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- PDB-6x8o: BimBH3 peptide tetramer -

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Basic information

Entry
Database: PDB / ID: 6x8o
TitleBimBH3 peptide tetramer
ComponentsBcl-2-like protein 11
KeywordsAPOPTOSIS / Bim / Cell Death / Bcl-2 / BH3
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 / ear development / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / FLT3 Signaling / response to endoplasmic reticulum stress / cell-matrix adhesion / post-embryonic development / thymus development / kidney development / positive regulation of protein-containing complex assembly / 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 / spermatogenesis / microtubule binding / regulation of apoptotic process / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / protein kinase binding / mitochondrion / cytosol
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
Similarity search - Domain/homology
THIOCYANATE ION / Bcl-2-like protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsRobin, A.Y. / Westphal, D. / Uson, I. / Czabotar, P.E.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079700 Australia
CitationJournal: Structure / Year: 2021
Title: Biophysical Characterization of Pro-apoptotic BimBH3 Peptides Reveals an Unexpected Capacity for Self-Association.
Authors: Assafa, T.E. / Nandi, S. / Smilowicz, D. / Galazzo, L. / Teucher, M. / Elsner, C. / Putz, S. / Bleicken, S. / Robin, A.Y. / Westphal, D. / Uson, I. / Stoll, R. / Czabotar, P.E. / Metzler- ...Authors: Assafa, T.E. / Nandi, S. / Smilowicz, D. / Galazzo, L. / Teucher, M. / Elsner, C. / Putz, S. / Bleicken, S. / Robin, A.Y. / Westphal, D. / Uson, I. / Stoll, R. / Czabotar, P.E. / Metzler-Nolte, N. / Bordignon, E.
History
DepositionJun 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2-like protein 11
B: Bcl-2-like protein 11
C: Bcl-2-like protein 11
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1495
Polymers13,0914
Non-polymers581
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-28 kcal/mol
Surface area6190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.560, 37.560, 128.480
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein/peptide
Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3272.698 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20% PEG600, 0.05 M Tris-HCl, 0.15 M potassium thiocyanate, 0.5% CHAPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.31→31.53 Å / Num. obs: 48375 / % possible obs: 99.67 % / Redundancy: 10.7 % / Rsym value: 0.068 / Net I/σ(I): 22.97
Reflection shell
Resolution (Å)Num. unique obsRsym valueDiffraction-ID
3.92-31.5318300.0241
2.78-3.9233040.0281
2.27-3.9242420.0411
1.97-2.2750250.0611
1.76-1.9757270.1011
1.61-1.7663510.1581
1.49-1.6168210.231
1.39-1.4973900.3941
1.31-1.3976850.5711

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.31→31.53 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1683 --
Rwork0.1398 --
obs-259981 99.66 %
Displacement parametersBiso mean: 12.19 Å2
Refinement stepCycle: LAST / Resolution: 1.31→31.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 3 177 1104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681053
X-RAY DIFFRACTIONf_angle_d0.99611432
X-RAY DIFFRACTIONf_chiral_restr0.0731135
X-RAY DIFFRACTIONf_plane_restr0.0059198
X-RAY DIFFRACTIONf_dihedral_angle_d18.9531659

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