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- PDB-5c3g: Crystal structure of Bcl-xl bound to BIM-MM -

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Basic information

Entry
Database: PDB / ID: 5c3g
TitleCrystal structure of Bcl-xl bound to BIM-MM
Components
  • Bcl-2-like protein 1,Bcl-2-like protein 1
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Complex / Bcl-2 Family / BH3 / Stapled Peptide
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / positive regulation of synaptic vesicle exocytosis / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of synaptic vesicle clustering / RAS processing ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / positive regulation of synaptic vesicle exocytosis / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of synaptic vesicle clustering / RAS processing / positive regulation of mitochondrial membrane permeability involved in apoptotic process / BH domain binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / Activation of BIM and translocation to mitochondria / apoptotic process involved in embryonic digit morphogenesis / developmental pigmentation / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / The NLRP1 inflammasome / ear development / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of synaptic vesicle endocytosis / 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 / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / mammary gland development / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / meiosis I / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / cellular response to glucocorticoid stimulus / response to cycloheximide / NRAGE signals death through JNK / thymocyte apoptotic process / STAT5 activation downstream of FLT3 ITD mutants / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / clathrin binding / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / hepatocyte apoptotic process / odontogenesis of dentin-containing tooth / negative regulation of intrinsic apoptotic signaling pathway / germ cell development / B cell homeostasis / T cell homeostasis / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / negative regulation of reproductive process / negative regulation of developmental process / positive regulation of ATP biosynthetic process / negative regulation of anoikis / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / ectopic germ cell programmed cell death / 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 / spleen development / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / regulation of long-term synaptic depression / positive regulation of cell cycle / endomembrane system / clathrin-coated pit / FLT3 Signaling / response to cytokine / MDM2/MDM4 family protein binding / epithelial cell proliferation / release of cytochrome c from mitochondria / response to endoplasmic reticulum stress / response to ischemia / thymus development / cell-matrix adhesion / negative regulation of autophagy / regulation of cytokinesis / post-embryonic development / regulation of mitochondrial membrane potential / kidney development / mitochondrion organization / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / response to radiation / male gonad development
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, 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-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 11 / Bcl-2-like protein 1 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMiles, J.A. / Yeo, D.J. / Rowell, P. / Rodriguez-Marin, S. / Pask, C.M. / Warriner, S.L. / Edwards, T.A. / Wilson, A.J.
CitationJournal: Chem Sci / Year: 2016
Title: Hydrocarbon constrained peptides - understanding preorganisation and binding affinity.
Authors: Miles, J.A. / Yeo, D.J. / Rowell, P. / Rodriguez-Marin, S. / Pask, C.M. / Warriner, S.L. / Edwards, T.A. / Wilson, A.J.
History
DepositionJun 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1,Bcl-2-like protein 1
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)20,1182
Polymers20,1182
Non-polymers00
Water543
1
A: Bcl-2-like protein 1,Bcl-2-like protein 1
B: Bcl-2-like protein 11

A: Bcl-2-like protein 1,Bcl-2-like protein 1
B: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)40,2354
Polymers40,2354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area7550 Å2
ΔGint-52 kcal/mol
Surface area14630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.220, 106.220, 92.760
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 17506.504 Da / Num. of mol.: 1 / Fragment: UNP residues 1-26,UNP residues 83-209
Source method: isolated from a genetically manipulated source
Details: Deletion mutation performed to remove flexible loop, removing residues 27-82. Numbering is correct in the pdb file.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Bcl2l1, Bcl2l, Bclx, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q64373, UniProt: Q07817
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 2611.031 Da / Num. of mol.: 1 / Fragment: UNP residues 56-76 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12% Peg 1500, 0.1M Sodium Acetate pH 5.5, 2.5M NaCl, 1.5% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→45.99 Å / Num. obs: 11587 / % possible obs: 98.1 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 29.2
Reflection shellResolution: 2.45→2.69 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 3.39 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FDL

3fdl


Resolution: 2.45→34.769 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 581 5.02 %
Rwork0.2244 --
obs0.2268 11577 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→34.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 3 1259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031297
X-RAY DIFFRACTIONf_angle_d0.6911754
X-RAY DIFFRACTIONf_dihedral_angle_d12.954459
X-RAY DIFFRACTIONf_chiral_restr0.029181
X-RAY DIFFRACTIONf_plane_restr0.002228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4504-2.69690.37581550.29732646X-RAY DIFFRACTION97
2.6969-3.08690.31671330.27782686X-RAY DIFFRACTION97
3.0869-3.88830.28831380.24532753X-RAY DIFFRACTION98
3.8883-34.77210.24551550.19622911X-RAY DIFFRACTION98

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