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- PDB-6uxr: Crystal structure of BAK core domain BH3-groove-dimer in complex ... -

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Basic information

Entry
Database: PDB / ID: 6uxr
TitleCrystal structure of BAK core domain BH3-groove-dimer in complex with LysoPC
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Pore-forming Protein
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / limb morphogenesis / Release of apoptotic factors from the mitochondria / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / 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 / 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 / positive regulation of calcium ion transport into cytosol / porin activity / pore complex / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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, 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-K6G / TRIETHYLENE GLYCOL / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCowan, A.D. / 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)1059290 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2020
Title: BAK core dimers bind lipids and can be bridged by them.
Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / ...Authors: Cowan, A.D. / Smith, N.A. / Sandow, J.J. / Kapp, E.A. / Rustam, Y.H. / Murphy, J.M. / Brouwer, J.M. / Bernardini, J.P. / Roy, M.J. / Wardak, A.Z. / Tan, I.K. / Webb, A.I. / Gulbis, J.M. / Smith, B.J. / Reid, G.E. / Dewson, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionNov 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)20,7909
Polymers19,0012
Non-polymers1,7887
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, The homodimers have been validated in previous publications by chemical crosslinking studies (Brouwer et al., Mol Cell, 2014)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-29 kcal/mol
Surface area9630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.921, 89.949, 77.572
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 9500.688 Da / Num. of mol.: 2 / Fragment: Core/dimerisation domain, residues 68-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Plasmid: pGEX-6P-3 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q16611
#2: Chemical ChemComp-K6G / [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate


Mass: 496.638 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H51NO7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: calcium chloride, PEG 3350, sodium acetate, sodium HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→30.041 Å / Num. obs: 18448 / % possible obs: 99.7 % / Redundancy: 14.493 % / Biso Wilson estimate: 44.11 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.061 / Χ2: 0.916 / Net I/σ(I): 28.1 / Num. measured all: 267375
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.9114.3642.6141.1241856293629140.7312.7199.3
1.91-2.0414.6411.0112.9640701278127800.9071.047100
2.04-2.214.6720.4286.9637809257925770.9760.44499.9
2.2-2.4114.6860.23112.5335100239123900.9940.239100
2.41-2.714.6710.13221.1431630215721560.9980.137100
2.7-3.1114.6330.06538.2328505195119480.9990.06899.8
3.11-3.8114.5530.0374.25238821641164110.032100
3.81-5.3714.160.021106.59182671292129010.02299.8
5.37-30.04112.7990.021105.82962578375210.02196

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.96 Å30.04 Å
Translation5.96 Å30.04 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASER2.6.0phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UXO

6uxo


Resolution: 1.8→30.041 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2323 1839 10 %
Rwork0.203 16544 -
obs0.206 18383 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 122.66 Å2 / Biso mean: 55.5178 Å2 / Biso min: 25.95 Å2
Refinement stepCycle: final / Resolution: 1.8→30.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 83 45 1398
Biso mean--68.72 52.03 -
Num. residues----159
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8002-1.84890.60651460.4998120097
1.8489-1.90330.39231340.3999126299
1.9033-1.96470.31151510.31271243100
1.9647-2.03490.27551390.24131266100
2.0349-2.11640.26081390.2141272100
2.1164-2.21270.25491420.20531250100
2.2127-2.32930.24351370.20241274100
2.3293-2.47520.2331390.19911261100
2.4752-2.66620.25951420.20141286100
2.6662-2.93430.25611430.20511293100
2.9343-3.35840.22451380.20321276100
3.3584-4.22930.18931390.18061310100
4.2293-30.0410.21881500.19135198
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)
16.987-1.65881.62040.8911-2.58157.0052-0.64621.1982-0.5733-0.27680.27480.44131.635-1.5240.1270.4594-0.17060.02140.5322-0.07690.3513-7.8632-27.30844.3046
21.725-1.35510.64896.06120.88275.9831-0.48570.118-0.31290.370.1897-0.2011.41881.03590.15280.56970.15870.18490.42070.01960.38876.4848-32.47411.0154
38.2892-6.2003-0.55578.0279-0.38216.7775-0.03960.40820.1175-0.4817-0.22590.0346-0.2030.15930.23810.183-0.10770.00390.32860.03890.28720.742-20.39032.2846
43.78221.1172-0.54475.4242-1.67067.3093-0.2091-0.12590.43610.53360.15510.3896-1.0967-1.21920.03190.40580.1538-0.09950.446-0.00030.3771-9.3965-14.152314.7224
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 100 )A69 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 146 )A101 - 146
3X-RAY DIFFRACTION3chain 'B' and (resid 67 through 100 )B67 - 100
4X-RAY DIFFRACTION4chain 'B' and (resid 101 through 147 )B101 - 147

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