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- PDB-6odh: BH3 domain swapped dimer of a BAK fragment -

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Basic information

Entry
Database: PDB / ID: 6odh
TitleBH3 domain swapped dimer of a BAK fragment
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / BAK
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 / limb morphogenesis / Release of apoptotic factors from the mitochondria ...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 / limb morphogenesis / Release of apoptotic factors from the mitochondria / 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 IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / positive regulation of proteolysis / vagina development / B cell homeostasis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / blood vessel remodeling / animal organ regeneration / Pyroptosis / 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 / response to gamma radiation / positive regulation of protein-containing complex assembly / 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 / 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 / identical protein binding / metal ion binding / cytosol
Similarity search - Function
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, 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
DI(HYDROXYETHYL)ETHER / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLiu, L.-K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA166741 United States
CitationJournal: To Be Published
Title: A BAK fragment that binds mitochondrial lipids and releases cytochrome c
Authors: Dai, H. / Liu, L.-K. / Kaufmann, S.
History
DepositionMar 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,93915
Polymers58,3436
Non-polymers1,5969
Water34219
1
A: Bcl-2 homologous antagonist/killer
B: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1176
Polymers19,4482
Non-polymers6694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-39 kcal/mol
Surface area8780 Å2
MethodPISA
2
C: Bcl-2 homologous antagonist/killer
D: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7924
Polymers19,4482
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-33 kcal/mol
Surface area8980 Å2
MethodPISA
3
E: Bcl-2 homologous antagonist/killer
F: Bcl-2 homologous antagonist/killer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0315
Polymers19,4482
Non-polymers5833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-22 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.043, 55.039, 55.682
Angle α, β, γ (deg.)117.130, 107.970, 97.550
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 72 or resid 74 through 75...
21(chain B and (resid 72 or resid 74 through 75...
31(chain C and (resid 72 or resid 74 through 75...
41(chain D and (resid 72 or resid 74 through 75...
51(chain E and (resid 72 or resid 74 through 75...
61(chain F and (resid 72 or resid 74 through 75...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYGLYGLY(chain A and (resid 72 or resid 74 through 75...AA722
12VALVALGLYGLY(chain A and (resid 72 or resid 74 through 75...AA74 - 754 - 5
13GLNGLNALAALA(chain A and (resid 72 or resid 74 through 75...AA77 - 797 - 9
14METMETGLYGLY(chain A and (resid 72 or resid 74 through 75...AA71 - 1461 - 76
15METMETGLYGLY(chain A and (resid 72 or resid 74 through 75...AA71 - 1461 - 76
16METMETGLYGLY(chain A and (resid 72 or resid 74 through 75...AA71 - 1461 - 76
17METMETGLYGLY(chain A and (resid 72 or resid 74 through 75...AA71 - 1461 - 76
21GLYGLYGLYGLY(chain B and (resid 72 or resid 74 through 75...BB722
22VALVALGLYGLY(chain B and (resid 72 or resid 74 through 75...BB74 - 754 - 5
23GLNGLNALAALA(chain B and (resid 72 or resid 74 through 75...BB77 - 797 - 9
24METMETGLNGLN(chain B and (resid 72 or resid 74 through 75...BB71 - 1441 - 74
25METMETGLNGLN(chain B and (resid 72 or resid 74 through 75...BB71 - 1441 - 74
26METMETGLNGLN(chain B and (resid 72 or resid 74 through 75...BB71 - 1441 - 74
27METMETGLNGLN(chain B and (resid 72 or resid 74 through 75...BB71 - 1441 - 74
31GLYGLYGLYGLY(chain C and (resid 72 or resid 74 through 75...CC722
32VALVALGLYGLY(chain C and (resid 72 or resid 74 through 75...CC74 - 754 - 5
33GLNGLNALAALA(chain C and (resid 72 or resid 74 through 75...CC77 - 797 - 9
34ILEILEILEILE(chain C and (resid 72 or resid 74 through 75...CC8010
35METMETGLUGLU(chain C and (resid 72 or resid 74 through 75...CC71 - 1481 - 78
36METMETGLUGLU(chain C and (resid 72 or resid 74 through 75...CC71 - 1481 - 78
37METMETGLUGLU(chain C and (resid 72 or resid 74 through 75...CC71 - 1481 - 78
41GLYGLYGLYGLY(chain D and (resid 72 or resid 74 through 75...DD722
42VALVALGLYGLY(chain D and (resid 72 or resid 74 through 75...DD74 - 754 - 5
43GLNGLNASNASN(chain D and (resid 72 or resid 74 through 75...DD77 - 867 - 16
44ARGARGASPASP(chain D and (resid 72 or resid 74 through 75...DD88 - 9018 - 20
45SERSERSERSER(chain D and (resid 72 or resid 74 through 75...DD9121
46METMETHISHIS(chain D and (resid 72 or resid 74 through 75...DD71 - 1451 - 75
47METMETHISHIS(chain D and (resid 72 or resid 74 through 75...DD71 - 1451 - 75
48METMETHISHIS(chain D and (resid 72 or resid 74 through 75...DD71 - 1451 - 75
49METMETHISHIS(chain D and (resid 72 or resid 74 through 75...DD71 - 1451 - 75
51GLYGLYGLYGLY(chain E and (resid 72 or resid 74 through 75...EE722
52VALVALGLYGLY(chain E and (resid 72 or resid 74 through 75...EE74 - 754 - 5
53GLNGLNALAALA(chain E and (resid 72 or resid 74 through 75...EE77 - 797 - 9
54ILEILEILEILE(chain E and (resid 72 or resid 74 through 75...EE8010
55METMETHISHIS(chain E and (resid 72 or resid 74 through 75...EE71 - 1451 - 75
56METMETHISHIS(chain E and (resid 72 or resid 74 through 75...EE71 - 1451 - 75
57METMETHISHIS(chain E and (resid 72 or resid 74 through 75...EE71 - 1451 - 75
61GLYGLYGLYGLY(chain F and (resid 72 or resid 74 through 75...FF722
62VALVALGLYGLY(chain F and (resid 72 or resid 74 through 75...FF74 - 754 - 5
63GLNGLNALAALA(chain F and (resid 72 or resid 74 through 75...FF77 - 797 - 9
64METMETGLNGLN(chain F and (resid 72 or resid 74 through 75...FF71 - 1441 - 74
65METMETGLNGLN(chain F and (resid 72 or resid 74 through 75...FF71 - 1441 - 74
66METMETGLNGLN(chain F and (resid 72 or resid 74 through 75...FF71 - 1441 - 74
67METMETGLNGLN(chain F and (resid 72 or resid 74 through 75...FF71 - 1441 - 74

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Components

#1: Protein
Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 9723.911 Da / Num. of mol.: 6 / Fragment: residues 71-147
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / 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 % sol: 35.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 12% PEG 3350 and 100 mM ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationMonochromator: Double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.95 Å / Num. obs: 18506 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 57.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.02 / Rrim(I) all: 0.038 / Net I/σ(I): 13.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.3-2.383.50.19818250.9610.1240.23497.4
8.91-46.953.60.0263180.9980.0160.03196.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.89 Å40.57 Å
Translation5.89 Å40.57 Å

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Processing

Software
NameVersionClassification
Aimless0.6.2data scaling
PHASER2.7.16phasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4u2v

4u2v


Resolution: 2.3→32.518 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 30.33
RfactorNum. reflection% reflection
Rfree0.2706 1695 4.78 %
Rwork0.2142 --
obs0.217 18506 93.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 216.63 Å2 / Biso mean: 80.3904 Å2 / Biso min: 33.39 Å2
Refinement stepCycle: final / Resolution: 2.3→32.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3616 0 159 19 3794
Biso mean--91.59 73.26 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033850
X-RAY DIFFRACTIONf_angle_d0.6935198
X-RAY DIFFRACTIONf_chiral_restr0.042533
X-RAY DIFFRACTIONf_plane_restr0.004649
X-RAY DIFFRACTIONf_dihedral_angle_d20.6482229
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1445X-RAY DIFFRACTION15.058TORSIONAL
12B1445X-RAY DIFFRACTION15.058TORSIONAL
13C1445X-RAY DIFFRACTION15.058TORSIONAL
14D1445X-RAY DIFFRACTION15.058TORSIONAL
15E1445X-RAY DIFFRACTION15.058TORSIONAL
16F1445X-RAY DIFFRACTION15.058TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.36780.34981580.28662874303294
2.3678-2.44420.33041490.26072818296795
2.4442-2.53160.35141240.26612920304495
2.5316-2.63290.30241440.2522875301995
2.6329-2.75260.37061300.25032869299994
2.7526-2.89770.33761700.25242846301695
2.8977-3.07910.2591290.24692850297995
3.0791-3.31660.28731040.24932877298193
3.3166-3.650.27171400.22552726286691
3.65-4.17720.24681250.18462712283790
4.1772-5.25920.29611500.19762734288491
5.2592-32.52150.22031720.19022679285190
Refinement TLS params.Method: refined / Origin x: -18.4608 Å / Origin y: 0.1186 Å / Origin z: 12.5672 Å
111213212223313233
T0.0876 Å20.0607 Å20.0229 Å2-0.2701 Å20.005 Å2--0.248 Å2
L1.5875 °21.5622 °20.2737 °2-4.8181 °20.8226 °2--3.5761 °2
S0.0367 Å °-0.1188 Å °0.0713 Å °-0.0998 Å °-0.105 Å °0.086 Å °-0.0814 Å °-0.0204 Å °-0.034 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA71 - 146
2X-RAY DIFFRACTION1allB71 - 144
3X-RAY DIFFRACTION1allC71 - 148
4X-RAY DIFFRACTION1allD71 - 145
5X-RAY DIFFRACTION1allE71 - 145
6X-RAY DIFFRACTION1allF71 - 144
7X-RAY DIFFRACTION1allG1 - 20
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allH3
10X-RAY DIFFRACTION1allI1 - 5
11X-RAY DIFFRACTION1allJ1
12X-RAY DIFFRACTION1allJ2

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