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- PDB-5fmk: Bcl-xL with Bak BH3 complex -

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Basic information

Entry
Database: PDB / ID: 5fmk
TitleBcl-xL with Bak BH3 complex
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
  • BCL-XL
KeywordsAPOPTOSIS / BCL-XL / BAK / BH3 DOMAIN / BCL-2 FAMILY
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process in bone marrow cell / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process in bone marrow cell / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / establishment or maintenance of transmembrane electrochemical gradient / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / 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 / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive 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 / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / porin activity / thymocyte apoptotic process / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / pore complex / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / germ cell development / apoptotic mitochondrial changes / BH3 domain binding / vagina development / B cell homeostasis / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / heat shock protein binding / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / negative regulation of autophagy / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / response to gamma radiation / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / establishment of localization in cell / cellular response to mechanical stimulus / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / cellular response to UV / synaptic vesicle membrane / protein-folding chaperone binding / channel activity / neuron apoptotic process / response to ethanol / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / nuclear membrane / defense response to virus
Similarity search - Function
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-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 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.731 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J. / Czabotar, P.E. / Colman, P.M.
CitationJournal: Genes Dev. / Year: 2016
Title: Physiological Restraint of Bak by Bcl-Xl is Essential for Cell Survival.
Authors: Lee, E.F. / Grabow, S. / Chappaz, S. / Dewson, G. / Hockings, C. / Kluck, R.M. / Gray, D.H. / Witkowski, M.T. / Evangelista, M. / Pettikiriarachchi, A. / Bouillet, P. / Lane, R.M. / ...Authors: Lee, E.F. / Grabow, S. / Chappaz, S. / Dewson, G. / Hockings, C. / Kluck, R.M. / Gray, D.H. / Witkowski, M.T. / Evangelista, M. / Pettikiriarachchi, A. / Bouillet, P. / Lane, R.M. / Czabotar, P.E. / Colman, P.M. / Smith, B.J. / Kile, B.T. / Fairlie, W.D.
History
DepositionNov 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1446
Polymers21,7752
Non-polymers3684
Water2,198122
1
A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules

A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,28712
Polymers43,5514
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area9860 Å2
ΔGint-58.1 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.668, 55.459, 61.053
Angle α, β, γ (deg.)90.00, 127.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 17933.959 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK / BCL-2-LIKE PROTEIN 7 / BCL2-L-7 / BAK


Mass: 3841.312 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, UNP RESIDUES 63-96 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16611
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN ...SEQUENCE LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN DELETED SEQUENCE OF PEPTIDES ON COVERS THE BH3 DOMAIN AND SURROUNDING RESIDUES

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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: 2.41 Å3/Da / Density % sol: 48.91 % / Description: NONE
Crystal growpH: 6.5
Details: 0.16M CALCIUM ACETATE, 0.08M SODIUM CACODYLATE, PH6.5, 20% GLYCEROL, 14.4% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364
DetectorType: ADSC Q210R / Detector: CCD / Date: Feb 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 1.73→19.4 Å / Num. obs: 21521 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.2
Reflection shellResolution: 1.73→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.73 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.4refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 1.731→19.401 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 1105 5.1 %RANDOM
Rwork0.1575 ---
obs0.159 21521 99.38 %-
Solvent computationShrinkage radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.731→19.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 24 122 1511
Refinement TLS params.Method: refined / Origin x: 13.216 Å / Origin y: -11.6307 Å / Origin z: -11.1698 Å
111213212223313233
T0.1067 Å2-0.02 Å20.0039 Å2-0.0972 Å2-0 Å2--0.1378 Å2
L0.6741 °2-0.195 °2-0.3678 °2-0.9503 °20.2357 °2--2.3104 °2
S-0.0287 Å °0.0736 Å °0.0151 Å °-0.0275 Å °-0.0581 Å °-0.0514 Å °0.0009 Å °-0.113 Å °0.0819 Å °

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