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- PDB-5fmj: Bcl-xL with mouse Bak BH3 Q75L complex -

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Basic information

Entry
Database: PDB / ID: 5fmj
TitleBcl-xL with mouse Bak BH3 Q75L complex
Components
  • BAK1 PROTEIN
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / BCL-XL / BAK / BH3 DOMAIN / BCL-2 FAMILY
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / Pyroptosis / leukocyte homeostasis / response to mycotoxin / BH domain binding / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / Pyroptosis / leukocyte homeostasis / response to mycotoxin / BH domain binding / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / apoptotic process in bone marrow cell / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mononuclear cell proliferation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / apoptotic mitochondrial changes / porin activity / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / thymocyte apoptotic process / hepatocyte apoptotic process / positive regulation of calcium ion transport into cytosol / pore complex / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / vagina development / germ cell development / BH3 domain binding / B cell homeostasis / positive regulation of proteolysis / negative regulation of anoikis / blood vessel remodeling / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / animal organ regeneration / negative regulation of protein localization to plasma membrane / 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 / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / response to cytokine / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to gamma radiation / establishment of localization in cell / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / mitochondrial membrane / cellular response to gamma radiation / : / response to hydrogen peroxide / synaptic vesicle membrane / cellular response to mechanical stimulus / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / RAS processing / cellular response to UV / protein-folding chaperone binding / channel activity / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / regulation of apoptotic process / spermatogenesis / nuclear membrane / defense response to virus / negative regulation of neuron apoptotic process
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 homologous antagonist/killer / Bcl-2-like protein 1 / BCL2-antagonist/killer 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J.
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 1.2Jan 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

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0246
Polymers21,7752
Non-polymers2484
Water1,58588
1
A: BCL-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules

A: BCL-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,04712
Polymers43,5514
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area9690 Å2
ΔGint-37.3 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.789, 57.789, 268.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

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Components

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


Mass: 17917.959 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Details: DELETION OF RESIDUES 27-82 / 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 BAK1 PROTEIN


Mass: 3857.354 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, UNP RESIDUES 61-94 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q91WX5, UniProt: O08734*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN ...CHAIN A LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN DELETED CHAIN B HAS Q75L MUTATION

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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: 2.97 Å3/Da / Density % sol: 58.58 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM THIOCYANATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.43→19.66 Å / Num. obs: 10808 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 19.2 % / Biso Wilson estimate: 47.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.6
Reflection shellResolution: 2.43→2.67 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.8 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 2.43→19.662 Å / SU ML: 0.24 / σ(F): 2.03 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 540 5 %
Rwork0.1799 --
obs0.1819 10808 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→19.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 16 88 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091471
X-RAY DIFFRACTIONf_angle_d0.9351980
X-RAY DIFFRACTIONf_dihedral_angle_d19.758869
X-RAY DIFFRACTIONf_chiral_restr0.048208
X-RAY DIFFRACTIONf_plane_restr0.005259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4295-2.67350.29151290.22392438X-RAY DIFFRACTION99
2.6735-3.05910.27741320.20972517X-RAY DIFFRACTION100
3.0591-3.84940.25371350.18642570X-RAY DIFFRACTION100
3.8494-19.66280.17231440.1592743X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.5981 Å / Origin y: 23.6931 Å / Origin z: 12.5338 Å
111213212223313233
T0.1284 Å2-0.0265 Å2-0.0223 Å2-0.3604 Å2-0.0518 Å2--0.2616 Å2
L1.1293 °20.3036 °2-0.2865 °2-0.9913 °20.1338 °2--0.8224 °2
S0.0383 Å °0.1728 Å °-0.2436 Å °0.107 Å °-0.0417 Å °-0.0806 Å °0.0463 Å °0.1399 Å °-0.0068 Å °
Refinement TLS groupSelection details: CHAIN A OR CHAIN B

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