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- PDB-5vwv: Bak core latch dimer in complex with Bim-BH3 - Cubic -

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Basic information

Entry
Database: PDB / ID: 5vwv
TitleBak core latch dimer in complex with Bim-BH3 - Cubic
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bcl-2 Family / Activator
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / BH domain binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / BH domain binding / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / Activation of BIM and translocation to mitochondria / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / apoptotic process involved in embryonic digit morphogenesis / developmental pigmentation / response to mycotoxin / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / apoptotic process involved in blood vessel morphogenesis / endocrine pancreas development / limb morphogenesis / ear development / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / meiosis I / mammary gland development / 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 / calcium ion transport into cytosol / regulation of mitochondrial membrane permeability / fibroblast apoptotic process / response to UV-C / Bcl-2 family protein complex / mitochondrial fusion / myeloid cell homeostasis / cellular response to glucocorticoid stimulus / thymocyte apoptotic process / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / porin activity / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / pore complex / odontogenesis of dentin-containing tooth / vagina development / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / positive regulation of calcium ion transport into cytosol / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / blood vessel remodeling / spleen development / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / positive regulation of cell cycle / FLT3 Signaling / endomembrane system / intrinsic apoptotic signaling pathway / epithelial cell proliferation / release of cytochrome c from mitochondria / response to endoplasmic reticulum stress / thymus development / cell-matrix adhesion / regulation of mitochondrial membrane potential / post-embryonic development / response to gamma radiation / apoptotic signaling pathway / kidney development / response to hydrogen peroxide / positive regulation of protein-containing complex assembly / cellular response to mechanical stimulus / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / protein-folding chaperone binding / channel activity / regulation of apoptotic process / spermatogenesis / microtubule binding / in utero embryonic development / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus
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, 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, 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, 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
trifluoroacetic acid / Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsBrouwer, J.M. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1058331 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Mol. Cell / Year: 2017
Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.
Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,67811
Polymers22,0642
Non-polymers6149
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-13 kcal/mol
Surface area12690 Å2
MethodPISA
2
A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules

A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,35522
Polymers44,1274
Non-polymers1,22818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area14470 Å2
ΔGint-112 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.404, 139.404, 139.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 19037.320 Da / Num. of mol.: 1 / Fragment: UNP residues 23-186 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3026.411 Da / Num. of mol.: 1 / Fragment: UNP residues 141-165 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521

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Non-polymers , 5 types, 195 molecules

#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 5.12 Å3/Da / Density % sol: 75.96 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2014
RadiationMonochromator: ADSC QUANTUM 315r / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.897→42.032 Å / Num. obs: 37157 / % possible obs: 100 % / Redundancy: 47.8 % / Rmerge(I) obs: 0.2162 / Net I/σ(I): 24.26
Reflection shellResolution: 1.898→1.966 Å / Redundancy: 47 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3647 / CC1/2: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.897→42.032 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3
RfactorNum. reflection% reflection
Rfree0.1771 1996 5.37 %
Rwork0.1568 --
obs0.1579 37157 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.897→42.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 38 186 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071625
X-RAY DIFFRACTIONf_angle_d0.7552188
X-RAY DIFFRACTIONf_dihedral_angle_d20.589950
X-RAY DIFFRACTIONf_chiral_restr0.048228
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8974-1.94480.30141390.29042462X-RAY DIFFRACTION100
1.9448-1.99740.26931390.24782455X-RAY DIFFRACTION100
1.9974-2.05620.28531410.22652461X-RAY DIFFRACTION100
2.0562-2.12260.22761390.20732465X-RAY DIFFRACTION100
2.1226-2.19840.22511410.1682471X-RAY DIFFRACTION100
2.1984-2.28640.161400.1592466X-RAY DIFFRACTION100
2.2864-2.39050.15321420.15622492X-RAY DIFFRACTION100
2.3905-2.51650.18081410.15142487X-RAY DIFFRACTION100
2.5165-2.67420.18061420.15072493X-RAY DIFFRACTION100
2.6742-2.88060.17661420.14482493X-RAY DIFFRACTION100
2.8806-3.17040.16811440.15132540X-RAY DIFFRACTION100
3.1704-3.62890.15011440.13632539X-RAY DIFFRACTION100
3.6289-4.57120.16081470.12972580X-RAY DIFFRACTION100
4.5712-42.04220.16781550.16172757X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9887-3.11340.60242.2619-1.20577.0027-0.46180.8847-2.1062-0.7168-0.9307-0.82461.48371.72991.32740.77510.22180.21720.7773-0.0411.126915.61699.795136.4117
27.17592.94220.56782.03452.06635.15950.1957-0.0660.02160.3056-0.198-0.0320.0897-0.1260.070.13810.07020.02510.228-0.02010.234913.728528.9185146.0283
35.349-3.688-1.62454.61912.05712.6544-0.0865-0.2024-0.12720.24410.00190.03930.17540.27560.07810.24360.02970.00770.2941-0.00160.293615.16430.2519152.541
48.0554-5.14610.15964.1541-1.01071.48890.24690.49240.7712-0.2376-0.249-0.5009-0.12690.1273-0.01330.2309-0.00470.02990.2558-0.00120.267312.195836.5061138.7494
54.0803-1.1416-1.02132.48731.32493.19490.10470.3995-0.0513-0.1335-0.10190.1391-0.0442-0.22340.00990.16520.0449-0.00850.20870.0360.19611.00832.7051141.0201
69.82321.0417-6.40346.1405-1.63114.8485-0.09650.1431-0.41330.08-0.13580.45350.7188-0.4790.13710.2626-0.02580.00720.2046-0.02410.2751-10.596336.0408167.9171
72.0596-0.82870.12646.08251.43392.7941-0.0873-0.28520.04010.73240.02190.65760.0403-0.31160.05170.29980.02530.13220.3045-0.00510.304-16.627346.7169179.9949
85.5166-5.6378-5.13187.57064.37635.62490.58551.07160.4984-0.9585-0.3335-0.3949-0.23650.1013-0.22280.35630.03760.03990.54240.06980.25654.716334.5216129.52
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 149 )
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 186 )
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 165 )

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