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- PDB-9clb: Crystal structure of Bak bound to the inhibitory aBAK -

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Basic information

Entry
Database: PDB / ID: 9clb
TitleCrystal structure of Bak bound to the inhibitory aBAK
Components
  • Bcl-2 homologous antagonist/killer
  • aBAK
KeywordsAPOPTOSIS / BAK / inhibitor / BH3-mimetic / computational design
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis ...Activation and oligomerization of BAK protein / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / myeloid cell homeostasis / mitochondrial fusion / Bcl-2 family protein complex / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / epithelial cell proliferation / response to gamma radiation / regulation of mitochondrial membrane potential / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / establishment of localization in cell / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / channel activity / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / 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 / metal ion binding / identical protein 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 ...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 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsBirkinshaw, R.W. / Berger, S.A. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. ...Birkinshaw, R.W. / Berger, S.A. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. / Miller, M.S. / Smyth, S. / Uren, R. / Kluck, R. / Colman, P.M. / Fairlie, W.D. / Czabotar, P.E. / Baker, D.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)2001406 Australia
National Health and Medical Research Council (NHMRC, Australia)2016894 Australia
CitationJournal: Sci Adv / Year: 2025
Title: Computational design of potent and selective binders of BAK and BAX.
Authors: Berger, S. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. / Miller, M.S. / Smyth, S. / Lutfi, M. / Uren, R.T. / Kluck, R.M. / ...Authors: Berger, S. / Lee, E.F. / Harris, T.J. / Tran, S. / Bera, A.K. / Arguinchona, L. / Kang, A. / Sankaran, B. / Kasapgil, S. / Miller, M.S. / Smyth, S. / Lutfi, M. / Uren, R.T. / Kluck, R.M. / Colman, P.M. / Fairlie, W.D. / Czabotar, P.E. / Baker, D. / Birkinshaw, R.W.
History
DepositionJul 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: aBAK
C: Bcl-2 homologous antagonist/killer
D: aBAK
E: Bcl-2 homologous antagonist/killer
F: aBAK
G: Bcl-2 homologous antagonist/killer
H: aBAK


Theoretical massNumber of molelcules
Total (without water)101,5238
Polymers101,5238
Non-polymers00
Water00
1
A: Bcl-2 homologous antagonist/killer
B: aBAK


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-14 kcal/mol
Surface area12210 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: aBAK


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-14 kcal/mol
Surface area12260 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: aBAK


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-14 kcal/mol
Surface area12360 Å2
MethodPISA
4
G: Bcl-2 homologous antagonist/killer
H: aBAK


Theoretical massNumber of molelcules
Total (without water)25,3812
Polymers25,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.497, 74.493, 76.315
Angle α, β, γ (deg.)113.130, 90.150, 105.510
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 86 through 135 or resid 137...
21(chain C and (resid 86 through 135 or resid 137 through 165))
31(chain E and (resid 86 through 135 or resid 137...
41(chain G and (resid 86 through 135 or resid 137 through 165))
12(chain B and ((resid 2 through 3 and (name N...
22(chain D and ((resid 2 through 3 and (name N...
32(chain F and ((resid 2 through 3 and (name N...
42(chain H and resid 2 through 114)

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLYGLY(chain A and (resid 86 through 135 or resid 137...AA86 - 1351 - 50
121ARGARGHISHIS(chain A and (resid 86 through 135 or resid 137...AA137 - 16452 - 79
131HISHISHISHIS(chain A and (resid 86 through 135 or resid 137...AA16580
141ASNASNHISHIS(chain A and (resid 86 through 135 or resid 137...AA86 - 1651 - 80
151ASNASNHISHIS(chain A and (resid 86 through 135 or resid 137...AA86 - 1651 - 80
161ASNASNHISHIS(chain A and (resid 86 through 135 or resid 137...AA86 - 1651 - 80
171ASNASNHISHIS(chain A and (resid 86 through 135 or resid 137...AA86 - 1651 - 80
211ASNASNGLYGLY(chain C and (resid 86 through 135 or resid 137 through 165))CC86 - 1351 - 50
221ARGARGHISHIS(chain C and (resid 86 through 135 or resid 137 through 165))CC137 - 16552 - 80
311ASNASNGLYGLY(chain E and (resid 86 through 135 or resid 137...EE86 - 1351 - 50
321ARGARGHISHIS(chain E and (resid 86 through 135 or resid 137...EE137 - 16452 - 79
331HISHISHISHIS(chain E and (resid 86 through 135 or resid 137...EE16580
341ASNASNHISHIS(chain E and (resid 86 through 135 or resid 137...EE86 - 1651 - 80
351ASNASNHISHIS(chain E and (resid 86 through 135 or resid 137...EE86 - 1651 - 80
361ASNASNHISHIS(chain E and (resid 86 through 135 or resid 137...EE86 - 1651 - 80
371ASNASNHISHIS(chain E and (resid 86 through 135 or resid 137...EE86 - 1651 - 80
411ASNASNGLYGLY(chain G and (resid 86 through 135 or resid 137 through 165))GG86 - 1351 - 50
421ARGARGHISHIS(chain G and (resid 86 through 135 or resid 137 through 165))GG137 - 16552 - 80
112ALAALAASPASP(chain B and ((resid 2 through 3 and (name N...BB2 - 33 - 4
122ALAALALEULEU(chain B and ((resid 2 through 3 and (name N...BB2 - 1153 - 116
132ALAALALEULEU(chain B and ((resid 2 through 3 and (name N...BB2 - 1153 - 116
142ALAALALEULEU(chain B and ((resid 2 through 3 and (name N...BB2 - 1153 - 116
152ALAALALEULEU(chain B and ((resid 2 through 3 and (name N...BB2 - 1153 - 116
212ALAALAASPASP(chain D and ((resid 2 through 3 and (name N...DD2 - 33 - 4
222ALAALALYSLYS(chain D and ((resid 2 through 3 and (name N...DD2 - 1143 - 115
232ALAALALYSLYS(chain D and ((resid 2 through 3 and (name N...DD2 - 1143 - 115
242ALAALALYSLYS(chain D and ((resid 2 through 3 and (name N...DD2 - 1143 - 115
252ALAALALYSLYS(chain D and ((resid 2 through 3 and (name N...DD2 - 1143 - 115
312ALAALAASPASP(chain F and ((resid 2 through 3 and (name N...FF2 - 33 - 4
322ALAALAGLUGLU(chain F and ((resid 2 through 3 and (name N...FF2 - 1163 - 117
332ALAALAGLUGLU(chain F and ((resid 2 through 3 and (name N...FF2 - 1163 - 117
342ALAALAGLUGLU(chain F and ((resid 2 through 3 and (name N...FF2 - 1163 - 117
352ALAALAGLUGLU(chain F and ((resid 2 through 3 and (name N...FF2 - 1163 - 117
412ALAALALYSLYS(chain H and resid 2 through 114)HH2 - 1143 - 115

NCS ensembles :
ID
1
2

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Components

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


Mass: 11515.069 Da / Num. of mol.: 4 / 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 BL21 (bacteria) / References: UniProt: Q16611
#2: Protein
aBAK


Mass: 13865.690 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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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: 1.88 Å3/Da / Density % sol: 34.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M 2-(N-Morpholino)ethanesulfonic acid (MES) pH 6.5, 0.2 M L-Proline and 10% (w/v) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9536 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 2.86→40.6 Å / Num. obs: 21041 / % possible obs: 96.92 % / Redundancy: 3.1 % / CC1/2: 0.983 / Rrim(I) all: 0.2 / Net I/σ(I): 4.7
Reflection shellResolution: 2.86→2.96 Å / Mean I/σ(I) obs: 1.44 / Num. unique obs: 1921 / CC1/2: 0.49 / Rrim(I) all: 1.22

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Processing

Software
NameVersionClassification
PHENIXdev_3965refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IMT

2imt


Resolution: 2.86→40.56 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2699 1078 5.14 %
Rwork0.221 19896 -
obs0.2236 20974 96.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.56 Å2 / Biso mean: 56.1151 Å2 / Biso min: 20.98 Å2
Refinement stepCycle: final / Resolution: 2.86→40.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6379 0 0 0 6379
Num. residues----778
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1481X-RAY DIFFRACTION8.953TORSIONAL
12C1481X-RAY DIFFRACTION8.953TORSIONAL
13E1481X-RAY DIFFRACTION8.953TORSIONAL
14G1481X-RAY DIFFRACTION8.953TORSIONAL
21B2356X-RAY DIFFRACTION8.953TORSIONAL
22D2356X-RAY DIFFRACTION8.953TORSIONAL
23F2356X-RAY DIFFRACTION8.953TORSIONAL
24H2356X-RAY DIFFRACTION8.953TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.86-2.990.34491180.27582291240990
2.99-3.150.26761280.25512489261798
3.15-3.350.33951460.25182538268498
3.35-3.60.27471150.23692514262997
3.61-3.970.2981280.2162531265998
3.97-4.540.22951540.19182497265198
4.54-5.720.27411590.21062509266899
5.72-40.560.23791300.20912527265798
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)
18.4376-0.70123.6614.2132-0.4644.9451.1427-0.2896-2.22530.4423-0.53350.62530.9913-0.4093-0.59430.33690.02040.00590.3835-0.02130.699-10.918-33.93869.4039
29.51250.12751.75111.4662-0.13652.07050.00180.2965-0.40530.0725-0.1636-0.13940.00360.55120.03870.2211-0.00420.08470.35050.11530.3478-3.2768-25.93269.6417
36.6173-0.1-2.34691.41490.34682.37420.680.48631.3229-0.2979-0.19920.1532-0.7665-0.2291-0.26790.4514-0.01240.07540.76280.16330.3263-7.27828.662612.0205
40.9150.35690.50151.5749-1.55077.77440.2036-0.05060.0648-0.214-0.05520.0595-0.07350.6291-0.18340.21870.06470.00030.2455-0.01710.2113-3.82892.85144.9413
54.23860.4916-1.04033.2937-0.17443.09320.1312-0.2340.01090.35190.0373-0.2914-0.034-0.0939-0.22070.33990.0660.0150.390.00010.2897-10.94329.265428.3077
69.55333.1045-2.37951.9051-1.31854.65610.405-0.09141.99490.09180.06150.8209-0.4575-0.5349-0.54050.38680.06720.11240.43860.08180.4751-22.632411.887424.8432
72.97771.0261-0.55375.1182-0.16252.71510.29230.10170.27270.3005-0.0940.29770.20390.2304-0.14380.25470.05890.00120.30080.14840.3478-16.665215.3844-8.2607
8-0.0244-1.19910.55533.5757-3.79275.72310.049-0.19470.06970.26550.3020.39080.1565-0.1337-0.35190.3051-0.0211-0.0510.2499-0.00220.3524-15.23341.88083.1387
94.9361.1891-0.83290.8910.44661.85410.38940.57270.782-0.2028-0.24980.2192-0.484-0.0328-0.19610.29910.0230.09140.33830.16560.4756-9.507627.5906-12.9158
106.2371-0.1173-5.38430.8959-1.71675.95390.3382-1.0341-0.12530.0796-0.4592-0.2726-0.44060.9201-0.01640.3173-0.0552-0.02890.5266-0.06780.46052.197626.5222-8.6994
114.582.38582.00743.56931.47385.33010.52440.137-0.22290.2609-0.04540.0050.576-0.1848-0.40550.34830.1190.04620.51150.14190.3492-3.9882-5.898-17.7525
120.176-0.0484-1.57740.1299-0.12734.8534-0.0625-0.02580.00730.2347-0.0812-0.0745-0.11540.5634-0.02290.3335-0.02330.03910.4563-0.00420.2262-5.6986-5.2576-0.347
133.7958-0.89760.94991.73630.09233.04860.76292.438-0.8918-0.3762-0.5824-0.03980.65740.607-0.31690.65650.2018-0.16520.7321-0.26260.56-13.0207-14.109-34.2764
141.70611.38090.91461.2151.15572.1450.30150.0311-0.6051-0.17060.2458-0.33430.6080.37510.61880.36281.1766-0.55211.9489-0.28881.193113.5002-21.726-23.0383
156.5697-2.19942.67373.7362-3.08414.7362-0.10111.45121.27390.0395-0.0736-0.3416-0.0919-0.03860.17070.32220.1532-0.04010.65210.02230.3296-12.3484-5.9027-27.2821
163.7485-0.15221.53211.3198-2.16614.41310.63590.8133-1.2005-0.0894-0.19160.58760.6791-0.4756-0.59350.4546-0.0398-0.11310.6473-0.01890.6084-23.6401-12.7449-26.8287
171.6381-1.38910.17733.9866-0.33831.51090.23170.1661-0.1134-0.567-0.19490.26530.05450.08530.06520.2521-0.02490.03340.39680.1410.3053-16.6564-16.66216.5861
180.10050.9153-0.9721.6281-1.80623.1420.03810.01630.064-0.47340.14670.04350.0863-0.217-0.07180.39980.0750.08390.26730.07150.3939-15.0942-2.8496-5.3768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'F' and (resid 2 through 39 )F2 - 39
2X-RAY DIFFRACTION2chain 'F' and (resid 40 through 116 )F40 - 116
3X-RAY DIFFRACTION3chain 'G' and (resid 86 through 106 )G86 - 106
4X-RAY DIFFRACTION4chain 'G' and (resid 107 through 166 )G107 - 166
5X-RAY DIFFRACTION5chain 'H' and (resid 2 through 78 )H2 - 78
6X-RAY DIFFRACTION6chain 'H' and (resid 79 through 116 )H79 - 116
7X-RAY DIFFRACTION7chain 'A' and (resid 86 through 124 )A86 - 124
8X-RAY DIFFRACTION8chain 'A' and (resid 125 through 165 )A125 - 165
9X-RAY DIFFRACTION9chain 'B' and (resid 2 through 78 )B2 - 78
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 115 )B79 - 115
11X-RAY DIFFRACTION11chain 'C' and (resid 86 through 124 )C86 - 124
12X-RAY DIFFRACTION12chain 'C' and (resid 125 through 165 )C125 - 165
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 34 )D2 - 34
14X-RAY DIFFRACTION14chain 'D' and (resid 35 through 39 )D35 - 39
15X-RAY DIFFRACTION15chain 'D' and (resid 40 through 78 )D40 - 78
16X-RAY DIFFRACTION16chain 'D' and (resid 79 through 114 )D79 - 114
17X-RAY DIFFRACTION17chain 'E' and (resid 86 through 124 )E86 - 124
18X-RAY DIFFRACTION18chain 'E' and (resid 125 through 165 )E125 - 165

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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