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

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Basic information

Entry
Database: PDB / ID: 6uxm
TitleCrystal structure of BAK core domain BH3-groove-dimer in complex with E. coli lipid
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Pore-forming Protein
Function / homologyT-superfamily conotoxin / chi-Conotoxin or t superfamily / toxin activity / extracellular region / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chi-conotoxin PnID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 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 2.0Oct 11, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

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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
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,46812
Polymers57,0046
Non-polymers4,4646
Water00
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-47 kcal/mol
Surface area9290 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-43 kcal/mol
Surface area9190 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4894
Polymers19,0012
Non-polymers1,4882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-45 kcal/mol
Surface area9280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.700, 55.040, 56.500
Angle α, β, γ (deg.)116.130, 109.670, 97.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 70 through 145 or (resid 200...
21(chain B and (resid 70 through 145 or (resid 200...
31(chain C and (resid 70 through 145 or (resid 200...
41(chain D and (resid 70 through 145 or (resid 200...
51(chain E and (resid 70 through 145 or (resid 200...
61(chain F and (resid 70 through 145 or (resid 200...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 70 through 145 or (resid 200...A0
211(chain B and (resid 70 through 145 or (resid 200...B0
311(chain C and (resid 70 through 145 or (resid 200...C0
411(chain D and (resid 70 through 145 or (resid 200...D0
511(chain E and (resid 70 through 145 or (resid 200...E0
611(chain F and (resid 70 through 145 or (resid 200...F0

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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.: 6 / 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-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
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: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ammonium sulphate, PEG 10000, sodium acetate, bis-tris chloride

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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: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.49→25.665 Å / Num. obs: 15495 / % possible obs: 97.4 % / Redundancy: 9.436 % / Biso Wilson estimate: 75.759 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.096 / Χ2: 1.016 / Net I/σ(I): 15.03 / Num. measured all: 146213 / Scaling rejects: 190
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
2.49-2.558.8061.9051.289449116610730.5182.02692
2.55-2.629.7821.41.910878114311120.7221.47797.3
2.62-2.79.7440.962.9510826113211110.8641.01498.1
2.7-2.789.7550.7743.7510028105810280.9260.81797.2
2.78-2.879.7410.6274.5410033104410300.9270.66198.7
2.87-2.989.7310.5195.51967310219940.9470.54897.4
2.98-3.099.680.3617.7693419819650.9750.38198.4
3.09-3.219.7690.24910.789299309140.9890.26298.3
3.21-3.369.670.16914.5187429299040.9940.17897.3
3.36-3.529.5920.11918.4581828588530.9960.12699.4
3.52-3.719.5560.10121.9276268167980.9970.10797.8
3.71-3.949.3780.07426.6572687937750.9970.07897.7
3.94-4.219.0990.06629.565067177150.9970.0799.7
4.21-4.559.1670.06130.9361606836720.9980.06598.4
4.55-4.988.8950.05832.1554886286170.9980.06198.2
4.98-5.578.8110.05533.0548555615510.9980.05998.2
5.57-6.438.7380.0632.3842644994880.9970.06497.8
6.43-7.879.1040.053538514344230.9980.05397.5
7.87-11.139.0430.04437.3329393313250.9970.04698.2
11.13-25.6657.9930.04235.4411751791470.9980.04582.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.49 Å46.91 Å
Translation2.49 Å46.91 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U2V

4u2v


Resolution: 2.49→25.665 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2372 1546 10 %
Rwork0.1872 13914 -
obs0.1922 15460 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 205.69 Å2 / Biso mean: 92.0494 Å2 / Biso min: 42.69 Å2
Refinement stepCycle: final / Resolution: 2.49→25.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 173 0 3948
Biso mean--86.52 --
Num. residues----470
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1871X-RAY DIFFRACTION12.566TORSIONAL
12B1871X-RAY DIFFRACTION12.566TORSIONAL
13C1871X-RAY DIFFRACTION12.566TORSIONAL
14D1871X-RAY DIFFRACTION12.566TORSIONAL
15E1871X-RAY DIFFRACTION12.566TORSIONAL
16F1871X-RAY DIFFRACTION12.566TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.49-2.57020.38371300.3108117592
2.5702-2.66190.31131420.262124098
2.6619-2.76840.29351440.2395128898
2.7684-2.89420.29481430.2196126799
2.8942-3.04660.27651370.2168128199
3.0466-3.23710.27691430.2009126899
3.2371-3.48650.21581410.1764128199
3.4865-3.83630.2491380.1883128499
3.8363-4.38910.21571430.178127299
4.3891-5.52070.23131420.1859128199
5.5207-25.6650.20841430.1601127799
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)
19.12685.4318-6.49382.04162.1139.49930.40612.20091.7497-1.8085-0.14623.4797-0.592-1.82642.35881.5139-0.0516-0.78110.67560.06890.60515.21785.080511.5144
25.83470.79320.1062.63330.14230.0383-0.96671.7243-1.2705-0.89450.45270.07820.52830.6633-0.69832.01790.25760.50011.2069-0.39710.86928.0572-9.22219.8518
38.85041.24451.0996.949-2.19129.1522-0.12251.211-0.6774-1.32030.1822-0.94250.28520.6405-0.23160.57480.13280.2510.6637-0.02420.485926.841-4.480418.0723
42.0571-4.23371.07874.86141.25870.95940.80543.10552.4431-2.2945-0.732-1.0734-0.59970.38740.54081.5222-0.13650.3920.9750.16770.678127.86574.254710.8991
57.8733-0.78592.77449.7094.30626.2505-0.2222-0.21661.1616-1.3598-0.29771.3878-0.9385-0.51360.43350.8440.0456-0.25970.6970.08941.02574.12728.383120.5441
64.07144.71311.65146.25991.42825.79260.1316-0.06670.5725-1.4258-0.2360.6976-0.8911-0.19540.33730.56380.0729-0.14530.4903-0.00270.628311.119410.54523.3452
73.9281-3.5167-0.09363.49-1.22845.62131.145-1.77691.2351.5002-1.00262.1685-1.2536-0.7574-0.52010.88420.10450.36420.9914-0.34331.07874.46127.64646.428
86.93880.01510.97684.2244-1.62777.93070.1430.35831.21790.2836-0.2472-0.7158-1.37390.46650.1140.75140.01410.02970.65510.05750.817229.205411.368835.7619
96.59790.49823.60376.85440.08896.57280.12250.19841.34940.5369-0.09121.1329-2.0245-1.72550.21950.56570.11660.04230.51560.10030.552621.702411.253933.9739
105.77811.8737-7.50254.4448-2.57672.10791.4472-1.78382.41831.1137-0.7314-1.1449-1.79462.0373-0.36310.8938-0.2073-0.05231.1536-0.09130.856327.723110.065445.8272
113.68643.54960.41254.85571.2912.0671.5977-1.464-0.56723.5292-1.10250.54210.5375-0.6235-0.351.2277-0.38040.1671.21360.00180.79886.4466-4.050851.3059
125.2422-1.385-0.54638.97650.51058.00870.531-0.97130.12450.1667-0.67361.11140.58590.14670.19460.4515-0.04410.16290.549-0.05320.67187.3443-1.521742.0695
135.6464-3.65050.48055.3721-3.47124.4776-0.3486-0.609-2.321.03750.00871.20570.6945-0.94280.11820.9221-0.06850.0430.6585-0.04721.14675.3904-23.607731.7084
145.1465-0.0029-0.55655.32646.5178.0874-0.1826-1.5564-1.21112.0344-0.4055-1.13741.89050.7227-0.91351.06060.0169-0.34271.08180.38250.904625.8311-21.631244.4313
152.41532.89651.72225.87554.84245.360.2817-0.2256-0.08380.78070.6143-1.08310.20131.1946-1.03240.78450.0548-0.21790.88560.09311.227831.8899-11.228637.2692
166.176-2.3189-2.7737.93514.42823.7289-0.3466-0.9098-0.63721.4244-0.52751.24891.0883-0.2560.29030.6471-0.0878-0.02590.67340.23150.52622.2454-13.880940.6366
179.92096.0473.68023.94852.01566.7131-0.31131.1963-1.2212-0.63840.0277-2.47521.40741.8073-1.35350.7090.3349-0.24760.61360.1421.572928.6954-23.230533.749
184.0713-3.16451.11787.3462-6.51446.9508-0.63351.7722-1.1577-1.9972-0.4033-0.16342.59010.5232-0.07561.2007-0.0217-0.15430.7999-0.14851.10779.1358-25.080621.6168
194.99953.4956-0.04228.17341.32787.4624-0.01560.95220.4005-0.98330.50621.3539-0.137-0.8565-0.38770.56160.0342-0.12130.58520.09640.59037.1347-15.067524.2216
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'E' and (resid 67 through 88 )E67 - 88
2X-RAY DIFFRACTION2chain 'E' and (resid 89 through 106 )E89 - 106
3X-RAY DIFFRACTION3chain 'E' and (resid 107 through 145 )E107 - 145
4X-RAY DIFFRACTION4chain 'F' and (resid 70 through 88 )F70 - 88
5X-RAY DIFFRACTION5chain 'F' and (resid 89 through 124 )F89 - 124
6X-RAY DIFFRACTION6chain 'F' and (resid 125 through 148 )F125 - 148
7X-RAY DIFFRACTION7chain 'A' and (resid 67 through 88 )A67 - 88
8X-RAY DIFFRACTION8chain 'A' and (resid 89 through 124 )A89 - 124
9X-RAY DIFFRACTION9chain 'A' and (resid 125 through 145 )A125 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 88 )B69 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 106 )B89 - 106
12X-RAY DIFFRACTION12chain 'B' and (resid 107 through 145 )B107 - 145
13X-RAY DIFFRACTION13chain 'C' and (resid 67 through 88 )C67 - 88
14X-RAY DIFFRACTION14chain 'C' and (resid 89 through 100 )C89 - 100
15X-RAY DIFFRACTION15chain 'C' and (resid 101 through 124 )C101 - 124
16X-RAY DIFFRACTION16chain 'C' and (resid 125 through 145 )C125 - 145
17X-RAY DIFFRACTION17chain 'D' and (resid 69 through 88 )D69 - 88
18X-RAY DIFFRACTION18chain 'D' and (resid 89 through 100 )D89 - 100
19X-RAY DIFFRACTION19chain 'D' and (resid 101 through 145 )D101 - 145

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