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- PDB-5vwv: Bak core latch dimer in complex with Bim-BH3 - Cubic -

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Basic information

Entry
Database: PDB / ID: 5vwv
TitleBak core latch dimer in complex with Bim-BH3 - Cubic
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bcl-2 Family / Activator
Function / homology
Function and homology information


dynorphin receptor activity / neuropeptide binding / neuropeptide signaling pathway / sensory perception of pain / toxin activity / neuron projection / extracellular region / membrane
Similarity search - Function
T-superfamily conotoxin / chi-Conotoxin or t superfamily / Kappa opioid receptor / Opioid receptor / Apoptosis regulator proteins, Bcl-2 family / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
trifluoroacetic acid / Kappa-type opioid receptor / Chi-conotoxin PnID
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 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

Downloads & links

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Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,67811
Polymers22,0642
Non-polymers6149
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-13 kcal/mol
Surface area12690 Å2
MethodPISA
2
A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules

A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,35522
Polymers44,1274
Non-polymers1,22818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
Buried area14470 Å2
ΔGint-112 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.404, 139.404, 139.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-437-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 19037.320 Da / Num. of mol.: 1 / Fragment: UNP residues 23-186 / 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 (E. coli) / References: UniProt: Q16611
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3026.411 Da / Num. of mol.: 1 / Fragment: UNP residues 141-165 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521

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Non-polymers , 5 types, 195 molecules

#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 5.12 Å3/Da / Density % sol: 75.96 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 18 % glycerol, 21.6 % PEG (poly-ethylene glycol) 1500 and 0.5 % ethyl acetate

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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: Jul 12, 2014
RadiationMonochromator: ADSC QUANTUM 315r / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.897→42.032 Å / Num. obs: 37157 / % possible obs: 100 % / Redundancy: 47.8 % / Rmerge(I) obs: 0.2162 / Net I/σ(I): 24.26
Reflection shellResolution: 1.898→1.966 Å / Redundancy: 47 % / Mean I/σ(I) obs: 1.48 / Num. unique obs: 3647 / CC1/2: 0.497 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.897→42.032 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.3
RfactorNum. reflection% reflection
Rfree0.1771 1996 5.37 %
Rwork0.1568 --
obs0.1579 37157 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.897→42.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1554 0 38 186 1778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071625
X-RAY DIFFRACTIONf_angle_d0.7552188
X-RAY DIFFRACTIONf_dihedral_angle_d20.589950
X-RAY DIFFRACTIONf_chiral_restr0.048228
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8974-1.94480.30141390.29042462X-RAY DIFFRACTION100
1.9448-1.99740.26931390.24782455X-RAY DIFFRACTION100
1.9974-2.05620.28531410.22652461X-RAY DIFFRACTION100
2.0562-2.12260.22761390.20732465X-RAY DIFFRACTION100
2.1226-2.19840.22511410.1682471X-RAY DIFFRACTION100
2.1984-2.28640.161400.1592466X-RAY DIFFRACTION100
2.2864-2.39050.15321420.15622492X-RAY DIFFRACTION100
2.3905-2.51650.18081410.15142487X-RAY DIFFRACTION100
2.5165-2.67420.18061420.15072493X-RAY DIFFRACTION100
2.6742-2.88060.17661420.14482493X-RAY DIFFRACTION100
2.8806-3.17040.16811440.15132540X-RAY DIFFRACTION100
3.1704-3.62890.15011440.13632539X-RAY DIFFRACTION100
3.6289-4.57120.16081470.12972580X-RAY DIFFRACTION100
4.5712-42.04220.16781550.16172757X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.9887-3.11340.60242.2619-1.20577.0027-0.46180.8847-2.1062-0.7168-0.9307-0.82461.48371.72991.32740.77510.22180.21720.7773-0.0411.126915.61699.795136.4117
27.17592.94220.56782.03452.06635.15950.1957-0.0660.02160.3056-0.198-0.0320.0897-0.1260.070.13810.07020.02510.228-0.02010.234913.728528.9185146.0283
35.349-3.688-1.62454.61912.05712.6544-0.0865-0.2024-0.12720.24410.00190.03930.17540.27560.07810.24360.02970.00770.2941-0.00160.293615.16430.2519152.541
48.0554-5.14610.15964.1541-1.01071.48890.24690.49240.7712-0.2376-0.249-0.5009-0.12690.1273-0.01330.2309-0.00470.02990.2558-0.00120.267312.195836.5061138.7494
54.0803-1.1416-1.02132.48731.32493.19490.10470.3995-0.0513-0.1335-0.10190.1391-0.0442-0.22340.00990.16520.0449-0.00850.20870.0360.19611.00832.7051141.0201
69.82321.0417-6.40346.1405-1.63114.8485-0.09650.1431-0.41330.08-0.13580.45350.7188-0.4790.13710.2626-0.02580.00720.2046-0.02410.2751-10.596336.0408167.9171
72.0596-0.82870.12646.08251.43392.7941-0.0873-0.28520.04010.73240.02190.65760.0403-0.31160.05170.29980.02530.13220.3045-0.00510.304-16.627346.7169179.9949
85.5166-5.6378-5.13187.57064.37635.62490.58551.07160.4984-0.9585-0.3335-0.3949-0.23650.1013-0.22280.35630.03760.03990.54240.06980.25654.716334.5216129.52
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 100 )
5X-RAY DIFFRACTION5chain 'A' and (resid 101 through 149 )
6X-RAY DIFFRACTION6chain 'A' and (resid 150 through 164 )
7X-RAY DIFFRACTION7chain 'A' and (resid 165 through 186 )
8X-RAY DIFFRACTION8chain 'B' and (resid 141 through 165 )

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