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- PDB-5vwy: Bak core latch dimer in complex with Bim-h3Pc-RT -

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Basic information

Entry
Database: PDB / ID: 5vwy
TitleBak core latch dimer in complex with Bim-h3Pc-RT
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bcl-2 Family / Inhibitor
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / developmental pigmentation / BAK complex ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / response to mycotoxin / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / developmental pigmentation / BAK complex / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / positive regulation of fibroblast apoptotic process / limb morphogenesis / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / endocrine pancreas development / post-embryonic camera-type eye morphogenesis / ear development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / meiosis I / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / positive regulation of T cell apoptotic process / tube formation / regulation of organ growth / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / cellular response to glucocorticoid stimulus / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / BH domain binding / FOXO-mediated transcription of cell death genes / positive regulation of calcium ion transport into cytosol / porin activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / 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 proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / endomembrane system / Pyroptosis / animal organ regeneration / positive regulation of cell cycle / positive regulation of intrinsic apoptotic signaling pathway / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / heat shock protein binding / FLT3 Signaling / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / cell-matrix adhesion / release of cytochrome c from mitochondria / post-embryonic development / thymus development / regulation of mitochondrial membrane potential / epithelial cell proliferation / kidney development / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / positive regulation of neuron apoptotic process / Signaling by BRAF and RAF1 fusions / protein-folding chaperone binding / spermatogenesis / microtubule binding / regulation of apoptotic process / response to ethanol / in utero embryonic development
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 / 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, Bim N-terminal / Bcl-2-like protein 11 / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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
PHOSPHATE ION / Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.555 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

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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-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3743
Polymers22,2792
Non-polymers951
Water2,486138
1
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)44,7486
Polymers44,5584
Non-polymers1902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12040 Å2
ΔGint-122 kcal/mol
Surface area16690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.890, 37.540, 69.560
Angle α, β, γ (deg.)90.00, 107.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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: 3241.641 Da / Num. of mol.: 1 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.84 Å3/Da / Density % sol: 33.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 15.8 % PEG 8000, 50 mM potassium dihydrogen phosphate, and 22.7 % glycerol

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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: Feb 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.555→32.45 Å / Num. obs: 21962 / % possible obs: 93 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06555 / Net I/σ(I): 13.68

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.555→32.45 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.11
RfactorNum. reflection% reflection
Rfree0.2156 1998 9.1 %
Rwork0.175 --
obs0.1787 21962 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.555→32.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 5 138 1595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071496
X-RAY DIFFRACTIONf_angle_d1.1382021
X-RAY DIFFRACTIONf_dihedral_angle_d22.434871
X-RAY DIFFRACTIONf_chiral_restr0.052209
X-RAY DIFFRACTIONf_plane_restr0.006269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5554-1.59430.4062990.3663991X-RAY DIFFRACTION65
1.5943-1.63740.35811110.3041086X-RAY DIFFRACTION72
1.6374-1.68550.26111450.25631401X-RAY DIFFRACTION94
1.6855-1.73990.27971450.23871484X-RAY DIFFRACTION97
1.7399-1.80210.29091440.2241462X-RAY DIFFRACTION96
1.8021-1.87430.22471460.20241457X-RAY DIFFRACTION96
1.8743-1.95960.22391500.20561472X-RAY DIFFRACTION98
1.9596-2.06290.23731460.17831493X-RAY DIFFRACTION98
2.0629-2.19210.19281450.1611510X-RAY DIFFRACTION98
2.1921-2.36130.19671540.16381492X-RAY DIFFRACTION98
2.3613-2.59880.21181440.15861497X-RAY DIFFRACTION99
2.5988-2.97470.21031540.16171509X-RAY DIFFRACTION99
2.9747-3.74690.19251530.15451541X-RAY DIFFRACTION99
3.7469-32.45660.19841620.15661569X-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)
14.7982-1.1475-0.31352.45293.2265.4198-0.1376-0.026-0.11810.49720.201-0.36140.2630.5202-0.13560.11650.0079-0.00940.16180.01260.1208-4.292813.732214.7633
26.6098-4.92793.68423.6895-2.70153.8532-0.71060.17150.80931.28960.2778-0.5455-0.73150.22350.46960.58410.0131-0.1020.4313-0.03110.3182-7.884624.566125.1403
34.8315-4.3843.71614.3033-2.1867.2099-0.4058-0.7772-0.21530.94091.0696-0.99422.09672.8889-0.58360.61680.2469-0.23260.7747-0.0791.09112.837617.453118.9594
44.4028-4.34650.29997.4808-2.03964.26080.04510.08430.6037-0.1238-0.1155-0.7991-0.22560.45680.01530.1172-0.04180.01280.17720.01290.1828-3.545819.27518.3108
58.88752.5956-5.96216.2799-4.52787.41090.2738-0.33760.50780.3736-0.01880.2686-0.5450.0287-0.30850.20650.0418-0.01570.1456-0.05090.1666-22.173122.823316.3912
64.62590.410.69483.77282.63992.04170.0768-0.6179-0.22730.6530.0290.07980.6519-0.3264-0.10780.22150.00370.02930.18850.03030.1689-21.0197.253322.5959
77.7353-0.66832.69193.7992.53553.02210.00880.0414-0.17090.0922-0.0043-0.01650.3037-0.28430.01540.1017-0.01060.00930.0754-0.01990.1113-20.04275.94795.5355
82.04430.95351.3491.86751.60889.04570.0762-0.27660.00030.1873-0.10220.0002-0.3051-0.16120.05740.09840.00340.00990.09190.0110.1041-14.756515.804917.4693
92.3442-1.65380.93686.4443-3.91543.52610.13430.3824-0.0811-1.05070.05960.2330.6543-0.1835-0.2220.2976-0.0545-0.02940.2042-0.03760.1567-12.29298.007443.4933
103.2714-0.478-0.767.31712.63853.370.1142-0.3082-0.11340.3393-0.17660.02690.1697-0.26250.07990.1116-0.03390.00940.19750.04710.0956-13.70158.471663.2936
119.12563.2213-6.55493.4736-3.00316.56430.0399-0.0869-0.06440.0199-0.01870.18130.1024-0.1793-0.04360.10220.0018-0.03370.08340.00970.1078-23.425215.45259.178
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 69 )
4X-RAY DIFFRACTION4chain 'A' and (resid 70 through 82 )
5X-RAY DIFFRACTION5chain 'A' and (resid 83 through 100 )
6X-RAY DIFFRACTION6chain 'A' and (resid 101 through 118 )
7X-RAY DIFFRACTION7chain 'A' and (resid 119 through 124 )
8X-RAY DIFFRACTION8chain 'A' and (resid 125 through 144 )
9X-RAY DIFFRACTION9chain 'A' and (resid 145 through 164 )
10X-RAY DIFFRACTION10chain 'A' and (resid 165 through 186 )
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 165 )

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