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- PDB-5vwz: Bak in complex with Bim-h3Pc -

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Basic information

Entry
Database: PDB / ID: 5vwz
TitleBak in complex with Bim-h3Pc
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bcl-2 Family / Inhibitor
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / developmental pigmentation ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / developmental pigmentation / BH domain binding / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / limb morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / ear development / establishment or maintenance of transmembrane electrochemical gradient / tube formation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of T cell apoptotic process / regulation of organ growth / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / positive regulation of calcium ion transport into cytosol / porin activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / endomembrane system / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / positive regulation of cell cycle / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway / spleen development / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / FLT3 Signaling / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / post-embryonic development / cell-matrix adhesion / release of cytochrome c from mitochondria / thymus development / regulation of mitochondrial membrane potential / epithelial cell proliferation / kidney development / establishment of localization in cell / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / male gonad development / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron apoptotic process / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / Signaling by BRAF and RAF1 fusions / protein-folding chaperone binding / microtubule binding / spermatogenesis / regulation of apoptotic process / response to ethanol / in utero embryonic development
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 regulator, Bcl-2, BH2 motif, conserved site ...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 (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
Similarity search - Domain/homology
Chem-1PG / AMMONIUM ION / Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.622 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

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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
C: Bcl-2 homologous antagonist/killer
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2637
Polymers44,7404
Non-polymers5233
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.237, 56.668, 79.291
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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.: 2 / 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: 3332.727 Da / Num. of mol.: 2 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#4: Chemical ChemComp-NH4 / AMMONIUM ION / Ammonium


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 10 % PEG 20000, 20 % PEG MME 550, 38 mM Imidazole pH 6.5, 20 mM ammonium acetate, 20 mM potassium sodium tartrate, 20 mM sodium formate, 62 mM sodium MES pH 6.5, 20 mM trisodium citrate, and 20 mM sodium oxamate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.622→38.58 Å / Num. obs: 41869 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1174 / Net I/σ(I): 15.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.622→38.579 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2
RfactorNum. reflection% reflection
Rfree0.1906 1996 4.77 %
Rwork0.154 --
obs0.1558 41867 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.622→38.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 31 390 3517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063307
X-RAY DIFFRACTIONf_angle_d1.1324482
X-RAY DIFFRACTIONf_dihedral_angle_d22.1791942
X-RAY DIFFRACTIONf_chiral_restr0.048457
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.622-1.66260.28431420.22272842X-RAY DIFFRACTION99
1.6626-1.70750.29391470.21172799X-RAY DIFFRACTION100
1.7075-1.75780.23331440.21122807X-RAY DIFFRACTION100
1.7578-1.81450.22221430.18982847X-RAY DIFFRACTION100
1.8145-1.87930.25911430.18412822X-RAY DIFFRACTION100
1.8793-1.95460.23371400.17922864X-RAY DIFFRACTION100
1.9546-2.04350.19121440.16052811X-RAY DIFFRACTION100
2.0435-2.15130.19131410.15282849X-RAY DIFFRACTION100
2.1513-2.2860.18481400.14682860X-RAY DIFFRACTION100
2.286-2.46250.20511410.14672834X-RAY DIFFRACTION100
2.4625-2.71030.16921410.14842875X-RAY DIFFRACTION100
2.7103-3.10230.17751410.14632850X-RAY DIFFRACTION100
3.1023-3.9080.16611400.12842875X-RAY DIFFRACTION100
3.908-38.590.14621490.13222936X-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)
12.1597-0.2157-0.01582.1560.33013.39890.0521-0.0860.09740.03530.02070.2313-0.1303-0.1462-0.08220.0022-0.01090.01990.08420.00470.1355-8.9232-50.79293.9929
20.8613-1.39772.00112.2644-3.2785.75270.0118-1.1269-1.23821.3497-0.496-0.27390.67490.01770.51560.6801-0.07870.0860.4210.22960.4677-5.9163-51.635324.1923
32.96180.5931.10720.33240.03670.591-0.0375-0.23320.13180.2229-0.03010.4078-0.1011-0.16260.0556-0.01030.00790.05510.1337-0.00350.2263-13.1147-50.30057.7924
41.90632.36560.34075.3367-1.26083.07390.3164-0.26010.06490.6974-0.3051-0.1059-0.12320.0838-0.01340.13350.0062-0.01010.0986-0.00950.10325.9454-56.195615.144
50.72150.00550.23661.35490.11931.30960.01450.0112-0.0171-0.0168-0.0287-0.0115-0.04260.0233-0.01490.01350.00250.01180.08150.00510.08360.1771-54.8361.7993
65.60551.1178-0.01871.93280.37172.14230.1334-0.1872-0.1093-0.0047-0.1379-0.29110.1515-0.0650.00010.040.02090.02630.07580.02130.13972.9764-65.5378.3332
72.6881-0.04711.10343.00110.5891.77520.1938-0.0991-0.2162-0.1446-0.04670.39030.4306-0.3855-0.13650.1822-0.0301-0.01720.12370.02670.1984-1.5384-78.321134.4191
83.2017-0.5991-1.28743.2745-1.21744.54790.05560.2182-0.0262-0.2147-0.03030.10720.1521-0.1788-0.06090.1306-0.0472-0.05720.0411-0.01880.07354.3061-70.988827.5112
91.6285-0.40240.13983.10340.62382.96450.04160.07140.0221-0.1729-0.0032-0.10690.18050.0201-0.0160.13570.00530.00310.07030.02810.052511.3878-73.322931.1297
102.5123-0.2685-0.52283.93471.17594.10320.0639-0.2250.08240.33640.0042-0.054-0.1075-0.0883-0.050.1709-0.00350.00350.11530.01930.05167.8572-72.744442.9873
117.9512-2.045-4.24795.25781.31656.59010.0204-0.070.1895-0.1612-0.0768-0.1634-0.15580.28530.02040.1234-0.0225-0.04060.07950.02840.076110.0437-61.904930.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 166 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 69 )
8X-RAY DIFFRACTION8chain 'C' and (resid 70 through 106 )
9X-RAY DIFFRACTION9chain 'C' and (resid 107 through 150 )
10X-RAY DIFFRACTION10chain 'C' and (resid 151 through 184 )
11X-RAY DIFFRACTION11chain 'D' and (resid 141 through 166 )

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