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- PDB-5vww: Bak core latch dimer in complex with Bim-RT - Tetragonal -

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Basic information

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


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / negative regulation of endoplasmic reticulum calcium ion concentration / developmental pigmentation / response to fungus / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / 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 / ear development / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / B cell apoptotic process / tube formation / mammary gland development / 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 / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / porin activity / thymocyte apoptotic process / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / pore complex / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / positive regulation of calcium ion transport into cytosol / T cell homeostasis / vagina development / B cell homeostasis / 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 / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / FLT3 Signaling / endomembrane system / intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / thymus development / release of cytochrome c from mitochondria / cell-matrix adhesion / epithelial cell proliferation / post-embryonic development / response to gamma radiation / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / kidney development / establishment of localization in cell / response to hydrogen peroxide / cellular response to mechanical stimulus / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / protein-folding chaperone binding / channel activity / response to ethanol / spermatogenesis / regulation of apoptotic process / microtubule binding / in utero embryonic development / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / positive regulation of apoptotic process
Similarity search - Function
Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BROMIDE ION / IMIDAZOLE / Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.802 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 homologous antagonist/killer
C: Bcl-2-like protein 11
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7898
Polymers44,4424
Non-polymers3474
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-126 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.790, 87.790, 95.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#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.: 2 / 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: 3183.605 Da / Num. of mol.: 2 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521

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Non-polymers , 4 types, 23 molecules

#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 12.5 % MPD (2-methyl-2,4-pentanediol), 38 mM imidazole pH 6.5, 12.5 % PEG 1000, 12.5 % PEG 3350, 30 mM sodium fluoride, 30 mM sodium iodide, 62 mM sodium MES pH 6.5 and 30 mM sodium bromide

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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: Apr 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.8→43.9 Å / Num. obs: 9619 / % possible obs: 100 % / Redundancy: 14 % / CC1/2: 0.99 / Rmerge(I) obs: 0.1196 / Net I/σ(I): 19.77

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.802→39.881 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.04
RfactorNum. reflection% reflection
Rfree0.2811 963 10.02 %
Rwork0.2245 --
obs0.2301 9611 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.802→39.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 15 19 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032784
X-RAY DIFFRACTIONf_angle_d0.4243753
X-RAY DIFFRACTIONf_dihedral_angle_d16.1121612
X-RAY DIFFRACTIONf_chiral_restr0.035393
X-RAY DIFFRACTIONf_plane_restr0.002489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8022-2.94980.32031320.30551189X-RAY DIFFRACTION99
2.9498-3.13460.33651360.29131201X-RAY DIFFRACTION100
3.1346-3.37650.30151280.26231219X-RAY DIFFRACTION100
3.3765-3.71610.28981420.22681215X-RAY DIFFRACTION100
3.7161-4.25330.3211330.21521231X-RAY DIFFRACTION100
4.2533-5.35660.26171420.20741255X-RAY DIFFRACTION100
5.3566-39.88480.25361500.20891338X-RAY DIFFRACTION100
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)
16.708-1.31934.44076.4679-1.98333.8005-0.4615-0.27960.84850.4019-0.2922-0.5573-2.48331.19940.53280.5702-0.1305-0.0640.5362-0.05940.649-25.956914.7226-18.8623
27.5441-2.167-2.20119.52698.48318.09981.137-0.93080.6266-0.4705-0.5174-1.1956-1.02810.8411-0.65130.6491-0.1466-0.18141.28760.58752.124-30.419320.165-9.3309
32.1038-2.10392.20436.4495-1.9838.9339-0.05930.20570.39920.2394-0.104-0.4904-0.29220.47690.10980.3943-0.08520.02140.49390.03490.5357-24.46272.4417-10.9415
44.58261.50284.35433.99241.68637.07810.4309-0.1435-0.27291.2367-0.2725-1.29760.3880.5322-0.21680.762-0.0603-0.32910.65190.0980.7269-7.60589.1624-3.2388
50.5705-0.88860.92941.3826-1.44491.5001-0.2674-1.15790.20690.0552-0.2996-0.0929-0.70120.4668-0.63543.19190.1695-2.3672.6173-0.05561.74389.425315.836820.8009
61.99084.9666-6.76067.0937-2.10488.1069-0.1038-3.4908-2.33841.2578-0.8688-1.12261.5055-0.69030.49592.1561-0.4473-0.54032.28340.10431.01340.711610.734813.2905
78.5186-3.3447-2.45676.23642.07230.96890.8039-2.16831.29210.84790.62730.19331.04-0.4774-0.79551.77420.015-0.55971.6983-0.24781.5659-5.498724.168511.6269
84.1416-2.72851.04574.7247-2.37692.1426-0.65970.14271.82410.3177-0.6933-2.1173-1.52261.3191.28451.3658-0.0239-0.74421.17170.12162.5875.272724.1834-0.079
99.09480.42656.82323.2240.8386.8143-0.403-0.25690.78340.0859-0.1002-0.7754-0.81540.40780.41160.6088-0.1356-0.10250.64190.06220.7043-16.590912.7676-12.5939
104.7087-4.68814.85394.6371-4.68895.06140.51460.1683-0.7854-0.2106-0.26140.90630.0557-0.0597-0.41090.63610.10660.02620.6404-0.05240.5582-31.9216-4.6896-14.7045
112.7166-0.43353.6783.563-2.4468.26340.7409-0.24812.20950.67750.276-0.31250.51361.0381-0.90381.4765-0.0373-0.51781.4113-0.66632.57432.682332.87947.5024
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 69 )
3X-RAY DIFFRACTION3chain 'A' and (resid 70 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 181 )
6X-RAY DIFFRACTION6chain 'B' and (resid 23 through 69 )
7X-RAY DIFFRACTION7chain 'B' and (resid 70 through 100 )
8X-RAY DIFFRACTION8chain 'B' and (resid 101 through 124 )
9X-RAY DIFFRACTION9chain 'B' and (resid 125 through 185 )
10X-RAY DIFFRACTION10chain 'C' and (resid 142 through 166 )
11X-RAY DIFFRACTION11chain 'D' and (resid 143 through 161 )

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