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- PDB-5agx: Bcl-2 alpha beta-1 LINEAR complex -

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Basic information

Entry
Database: PDB / ID: 5agx
TitleBcl-2 alpha beta-1 LINEAR complex
Components
  • (APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2) x 2
  • BCL-2-LIKE PROTEIN 11
KeywordsAPOPTOSIS / FOLDAMER / BIM
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / regulation of developmental pigmentation / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process ...BIM-BCL-xl complex / BIM-BCL-2 complex / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / regulation of developmental pigmentation / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / RUNX3 regulates BCL2L11 (BIM) transcription / cochlear nucleus development / osteoblast proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / developmental pigmentation / positive regulation of fibroblast apoptotic process / stem cell development / apoptotic process involved in embryonic digit morphogenesis / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / negative regulation of calcium ion transport into cytosol / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / negative regulation of dendritic cell apoptotic process / glomerulus development / focal adhesion assembly / regulation of transmembrane transporter activity / negative regulation of T cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / oocyte development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / B cell apoptotic process / tube formation / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / mammary gland development / Regulation of MITF-M-dependent genes involved in apoptosis / positive regulation of multicellular organism growth / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / calcium ion transport into cytosol / response to UV-B / negative regulation of ossification / response to iron ion / epithelial cell apoptotic process / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / axon regeneration / myeloid cell homeostasis / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / organ growth / cellular response to glucocorticoid stimulus / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / response to cycloheximide / NRAGE signals death through JNK / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / B cell lineage commitment / hepatocyte apoptotic process / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle
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-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site ...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-2 / 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 / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSmith, B.J. / F Lee, E. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Alpha Beta Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity on Living Cells
Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / ...Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / Murphy, W.L. / Smith, B.J. / Gellman, S.H. / Fairlie, W.D.
History
DepositionFeb 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
C: BCL-2-LIKE PROTEIN 11
D: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)44,1374
Polymers44,1374
Non-polymers00
Water79344
1
A: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
D: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)22,0692
Polymers22,0692
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-15.4 kcal/mol
Surface area8110 Å2
MethodPISA
2
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
C: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)22,0692
Polymers22,0692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-13.9 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.054, 86.054, 108.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 19357.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-34,29-44,92-207
Source method: isolated from a genetically manipulated source
Details: CONTAINS RESIDUES 1-34,92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817
#2: Protein APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2 / BCL2-L-1 / APOPTOSIS REGULATOR BCL-X


Mass: 19357.557 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-34,29-44,92-207
Source method: isolated from a genetically manipulated source
Details: CONTAINS RESIDUES 1-34,92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817
#3: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 2711.190 Da / Num. of mol.: 2 / Fragment: BIM BH3, RESIDUES 146-166 / Source method: obtained synthetically
Details: BIM BH3 WITH CYCLIC BETA AMINO ACIDS AT RESIDUES 2,6,16 AND PENTENY AMINO ACIDS AT RESIDUES 9,13
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: O43521
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBCL-2 WITH THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED WITH RESIDUES 35-50 OF BCL-XL

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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: 2.34 Å3/Da / Density % sol: 47.4 % / Description: NONE
Crystal growpH: 7 / Details: PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.24→40 Å / Num. obs: 20251 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 29.2
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 14 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 3.89 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED BCL-2 BECLIN BH3 COMPLEX

Resolution: 2.24→40.009 Å / SU ML: 0.29 / σ(F): 1.36 / Phase error: 25.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1013 5 %
Rwork0.1878 --
obs0.1906 20250 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→40.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2643 0 0 44 2687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072773
X-RAY DIFFRACTIONf_angle_d1.1053773
X-RAY DIFFRACTIONf_dihedral_angle_d23.2311008
X-RAY DIFFRACTIONf_chiral_restr0.042391
X-RAY DIFFRACTIONf_plane_restr0.005483
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2403-2.35840.38231400.2632665X-RAY DIFFRACTION99
2.3584-2.50610.26131430.21472703X-RAY DIFFRACTION100
2.5061-2.69960.30841420.20172705X-RAY DIFFRACTION100
2.6996-2.97110.23431430.20222723X-RAY DIFFRACTION100
2.9711-3.40090.26621450.20972743X-RAY DIFFRACTION100
3.4009-4.2840.22561450.17282767X-RAY DIFFRACTION100
4.284-40.01510.21371550.16472931X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 96.644 Å / Origin y: 79.1155 Å / Origin z: 8.9341 Å
111213212223313233
T0.1879 Å20.0486 Å2-0.0111 Å2-0.2929 Å2-0.0035 Å2--0.2442 Å2
L1.6971 °21.4727 °20.7502 °2-4.117 °21.9377 °2--2.9561 °2
S-0.034 Å °0.0672 Å °-0.0838 Å °-0.0545 Å °-0.1406 Å °0.1295 Å °0.0744 Å °-0.0622 Å °0.1575 Å °
Refinement TLS groupSelection details: ALL

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