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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 / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / apoptotic process involved in embryonic digit morphogenesis / B cell negative selection / BAK complex / positive regulation of fibroblast apoptotic process ...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 / apoptotic process involved in embryonic digit morphogenesis / B cell negative selection / BAK complex / positive regulation of fibroblast apoptotic process / response to fungus / BH domain binding / 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 / Activation of BIM and translocation to mitochondria / limb morphogenesis / developmental pigmentation / response to mycotoxin / Release of apoptotic factors from the mitochondria / endocrine pancreas development / post-embryonic camera-type eye 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 / regulation of organ growth / positive regulation of T cell apoptotic process / tube formation / mammary gland development / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / meiosis I / calcium ion transport into cytosol / fibroblast apoptotic process / regulation of mitochondrial membrane permeability / mitochondrial fusion / myeloid cell homeostasis / response to UV-C / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / odontogenesis of dentin-containing tooth / NRAGE signals death through JNK / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / porin activity / FOXO-mediated transcription of cell death genes / B cell homeostasis / positive regulation of IRE1-mediated unfolded protein response / pore complex / T cell homeostasis / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / animal organ regeneration / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / positive regulation of calcium ion transport into cytosol / Pyroptosis / blood vessel remodeling / spleen development / epithelial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / heat shock protein binding / endomembrane system / FLT3 Signaling / positive regulation of cell cycle / thymus development / release of cytochrome c from mitochondria / post-embryonic development / intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / cell-matrix adhesion / regulation of mitochondrial membrane potential / kidney development / response to gamma radiation / apoptotic signaling pathway / response to hydrogen peroxide / cellular response to mechanical stimulus / positive regulation of protein-containing complex assembly / 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 / in utero embryonic development / protein-folding chaperone binding / channel activity / regulation of apoptotic process / spermatogenesis / microtubule binding / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process
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 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 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 / 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-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 / Orthogonal Bundle / Mainly Alpha
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
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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


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


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


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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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