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- PDB-6mcy: Crystal structure of mouse Bak -

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Basic information

Entry
Database: PDB / ID: 6mcy
TitleCrystal structure of mouse Bak
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Bcl-2 family / Bak / alpha-helical
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / 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 / 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 / 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 release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / mitochondrial membrane / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / 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 / 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
FORMIC ACID / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.748 Å
AuthorsBrouwer, J.M. / Czabotar, P.E. / Colman, P.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A small molecule interacts with VDAC2 to block mouse BAK-driven apoptosis.
Authors: van Delft, M.F. / Chappaz, S. / Khakham, Y. / Bui, C.T. / Debrincat, M.A. / Lowes, K.N. / Brouwer, J.M. / Grohmann, C. / Sharp, P.P. / Dagley, L.F. / Li, L. / McArthur, K. / Luo, M.X. / ...Authors: van Delft, M.F. / Chappaz, S. / Khakham, Y. / Bui, C.T. / Debrincat, M.A. / Lowes, K.N. / Brouwer, J.M. / Grohmann, C. / Sharp, P.P. / Dagley, L.F. / Li, L. / McArthur, K. / Luo, M.X. / Chin, H.S. / Fairlie, W.D. / Lee, E.F. / Segal, D. / Duflocq, S. / Lessene, R. / Bernard, S. / Peilleron, L. / Nguyen, T. / Miles, C. / Wan, S.S. / Lane, R.M. / Wardak, A. / Lackovic, K. / Colman, P.M. / Sandow, J.J. / Webb, A.I. / Czabotar, P.E. / Dewson, G. / Watson, K.G. / Huang, D.C.S. / Lessene, G. / Kile, B.T.
History
DepositionSep 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: 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 27, 2019Group: 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 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)76,25712
Polymers75,8734
Non-polymers3848
Water7,566420
1
A: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1685
Polymers18,9681
Non-polymers2004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1064
Polymers18,9681
Non-polymers1383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)18,9681
Polymers18,9681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0142
Polymers18,9681
Non-polymers461
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.951, 59.261, 79.207
Angle α, β, γ (deg.)93.14, 93.35, 97.63
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK


Mass: 18968.244 Da / Num. of mol.: 4 / Mutation: C154S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bak1, Bak / Production host: Escherichia coli (E. coli) / References: UniProt: O08734
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 200 mM ammonium formate

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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: Mar 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.748→36.54 Å / Num. obs: 65510 / % possible obs: 97.55 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1098 / Rpim(I) all: 0.06454 / Net I/σ(I): 9.08
Reflection shellResolution: 1.748→1.811 Å / Mean I/σ(I) obs: 0.72 / Num. unique obs: 6395 / CC1/2: 0.326 / % possible all: 95.24

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IMT

2imt


Resolution: 1.748→36.543 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 1998 3.05 %
Rwork0.1809 --
obs0.182 65460 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.748→36.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5285 0 25 420 5730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065679
X-RAY DIFFRACTIONf_angle_d0.757745
X-RAY DIFFRACTIONf_dihedral_angle_d17.7983313
X-RAY DIFFRACTIONf_chiral_restr0.045831
X-RAY DIFFRACTIONf_plane_restr0.0051035
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7485-1.79220.38571390.37244403X-RAY DIFFRACTION95
1.7922-1.84060.40761480.34234488X-RAY DIFFRACTION96
1.8406-1.89480.34921270.29994491X-RAY DIFFRACTION97
1.8948-1.9560.30391560.26544489X-RAY DIFFRACTION97
1.956-2.02590.29681330.25674513X-RAY DIFFRACTION97
2.0259-2.1070.2891450.21894515X-RAY DIFFRACTION97
2.107-2.20280.25591430.19814517X-RAY DIFFRACTION97
2.2028-2.3190.22431410.18994573X-RAY DIFFRACTION98
2.319-2.46420.20521560.17734554X-RAY DIFFRACTION98
2.4642-2.65440.22631350.17624550X-RAY DIFFRACTION98
2.6544-2.92150.18661340.17434569X-RAY DIFFRACTION98
2.9215-3.3440.23921500.17554605X-RAY DIFFRACTION99
3.344-4.2120.16411440.14174581X-RAY DIFFRACTION99
4.212-36.55070.1691470.13244614X-RAY DIFFRACTION99
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)
11.5589-0.35442.09741.941-0.58726.50820.24920.52370.0448-0.749-0.2689-0.18490.13960.66740.05120.45610.12550.02630.29460.05360.2139-7.0866-4.7771-52.1033
22.0099-3.7464-5.68562.64580.71564.82490.2551-0.2251.2198-0.1234-0.1516-1.0098-2.40970.6303-0.20410.7559-0.0018-0.03540.30990.01430.3513-10.34128.3576-39.6366
32.70250.6352.38283.70564.85228.87020.0747-0.25130.02760.3714-0.17660.20770.1949-0.25460.1090.1888-0.02310.02540.15820.04340.1624-9.94244.502-13.5863
47.9649-7.1716-0.3875.87870.47180.847-0.2455-0.4731-0.81070.18990.37031.2020.3578-0.2528-0.1440.3099-0.06110.0240.24050.06240.3197-13.7603-4.4294-15.4038
57.9222-5.91150.88656.442-1.13642.69290.50680.98180.0062-0.6041-0.4567-0.23010.04210.2273-0.05970.2313-0.0485-0.01730.1528-0.04230.1993-1.42174.2357-20.688
62.0657-0.15881.02555.2374-0.1352.3903-0.0661-0.05030.01160.46090.0106-0.71920.11460.19650.05290.1557-0.0044-0.03410.1370.0120.20133.81522.1918-12.0921
71.5976-0.90840.98248.8580.72773.1095-0.0507-0.12210.01490.8108-0.0267-0.34640.06080.01320.07890.2195-0.0145-0.0250.14780.01820.1304-1.94227.1955-6.8283
88.6285-4.4211-4.31668.9251-1.979.66670.47180.62270.0113-0.9350.0527-0.1034-0.2221-0.5981-0.47390.2446-0.0226-0.01650.1339-0.00380.2924-11.162316.0039-18.7543
95.4721-6.08695.90884.4718-5.2464.2143-0.1954-0.23090.23780.14350.0638-0.3460.0068-0.28450.02830.30120.0145-0.06630.19580.01850.308-1.5831-28.8486-30.0338
102.7103-2.17933.34462.3418-1.23898.27530.7983-0.6315-0.31060.2791-0.3226-0.24070.7026-0.8764-0.47330.4232-0.03390.00780.24030.01940.3979-0.9755-31.9362-20.7783
117.91373.1327-0.56646.90530.1253.74680.17360.2135-0.5374-0.09570.2263-1.06830.49760.7137-0.36440.26410.0807-0.06810.3095-0.05940.30148.6265-28.0616-34.1158
121.69470.29110.93053.54523.6378.33840.2270.10360.15160.09110.3161-0.6212-0.0980.7282-0.50.1199-0.00230.03060.1919-0.03030.3766.3406-18.6566-32.6893
132.39790.27821.88393.2841-0.21535.28290.16710.0488-0.14950.08280.0762-0.37270.27080.0713-0.24040.13530.0313-0.01640.110.01440.1632-2.3707-22.5486-35.5976
142.57892.04321.78538.26694.23926.041-0.0742-0.1620.1348-0.2342-0.40560.7389-0.1978-0.67480.45910.35880.1108-0.08920.3652-0.03920.2139-24.5657-29.7183-58.51
157.0314.1469-3.93248.0091-5.15348.32260.3249-0.6836-0.22890.528-0.6838-0.9925-1.04320.73170.33430.42240.0053-0.05420.2708-0.07890.2665-12.7363-29.5852-61.0235
161.7782-0.42870.05245.7004-0.20082.51090.0470.01650.0996-0.678-0.1939-0.053-0.3285-0.13230.120.48680.1077-0.07270.2258-0.00310.1422-18.2518-31.5935-68.8273
171.1381-1.79982.21213.7715-4.75573.78240.1350.20520.0648-0.4926-0.1889-0.04250.24760.085-0.01720.47490.066-0.03250.21440.00450.2631-15.60532.8935-52.9717
188.5494-1.2243-1.72116.1432-2.29488.5006-0.35230.12430.4733-0.4412-0.0791-0.0671-0.79950.17970.37760.64850.0451-0.1230.2190.02820.2923-13.22469.6316-50.2797
195.32873.1141.8765.73754.87124.25650.20591.4913-0.0624-1.6103-0.4909-1.3004-0.52121.52570.03680.58450.18360.23631.09360.25350.51291.1285-1.3871-60.9721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 98 through 172 )
2X-RAY DIFFRACTION2chain 'D' and (resid 173 through 181 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 51 )
4X-RAY DIFFRACTION4chain 'A' and (resid 52 through 67 )
5X-RAY DIFFRACTION5chain 'A' and (resid 68 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 142 )
7X-RAY DIFFRACTION7chain 'A' and (resid 143 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 182 )
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 67 )
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 97 )
12X-RAY DIFFRACTION12chain 'B' and (resid 98 through 142 )
13X-RAY DIFFRACTION13chain 'B' and (resid 143 through 182 )
14X-RAY DIFFRACTION14chain 'C' and (resid 16 through 67 )
15X-RAY DIFFRACTION15chain 'C' and (resid 68 through 97 )
16X-RAY DIFFRACTION16chain 'C' and (resid 98 through 182 )
17X-RAY DIFFRACTION17chain 'D' and (resid 16 through 59 )
18X-RAY DIFFRACTION18chain 'D' and (resid 60 through 86 )
19X-RAY DIFFRACTION19chain 'D' and (resid 87 through 97 )

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