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- PDB-5vx1: Bak L100A -

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Basic information

Entry
Database: PDB / ID: 5vx1
TitleBak L100A
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Bcl-2 Family / Mutant
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 / Release of apoptotic factors from the mitochondria / limb morphogenesis ...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 / Release of apoptotic factors from the mitochondria / limb morphogenesis / 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 / mitochondrial fusion / fibroblast apoptotic process / myeloid cell homeostasis / Bcl-2 family protein complex / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / 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 / cellular response to unfolded protein / animal organ regeneration / Pyroptosis / negative regulation of peptidyl-serine phosphorylation / 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 / apoptotic signaling pathway / establishment of localization in cell / 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 / 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
Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.224 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,9902
Polymers37,9902
Non-polymers00
Water8,683482
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.497, 39.488, 108.107
Angle α, β, γ (deg.)90.00, 91.25, 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: 18995.240 Da / Num. of mol.: 2 / Fragment: UNP residues 23-186 / Mutation: L100A, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 1M sodium malonate-malonic acid pH 7.0 and 10 % DL-malate-MES-tris pH 9

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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: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.224→36.027 Å / Num. obs: 98200 / % possible obs: 95 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04585 / Net I/σ(I): 14.94

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.224→36.027 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 2008 2.05 %
Rwork0.1678 --
obs0.1684 97795 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.224→36.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2598 0 0 482 3080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122984
X-RAY DIFFRACTIONf_angle_d1.334098
X-RAY DIFFRACTIONf_dihedral_angle_d24.6351095
X-RAY DIFFRACTIONf_chiral_restr0.086422
X-RAY DIFFRACTIONf_plane_restr0.011564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2241-1.25470.27541460.26486514X-RAY DIFFRACTION91
1.2547-1.28860.27291280.25596633X-RAY DIFFRACTION93
1.2886-1.32650.20951480.23386733X-RAY DIFFRACTION93
1.3265-1.36940.23951440.2236749X-RAY DIFFRACTION94
1.3694-1.41830.22051460.21056730X-RAY DIFFRACTION94
1.4183-1.47510.21641500.19576790X-RAY DIFFRACTION94
1.4751-1.54220.2091390.17826841X-RAY DIFFRACTION95
1.5422-1.62350.17941350.17256861X-RAY DIFFRACTION95
1.6235-1.72520.20861410.16976959X-RAY DIFFRACTION96
1.7252-1.85840.18171450.17416937X-RAY DIFFRACTION96
1.8584-2.04550.20721420.16817008X-RAY DIFFRACTION96
2.0455-2.34140.17931470.15616989X-RAY DIFFRACTION96
2.3414-2.94970.19471500.15457077X-RAY DIFFRACTION97
2.9497-36.04260.17081470.14616966X-RAY DIFFRACTION93
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)
17.28971.70050.38795.6798-0.0084.88550.03740.36560.1133-0.1332-0.03910.2137-0.1293-0.13330.0380.13490.0281-0.00570.14770.00190.0271-1.60968.4254-18.6249
23.8510.01410.53994.8262-2.44653.2159-0.41670.6948-1.4121-1.00980.7356-0.50770.6957-0.1813-0.35410.49310.04690.10420.5076-0.06540.512-16.58050.5446-16.9147
37.3812-0.1909-3.16691.1509-0.99586.51730.03870.55390.1005-0.04590.05850.22560.0198-0.5129-0.11270.1738-0.0207-0.02020.2609-0.00170.0889-3.1986.7502-23.241
43.4055-2.1494-0.58077.22991.07341.37310.0474-0.0191-0.2382-0.22030.00990.15940.02220.0187-0.01950.0987-0.0073-0.02370.1070.01630.0833-7.0828-0.9453-4.6332
53.3473-1.2306-0.29821.3220.10721.88670.00080.0709-0.04960.00070.00120.05990.0051-0.1143-0.01130.0979-0.0170.0030.06730.00930.0584-2.11575.3573-5.3569
65.356-1.1571-0.81221.64420.34842.68550.06080.19670.1214-0.0668-0.0464-0.0621-0.0423-0.00210.00090.1043-0.0188-0.00160.0820.01780.07314.749910.0638-11.722
75.1591-2.54360.50146.3937-0.31444.4813-0.1001-0.30630.22950.207-0.01810.37380.0896-0.17220.10490.1276-0.03650.04640.1478-0.0050.143215.85167.3034-36.7732
87.38231.38116.91040.28381.0168.72150.1502-0.53030.03950.09940.02030.04510.4248-0.1854-0.14680.19410.02250.0480.28830.01880.11526.29114.8335-35.278
96.9698-3.31211.72639.3244-6.0188.1644-0.2269-0.29780.77250.8425-0.18140.0442-0.59970.21420.40810.1919-0.0168-0.00780.2789-0.06140.258918.580812.9617-31.7477
103.82532.10211.72857.75191.92433.3187-0.0310.00980.26150.10680.02070.2404-0.07090.01130.06390.08960.00640.03230.08750.02190.093514.091815.402-51.5471
113.4320.8680.32830.72570.13511.1802-0.0084-0.05740.006-0.02110.00280.07630.0303-0.09060.00510.10390.01130.00120.06740.00750.093418.15377.0917-48.5795
122.66120.8289-0.42493.81852.71892.3727-0.0769-0.61980.09910.1549-0.05940.0991-0.25670.04610.09820.12150.0271-0.00670.2274-0.01740.098731.2128.1772-36.8418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 47 )
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 145 )
6X-RAY DIFFRACTION6chain 'A' and (resid 146 through 183 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 50 )
8X-RAY DIFFRACTION8chain 'B' and (resid 51 through 69 )
9X-RAY DIFFRACTION9chain 'B' and (resid 70 through 83 )
10X-RAY DIFFRACTION10chain 'B' and (resid 84 through 106 )
11X-RAY DIFFRACTION11chain 'B' and (resid 107 through 164 )
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 182 )

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