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- PDB-3io8: BimL12F in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 3io8
TitleBimL12F in complex with Bcl-xL
Components
  • Bcl-2-like protein 1
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / helical bundle / Bcl-2-like fold / Alternative splicing / Membrane / Mitochondrion / Nucleus / Transmembrane / Phosphoprotein
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 / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / 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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / 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 / NFE2L2 regulating tumorigenic genes / FOXO-mediated transcription of cell death 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 / hepatocyte apoptotic process / thymocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / BH3 domain binding / 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 / response to cytokine / kidney development / 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 / spermatogenesis / microtubule binding / 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 / 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 (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 / Orthogonal Bundle / Mainly Alpha
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: 2.3 Å
AuthorsColman, P.M. / Lee, E.F. / Fairlie, W.D. / Smith, B.J. / Czabotar, P.E. / Yang, H. / Sleebs, B.E. / Lessene, G.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Conformational changes in Bcl-2 pro-survival proteins determine their capacity to bind ligands.
Authors: Lee, E.F. / Czabotar, P.E. / Yang, H. / Sleebs, B.E. / Lessene, G. / Colman, P.M. / Smith, B.J. / Fairlie, W.D.
History
DepositionAug 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 26, 2017Group: Advisory / Data collection ...Advisory / Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_detector.detector
Revision 1.3Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Bcl-2-like protein 1
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6507
Polymers42,4534
Non-polymers1963
Water52229
1
A: Bcl-2-like protein 1
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2923
Polymers21,2272
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-45 kcal/mol
Surface area10670 Å2
MethodPISA
2
C: Bcl-2-like protein 1
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3574
Polymers21,2272
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-27 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.717, 65.717, 170.094
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-36-

HOH

DetailsThe biological assembly is one half of the asymmetric unit.

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Components

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


Mass: 17917.959 Da / Num. of mol.: 2 / Fragment: residues 1-26, and residues 83-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pGEX / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07817
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3308.707 Da / Num. of mol.: 2 / Fragment: BH3 peptide, residues 141-166 / Mutation: L152P / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.02M Zinc Acetate 2.5M Sodium Chloride 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9566 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 24, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9566 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 18501 / Num. obs: 18464 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.147
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.835 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID: 2P1L

2p1l


Resolution: 2.3→47.299 Å / σ(F): 1.35 / Phase error: 39.78 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2307 948 5.15 %
Rwork0.185 --
obs0.1873 18425 99.8 %
all-18462 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.176 Å2 / ksol: 0.36 e/Å3
Refinement stepCycle: LAST / Resolution: 2.3→47.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 3 29 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042754
X-RAY DIFFRACTIONf_angle_d0.7653721
X-RAY DIFFRACTIONf_dihedral_angle_d15.845967
X-RAY DIFFRACTIONf_chiral_restr0.055380
X-RAY DIFFRACTIONf_plane_restr0.002482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.31931110.31651925X-RAY DIFFRACTION98
2.3921-2.5010.3111950.29541944X-RAY DIFFRACTION98
2.501-2.63280.33071080.30391966X-RAY DIFFRACTION98
2.6328-2.79780.2822960.2731918X-RAY DIFFRACTION98
2.7978-3.01380.27551150.25341932X-RAY DIFFRACTION98
3.0138-3.3170.23611080.23861947X-RAY DIFFRACTION98
3.317-3.79680.22461140.20131935X-RAY DIFFRACTION98
3.7968-4.78280.19881000.13581958X-RAY DIFFRACTION98
4.7828-47.3090.1904990.10281954X-RAY DIFFRACTION98

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