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- PDB-5vx0: Bak in complex with Bim-h3Glg -

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Basic information

Entry
Database: PDB / ID: 5vx0
TitleBak in complex with Bim-h3Glg
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 / Activation of BIM and translocation to mitochondria ...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 / Activation of BIM and translocation to mitochondria / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / response to fungus / limb morphogenesis / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / ear development / establishment or maintenance of transmembrane electrochemical gradient / 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 / tube formation / 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 / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / cellular response to glucocorticoid stimulus / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / BH domain binding / porin activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / endomembrane system / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / heat shock protein binding / FLT3 Signaling / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / epithelial cell proliferation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / kidney development / establishment of localization in cell / response to gamma radiation / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / : / cellular response to mechanical stimulus / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular response to UV / Signaling by BRAF and RAF1 fusions / protein-folding chaperone binding / spermatogenesis / microtubule binding / 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, 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
Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsBrouwer, J.M. / Lan, P. / Lessene, G. / 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)44,79611
Polymers44,5884
Non-polymers2087
Water7,819434
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.092, 63.231, 121.038
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 3256.613 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 200 mM magnesium chloride, 25 % PEG 3350, and 100 mM bis-tris chloride (pH 6.5)

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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: Apr 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.599→44.693 Å / Num. obs: 49543 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1559 / Net I/σ(I): 11.78

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→44.693 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2003 1995 4.03 %
Rwork0.1649 --
obs0.1663 49528 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→44.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3041 0 10 434 3485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063188
X-RAY DIFFRACTIONf_angle_d0.8574325
X-RAY DIFFRACTIONf_dihedral_angle_d18.0461874
X-RAY DIFFRACTIONf_chiral_restr0.049454
X-RAY DIFFRACTIONf_plane_restr0.005578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.599-1.6390.4091360.3693233X-RAY DIFFRACTION98
1.639-1.68330.37221410.33463362X-RAY DIFFRACTION100
1.6833-1.73280.33761390.31353352X-RAY DIFFRACTION100
1.7328-1.78870.31221420.27623368X-RAY DIFFRACTION100
1.7887-1.85270.28731420.25673371X-RAY DIFFRACTION100
1.8527-1.92690.25131400.21613371X-RAY DIFFRACTION100
1.9269-2.01460.26591410.17883353X-RAY DIFFRACTION100
2.0146-2.12080.21931420.16073364X-RAY DIFFRACTION100
2.1208-2.25360.18991430.14673409X-RAY DIFFRACTION100
2.2536-2.42760.18261430.14683397X-RAY DIFFRACTION100
2.4276-2.67190.20541440.1443419X-RAY DIFFRACTION100
2.6719-3.05850.16641440.13953419X-RAY DIFFRACTION100
3.0585-3.8530.15021450.12753474X-RAY DIFFRACTION100
3.853-44.71080.1571530.13733641X-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)
11.36670.06020.15611.10870.27251.0480.0102-0.12070.06990.1167-0.00460.0197-0.0302-0.0194-0.00010.15680.00630.00280.17210.00030.17381.434425.293123.6969
24.5848-5.89020.13667.5652-0.3451.2898-0.1889-0.18450.05430.26920.1525-0.08180.0966-0.03730.04830.2544-0.0311-0.00820.23350.00730.17175.123611.858736.074
38.37466.70847.14397.2745.7498.4956-0.13280.0999-0.6585-0.210.1417-0.62260.05710.341-0.04170.17490.04120.04160.16010.04330.245415.33559.083723.5192
44.34841.97861.62541.20721.02191.75330.02420.032-0.10120.02930.0067-0.07030.10970.0375-0.0380.12520.02620.00230.09910.01160.14138.471715.534522.8759
56.3584-2.784-0.51865.93082.88425.4688-0.0582-0.0652-0.28590.13970.08330.09640.16740.02660.0570.1426-0.018-0.00990.09680.01850.1337-4.279714.278714.1239
63.5934-5.16523.16938.2083-3.43445.12950.0982-0.1304-0.19380.0926-0.0321-0.03150.1558-0.0297-0.08870.1713-0.03040.02080.12620.01460.12511.355.530629.0148
73.7237-0.0405-0.88027.18932.51183.53770.0368-0.26840.24630.1320.1055-0.1383-0.04940.2525-0.14420.08450.0041-0.00290.1889-0.00720.123423.243429.723215.5583
84.087-0.4752-1.95790.8044-0.39272.56980.0303-0.08390.22830.0076-0.0134-0.0507-0.16370.0786-0.01320.1551-0.0219-0.02290.1604-0.04050.172324.052734.345719.2691
94.0841-2.94855.04363.0725-3.33016.5081-0.2553-0.08280.55330.04770.02-0.1959-0.32080.04730.33590.22750.00780.03130.135-0.02460.236420.51544.70553.5616
105.2117-5.2332-4.83116.22453.8165.68620.04180.5904-0.24240.0349-0.21490.37110.2669-0.56210.12470.1974-0.0301-0.04760.19070.01980.157113.823830.9971-0.3436
112.4081-1.0617-0.90711.47350.74271.01020.00870.0529-0.0252-0.00040.01540.04980.0059-0.0097-0.02320.13750.0002-0.0170.16760.00370.12718.185529.30147.4354
128.4976-2.28124.68399.29894.74998.1048-0.19470.10490.6493-0.30420.0122-0.433-0.2610.45230.08340.16510.0105-0.01420.1903-0.00920.14735.022226.91110.4398
133.5577-2.21964.48224.5119-1.36946.41920.15280.24590.278-0.3514-0.1024-0.1183-0.08510.0103-0.00610.2307-0.01090.04270.19270.0240.158824.778937.5906-2.2502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 82 )
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 118 )
4X-RAY DIFFRACTION4chain 'A' and (resid 119 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 185 )
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 165 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 48 )
8X-RAY DIFFRACTION8chain 'C' and (resid 49 through 82 )
9X-RAY DIFFRACTION9chain 'C' and (resid 83 through 100 )
10X-RAY DIFFRACTION10chain 'C' and (resid 101 through 124 )
11X-RAY DIFFRACTION11chain 'C' and (resid 125 through 174 )
12X-RAY DIFFRACTION12chain 'C' and (resid 175 through 185 )
13X-RAY DIFFRACTION13chain 'D' and (resid 142 through 165 )

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