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- PDB-6yld: Crystal structure of Trichoplax adhaerens trBcl-2L2 bound to trBak BH3 -

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Basic information

Entry
Database: PDB / ID: 6yld
TitleCrystal structure of Trichoplax adhaerens trBcl-2L2 bound to 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


BH domain binding / porin activity / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of apoptotic process / mitochondrial outer membrane / apoptotic process / membrane
Similarity search - Function
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
Similarity search - Domain/homology
D(-)-TARTARIC ACID / Bcl-2-like protein 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesTrichoplax sp. H2 (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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)42,08510
Polymers41,4494
Non-polymers6366
Water5,837324
1
A: Bcl-2-like protein 1
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0875
Polymers20,7242
Non-polymers3623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-11 kcal/mol
Surface area8730 Å2
MethodPISA
2
C: Bcl-2-like protein 1
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9995
Polymers20,7242
Non-polymers2743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-13 kcal/mol
Surface area8960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.297, 40.859, 56.721
Angle α, β, γ (deg.)97.300, 90.085, 101.088
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Bcl-2-like protein 1


Mass: 17845.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplax sp. H2 (invertebrata) / Gene: TrispH2_005532 / Plasmid: pGEX-6P1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A369S2N9
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 33.6 % / Description: rectangular shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 5.8, 29 % w/v PEG 4000

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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 EIGER2 X 16M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→39.81 Å / Num. obs: 56421 / % possible obs: 95.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Net I/σ(I): 6.7
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.161 / Num. unique obs: 2489 / CC1/2: 0.358 / % possible all: 84

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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: 1.4→30.64 Å / SU ML: 0.205 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.4603
RfactorNum. reflection% reflection
Rfree0.2125 2350 4.17 %
Rwork0.186 --
obs0.1871 56386 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.3 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2830 0 42 324 3196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512977
X-RAY DIFFRACTIONf_angle_d0.87454018
X-RAY DIFFRACTIONf_chiral_restr0.0586429
X-RAY DIFFRACTIONf_plane_restr0.004512
X-RAY DIFFRACTIONf_dihedral_angle_d17.04291079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.35821180.35322730X-RAY DIFFRACTION81.16
1.42-1.460.35191380.34193172X-RAY DIFFRACTION93.69
1.46-1.490.3461360.30313129X-RAY DIFFRACTION93.37
1.49-1.530.28981360.27553118X-RAY DIFFRACTION94.24
1.53-1.570.33021390.25893195X-RAY DIFFRACTION94.64
1.57-1.610.27411380.24193167X-RAY DIFFRACTION94.75
1.61-1.670.25051380.21893174X-RAY DIFFRACTION94.6
1.67-1.730.24091370.20343200X-RAY DIFFRACTION95.51
1.73-1.80.25021330.20673225X-RAY DIFFRACTION95.83
1.8-1.880.24011420.19513185X-RAY DIFFRACTION95.69
1.88-1.980.20521390.17283207X-RAY DIFFRACTION95.82
1.98-2.10.18561420.1653223X-RAY DIFFRACTION96.28
2.1-2.260.17051500.15563280X-RAY DIFFRACTION96.95
2.26-2.490.1911370.15173210X-RAY DIFFRACTION96.76
2.49-2.850.17911460.16373292X-RAY DIFFRACTION97.23
2.85-3.590.18341360.16343226X-RAY DIFFRACTION96.72
3.59-30.640.19231450.16683303X-RAY DIFFRACTION98.26
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)
15.16716394766-0.7325366836-0.252111165551.823750105490.1460235356731.90477895956-0.008740984756250.08766753477870.384114448614-0.0540842916761-0.03323762639720.0717282971947-0.253057400560.1794154357350.0323638726990.162393730967-0.0247781609377-0.02648244748480.1962952526890.04664185040730.1603488385443.0818196627738.767666606824.0332493059
21.36076498151-1.40206612228-1.723119596281.43899178051.775584510282.193883340870.2504611155130.1018808210670.248409182176-0.662330665489-0.10706483105-0.0683262167153-0.4086351983420.0390670252115-0.06062436098690.2794957235190.00764739739882-0.01756390913180.3153251009430.04951946675030.31348902591911.011955098540.701094416320.7018901836
32.41351431563-2.094181782980.7455224774337.34596425023-1.634118309852.15570273119-0.0775912516942-0.07501213383050.2267784055830.01847257777930.0794873485557-0.0528991034206-0.3160612758790.121988453444-0.02587062890540.160186679791-0.0168894378529-0.01049113760740.1511786130410.007846505247550.1574891754136.4543005301639.246677220834.5099325417
42.1387461342-0.01438260965992.970926447452.18583839312.845552416527.915998618670.03648633207460.132115130973-0.11265079644-0.139725174992-0.04428967713490.1379112341790.2739706606750.2748297452560.05198526971980.2016537318470.001528055336470.005035208178860.1295051639140.02346492771980.1782364040786.4069145171319.651344616930.9419048955
50.5284935480660.1969118742870.1572686966970.5202619304160.01460843875671.351860429130.00264774172590.0939231827756-0.01610438414540.0033695408289-0.0270035405874-0.01721044610640.08243068016270.01993786213440.02283675910550.1022270165570.00560880252113-0.005064510805830.1401580230550.00173123452670.10668049047-1.7862712396627.497446010124.590355973
62.788487625330.6728770624050.5248246021831.73317431156-0.05130175511240.8634858623190.0279013224711-0.01175968324480.364235336194-0.00650770944962-0.0103818421383-0.00578553658055-0.479161411775-0.232671204088-0.01303515315160.2426049912470.07005737337940.02472542188030.205380780946-0.0211216800690.168404639538-6.7314027496640.994656616337.3040812324
72.81737533860.3295411405260.3444154242674.050954138751.862641708464.84776838613-0.0129180357096-0.0447720963362-0.1057135327050.1144469741650.04165563652040.03151199990650.139241627840.111849626491-0.02545327557070.115338736906-0.004170992496050.006955422331290.1131332273740.01950670643370.0973602033552-1.3736414732324.491491366339.6864877694
81.5635192947-0.2105136881240.08475954079211.480226123750.0474212667641.083102231220.04380036557670.0194267952675-0.198346882574-0.1492116662450.01786997602320.01553886112610.09482461963250.0342252064267-0.05378367484980.1520202352120.0002279185297620.0006451846390960.15726687806-0.02463593317090.138218345631-17.197862676212.641767327148.1894468269
91.38559738276-0.161438884760.103481310531.620236713960.1641948523551.39689101087-0.0350041488215-0.1579394325540.107204959647-0.1036902832610.06589046036810.0695588713105-0.0506598518857-0.07792611736840.0007778715904720.1367126207240.001414903917860.009232705956060.17045094837-0.006466746097930.164131264957-18.015561305818.166728056660.0358460834
100.5870077519470.170003541888-0.131350535660.506065777481-0.1729888020831.47535653148-0.00248935532867-0.00445627564209-0.0122232069960.0154862307480.01280949733175.77763039289E-50.05418611873640.0829529510855-0.0117068153570.1032546571040.01277065796580.001975678794650.133461758825-0.005464908240650.109609677632-8.6419826155819.979250487254.9825671356
112.021536275920.138534369354-0.1582826517464.02390889006-1.747111858243.409220324110.108572642282-0.1704031877430.09513791937380.217353696011-0.009993832139580.139089756232-0.09365177885420.025339918442-0.06580751324670.1278222737090.01985154292850.01071237569630.219319979013-0.01558979444180.11313510153-10.322399341623.577840063167.4551421877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 38 )
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 58 )
4X-RAY DIFFRACTION4chain 'A' and (resid 59 through 70 )
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 154 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 25 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 38 )
9X-RAY DIFFRACTION9chain 'C' and (resid 39 through 70 )
10X-RAY DIFFRACTION10chain 'C' and (resid 71 through 154 )
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 23 )

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