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- PDB-3qbr: BakBH3 in complex with sjA -

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Basic information

Entry
Database: PDB / ID: 3qbr
TitleBakBH3 in complex with sjA
Components
  • Bcl-2 homologous antagonist/killer
  • SJCHGC06286 protein
KeywordsAPOPTOSIS / helical bundle / Bcl-2-like fold
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / Release of apoptotic factors from the mitochondria / limb morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / response to UV-C / mitochondrial fusion / fibroblast apoptotic process / Bcl-2 family protein complex / myeloid cell homeostasis / positive regulation of calcium ion transport into cytosol / porin activity / thymocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / animal organ regeneration / negative regulation of peptidyl-serine phosphorylation / extrinsic apoptotic signaling pathway in absence of ligand / heat shock protein binding / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / epithelial cell proliferation / establishment of localization in cell / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / response to gamma radiation / response to hydrogen peroxide / response to organic cyclic compound / cellular response to mechanical stimulus / cellular response to UV / intrinsic apoptotic signaling pathway in response to DNA damage / protein-folding chaperone binding / regulation of apoptotic process / response to ethanol / mitochondrial outer membrane / transmembrane transporter binding / regulation of cell cycle / response to xenobiotic stimulus / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / membrane / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family ...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 (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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2 homologous antagonist/killer / SJCHGC06286 protein
Similarity search - Component
Biological speciesSchistosoma japonicum (invertebrata)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.601 Å
AuthorsLee, E.F. / Clarke, O.B. / Fairlie, W.D. / Colman, P.M. / Evangelista, M. / Feng, Z. / Speed, T.P. / Tchoubrieva, E. / Strasser, A. / Kalinna, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Discovery and molecular characterization of a Bcl-2-regulated cell death pathway in schistosomes.
Authors: Lee, E.F. / Clarke, O.B. / Evangelista, M. / Feng, Z. / Speed, T.P. / Tchoubrieva, E.B. / Strasser, A. / Kalinna, B.H. / Colman, P.M. / Fairlie, W.D.
History
DepositionJan 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SJCHGC06286 protein
B: Bcl-2 homologous antagonist/killer
X: SJCHGC06286 protein
Y: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8405
Polymers48,6334
Non-polymers2071
Water2,630146
1
A: SJCHGC06286 protein
B: Bcl-2 homologous antagonist/killer


Theoretical massNumber of molelcules
Total (without water)24,3162
Polymers24,3162
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-13 kcal/mol
Surface area9340 Å2
MethodPISA
2
X: SJCHGC06286 protein
Y: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5243
Polymers24,3162
Non-polymers2071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-16 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.625, 148.625, 148.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein SJCHGC06286 protein / sjA


Mass: 20475.078 Da / Num. of mol.: 2 / Fragment: C-terminal truncation (RESIDUES 21-189)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Plasmid: pDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5BWX6
#2: Protein/peptide Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 3841.312 Da / Num. of mol.: 2 / Fragment: BH3 (UNP RESIDUES 63-96) / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16611
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES / CHES (buffer)


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1M tri-sodium citrate, 0.1M CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.991874, 1.009234
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9918741
21.0092341
ReflectionResolution: 2.6→50 Å / Num. all: 16915 / Num. obs: 16915 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 33.4
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.946 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameClassification
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.601→29.148 Å / SU ML: 2.36 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2339 1639 10.05 %random
Rwork0.1713 ---
all0.1777 16915 --
obs0.1777 16303 96.38 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.284 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.601→29.148 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2960 0 13 146 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093015
X-RAY DIFFRACTIONf_angle_d1.1274084
X-RAY DIFFRACTIONf_dihedral_angle_d17.0481073
X-RAY DIFFRACTIONf_chiral_restr0.072468
X-RAY DIFFRACTIONf_plane_restr0.004519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6015-2.6780.30721220.2161095109588
2.678-2.76430.27421250.2026117393
2.7643-2.8630.29371280.2088117193
2.863-2.97760.28431340.199117895
2.9776-3.11290.27881320.2053120595
3.1129-3.27690.28911380.2122197
3.2769-3.48180.27241410.1816124598
3.4818-3.75020.23581410.1703124399
3.7502-4.12660.19771400.1618126699
4.1266-4.72160.20691420.13631253100
4.7216-5.94040.2241450.15791299100
5.9404-29.14960.19731510.15671315100
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)
11.3310.5020.94332.1498-0.01592.87930.05350.04150.0054-0.1613-0.0799-0.0474-0.02330.253600.2610.00720.07150.42870.03320.259552.214710.680954.3188
20.1444-0.12320.17450.0573-0.00620.2877-0.12440.4225-0.0972-0.6020.1516-0.0010.23120.45500.63530.13340.16380.87890.09180.436358.09874.535441.3171
30.8826-0.7737-0.21822.7314-0.04051.74460.09010.1564-0.1166-0.3978-0.1939-0.09190.1378-0.006700.38390.02620.03010.363-0.10580.455715.130217.223950.0572
40.1818-0.1513-0.12270.1310.34040.3080.3618-0.02570.2243-0.03030.13630.93750.1542-0.1205-00.4655-0.04190.04660.4896-0.12630.58571.787420.152957.4195
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN X
4X-RAY DIFFRACTION4CHAIN Y

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