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- PDB-6yli: Crystal structure of human bcl-xL bound to trichoplax adhaerens t... -

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Basic information

Entry
Database: PDB / ID: 6yli
TitleCrystal structure of human bcl-xL bound to trichoplax adhaerens trBak BH3
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS / Bcl-2 / Bak / trichoplax adhaerens
Function / homology
Function and homology information


apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / regulation of apoptotic process / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / apoptotic process / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / 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
Bcl-2 homologous antagonist/killer / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Trichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsD Sa, J. / Banjara, S. / Kvansakul, M.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190103591 Australia
CitationJournal: Sci Adv / Year: 2020
Title: Ancient and conserved functional interplay between Bcl-2 family proteins in the mitochondrial pathway of apoptosis.
Authors: Popgeorgiev, N. / Sa, J.D. / Jabbour, L. / Banjara, S. / Nguyen, T.T.M. / Akhavan-E-Sabet, A. / Gadet, R. / Ralchev, N. / Manon, S. / Hinds, M.G. / Osigus, H.J. / Schierwater, B. / Humbert, ...Authors: Popgeorgiev, N. / Sa, J.D. / Jabbour, L. / Banjara, S. / Nguyen, T.T.M. / Akhavan-E-Sabet, A. / Gadet, R. / Ralchev, N. / Manon, S. / Hinds, M.G. / Osigus, H.J. / Schierwater, B. / Humbert, P.O. / Rimokh, R. / Gillet, G. / Kvansakul, M.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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-like protein 1
B: Bcl-2 homologous antagonist/killer
C: Bcl-2-like protein 1
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39813
Polymers46,5334
Non-polymers8659
Water2,396133
1
A: Bcl-2-like protein 1
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8438
Polymers23,2672
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-98 kcal/mol
Surface area8920 Å2
MethodPISA
2
C: Bcl-2-like protein 1
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5555
Polymers23,2672
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-51 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.141, 63.801, 69.761
Angle α, β, γ (deg.)90.000, 94.566, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 20387.490 Da / Num. of mol.: 2 / Mutation: delta45-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q07817
#2: Protein/peptide Bcl-2 homologous antagonist/killer


Mass: 2879.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trichoplax sp. H2 (invertebrata) / References: UniProt: A0A369S334
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.87 Å3/Da / Density % sol: 35.6 % / Description: plate like
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium sulfate and 30 % w/v PEG 8000

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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: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→47.07 Å / Num. obs: 26735 / % possible obs: 98.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 32.98 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.125 / Net I/σ(I): 6.4
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 1.737 / Num. unique obs: 1963 / CC1/2: 0.351 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PQ1

1pq1


Resolution: 1.9→39.02 Å / SU ML: 0.2829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1892
RfactorNum. reflection% reflection
Rfree0.2359 1310 4.91 %
Rwork0.1988 --
obs0.2007 26699 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 45 133 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00822942
X-RAY DIFFRACTIONf_angle_d0.91423980
X-RAY DIFFRACTIONf_chiral_restr0.0422410
X-RAY DIFFRACTIONf_plane_restr0.0052513
X-RAY DIFFRACTIONf_dihedral_angle_d5.1195386
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.38581520.35412789X-RAY DIFFRACTION96.33
1.97-2.060.3131450.28832766X-RAY DIFFRACTION97.1
2.06-2.170.30031290.24632796X-RAY DIFFRACTION97.37
2.17-2.310.29511500.22192781X-RAY DIFFRACTION97.83
2.31-2.490.2291510.20092814X-RAY DIFFRACTION97.95
2.49-2.740.24831420.19342811X-RAY DIFFRACTION98.53
2.74-3.130.23711430.19222850X-RAY DIFFRACTION98.68
3.13-3.940.21061540.17182870X-RAY DIFFRACTION98.95
3.94-39.020.20521440.1842912X-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)
10.410728559392-0.410497172496-0.004224700730350.514451286441-0.3000910026630.847290980355-0.2482067146620.385317857838-0.0998088512493-0.03979003989880.0959800531464-0.2926613175230.4023260398260.512556005787-0.01271136398620.2467834635060.04223472144810.02971490085380.3660137015440.07816516748040.36239224713912.4706210567-16.67605499823.76260017284
20.2253775140290.381626069259-0.0531837214120.4530418019780.09598065276170.206683714147-0.0839568950269-0.22068181019-0.2328423679530.07859296655950.000126607988003-0.3472114069410.250845905940.205331851472-0.0003658477290220.3183078935810.0258406323730.0006329728950180.3580487327080.05020029459320.3675115223819.05497782998-17.561785721212.3641032417
3-0.01132626281090.0326673957470.001925448984070.1406827458940.1265631555620.06995652688210.02289755443130.0286669409399-0.138593137633-0.3629203480270.3959227604610.4285328904350.489941663744-1.00614243571-0.00657793527980.375941827566-0.0557374162938-0.06904287157560.5471247110010.1143582858180.499396998029-7.19659175724-11.77939718021.4391449093
40.4485525628570.169837457289-0.4916825272650.492972985091-0.5728884163451.568452047060.0297445510928-0.08524060495710.000726945280867-0.0463677778735-0.150721429029-0.0656707000847-0.2046111918950.1442260206760.0001594276104520.277122742168-0.00591103391493-0.01069615974020.2261585062120.03045857245520.2772356939516.37382309367-7.9540618516.23503238742
50.845114904040.32561556815-0.4800670370170.62718849040.04892541278370.326089663534-0.0950069303539-0.001920613986240.40305923497-0.0533184929993-0.0952496522930.192113344735-0.351893967469-0.404023831259-0.004834279356110.392221159470.03977708196210.02438336826260.3036986413340.0174766037420.355402583262-3.63644590281-5.9871130242413.5840440123
60.6770303512450.565865119855-0.1278694933150.706239302651-0.4029770387090.306899887779-0.0966077993157-0.0914286161268-0.128823817641-0.3678790149950.176607574030.3404598301680.276083006819-0.2550793151980.01137678781790.269890085629-0.0522192563246-0.03428096133330.3513792595670.04301765195090.343558935087-17.8506841403-33.834497220520.716586399
70.2247622942080.024616139276-0.2462115587140.284297601054-0.1499522756820.2099007047950.2551751113630.247471100130.299167599513-0.156715613871-0.1432769125820.1153414341180.202529020791-0.178133523234-0.002178953181240.202944556949-0.01203726474550.008826750603510.230300166930.02161363158160.226828702666-11.2407174923-24.182359202220.5928978008
8-0.0106620967191-0.07110427781530.008860439959010.0730538990070.01744462450460.3895819134690.03418494217930.1861175166710.0110791230523-0.611334109168-0.128929136609-0.9116326910240.5505570243480.2661179616370.002218082853780.3826978187310.06993280983980.04767468500890.4101276689280.03838855545610.5606527084322.08328245826-37.380667700826.1954477436
91.04149438395-0.490981253520.3207173519931.60837789841-0.05168401950321.53706578913-0.00348137556025-0.166752612648-0.03417797727290.136665386980.0995251861402-0.04245585171620.204204655936-0.07932536790920.0005625770642690.205013122010.01408549199920.002121613234860.2473016060640.0268110144270.196064689605-11.5441558777-32.69065888929.9934408256
100.6006679057720.420517885237-0.06794136229290.2617910810610.04853848251720.2657280744910.2252287025140.06567995354240.247588530086-0.120408840701-0.419005046677-0.6187617525920.1477019746650.3406993633310.000822523745640.312448613793-0.00661657497608-0.05897830065450.387353200610.04038033108440.334330679693-1.80964721743-24.663583080432.1877316355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 30 )
2X-RAY DIFFRACTION2chain 'A' and (resid 31 through 64 )
3X-RAY DIFFRACTION3chain 'A' and (resid 65 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 164 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 26 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3 through 46 )
7X-RAY DIFFRACTION7chain 'C' and (resid 47 through 64 )
8X-RAY DIFFRACTION8chain 'C' and (resid 65 through 82 )
9X-RAY DIFFRACTION9chain 'C' and (resid 83 through 165 )
10X-RAY DIFFRACTION10chain 'D' and (resid 4 through 26 )

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