic process / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / T cell homeostasis / germ cell development / odontogenesis of dentin-containing tooth / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / endomembrane system / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of cell cycle / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of 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 / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / negative regulation of autophagy / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / kidney development / response to cytokine / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / 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 / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane
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 / 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 ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 11 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsSmith, B.J. / Czabotar, P.E.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Stabilizing the Pro-Apoptotic Bimbh3 Helix (Bimsahb) Does not Necessarily Enhance Affinity or Biological Activity.
Authors: Okamoto, T. / Zobel, K. / Fedorova, A. / Quan, C. / Yang, H. / Fairbrother, W.J. / Huang, D.C.S. / Smith, B.J. / Deshayes, K. / Czabotar, P.E.
History
DepositionNov 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2243
Polymers20,1312
Non-polymers921
Water2,162120
1
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 11
hetero molecules

A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4476
Polymers40,2634
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area9880 Å2
ΔGint-62.3 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.803, 35.223, 61.363
Angle α, β, γ (deg.)90.00, 101.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BCL-2-LIKE PROTEIN 1 / / BCL-XL / BCL2-L-1 / APOPTOSIS REGULATOR BCL-X


Mass: 17917.959 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q07817
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BIM BETA 5 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH / BIMEL


Mass: 2213.471 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, RESIDUES 147-164 / Mutation: YES / Source method: obtained synthetically
Details: SIDE CHAINS OF AMINO ACIDS AT POSITIONS 154 AND 158 LINKED THROUGH A LACTAM BRIDGE.
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43521
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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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: 1.92 Å3/Da / Density % sol: 35.98 % / Description: NONE
Crystal growDetails: 15 % (W/V) PEG 400, 5 % PEG 3000, 10 % GLYCEROL AND 0.1 M MES PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.0092
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0092 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12014 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 23.59 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→2.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2 / % possible all: 80.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FDL CHAIN A

3fdl


Resolution: 1.901→34.068 Å / SU ML: 0.21 / σ(F): 1.36 / Phase error: 23.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2078 593 4.9 %
Rwork0.163 --
obs0.1653 12009 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.901→34.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1322 0 6 120 1448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061368
X-RAY DIFFRACTIONf_angle_d0.9411849
X-RAY DIFFRACTIONf_dihedral_angle_d14.888484
X-RAY DIFFRACTIONf_chiral_restr0.066189
X-RAY DIFFRACTIONf_plane_restr0.004236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.901-2.09230.30111200.21052612X-RAY DIFFRACTION89
2.0923-2.3950.21441620.15872885X-RAY DIFFRACTION99
2.395-3.01720.19551470.16882907X-RAY DIFFRACTION99
3.0172-34.07340.19651640.15243012X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -7.4778 Å / Origin y: 0.2983 Å / Origin z: 16.9716 Å
111213212223313233
T0.1311 Å20.006 Å2-0.007 Å2-0.0925 Å2-0.0082 Å2--0.1526 Å2
L1.0738 °20.1548 °2-0.3597 °2-0.5141 °2-0.1652 °2--2.0175 °2
S-0.0364 Å °0.1145 Å °0.0904 Å °-0.0311 Å °0.0452 Å °0.0774 Å °-0.0039 Å °-0.0742 Å °-0.0023 Å °
Refinement TLS groupSelection details: ALL

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