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- PDB-4u2u: Bak domain swapped dimer induced by BidBH3 with CHAPS -

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Basic information

Entry
Database: PDB / ID: 4u2u
TitleBak domain swapped dimer induced by BidBH3 with CHAPS
ComponentsBcl-2 homologous antagonist/killer
KeywordsAPOPTOSIS / Bak / Bcl-2
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 / myeloid cell homeostasis / Bcl-2 family protein complex / 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 / 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 / apoptotic signaling pathway / establishment of localization in cell / 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 / 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
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsBrouwer, J.M. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1059331 Australia
National Health and Medical Research Council (NHMRC, Australia)1023055 Australia
National Health and Medical Research Council (NHMRC, Australia)1016701 Australia
CitationJournal: Mol.Cell / Year: 2014
Title: Bak Core and Latch Domains Separate during Activation, and Freed Core Domains Form Symmetric Homodimers.
Authors: Brouwer, J.M. / Westphal, D. / Dewson, G. / Robin, A.Y. / Uren, R.T. / Bartolo, R. / Thompson, G.V. / Colman, P.M. / Kluck, R.M. / Czabotar, P.E.
History
DepositionJul 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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


Theoretical massNumber of molelcules
Total (without water)37,9612
Polymers37,9612
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-77 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.646, 39.482, 88.147
Angle α, β, γ (deg.)90.000, 117.710, 90.000
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: 18980.270 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 26.7% PEG 3350, 0.05 M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 25, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953726 Å / Relative weight: 1
ReflectionResolution: 2.9→48.98 Å / Num. obs: 7712 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 61 Å2 / Rmerge F obs: 0.976 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.267 / Χ2: 0.876 / Net I/av σ(I): 6.37 / Net I/σ(I): 6.33 / Num. measured all: 28181
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.9-3.073.70.3991.0831.314369124911931.26995.5
3.07-3.280.6270.7122.084385118211750.83399.4
3.28-3.550.8520.3893.584009107810730.45699.5
3.55-3.880.920.2784.93368510089980.32699
3.88-4.340.960.1787.6432939058990.20999.3
4.34-50.9790.12310.0729368178110.14599.3
5-6.110.970.1657.7924936896870.19499.7
6.11-8.570.9870.10411.8118995505430.12398.7
8.570.9980.03427.7111123393330.04198.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.14data extraction
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IMS

2ims


Resolution: 2.9→48.98 Å / Cor.coef. Fo:Fc: 0.8962 / Cor.coef. Fo:Fc free: 0.8511 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.415
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 744 9.76 %RANDOM
Rwork0.2091 ---
obs0.2142 7624 98.71 %-
Displacement parametersBiso max: 158.38 Å2 / Biso mean: 60.31 Å2 / Biso min: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.0297 Å20 Å2-4.3286 Å2
2--1.5689 Å20 Å2
3---2.4608 Å2
Refine analyzeLuzzati coordinate error obs: 0.438 Å
Refinement stepCycle: final / Resolution: 2.9→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 0 20 2357
Biso mean---33.02 -
Num. residues----287
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d822SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes65HARMONIC2
X-RAY DIFFRACTIONt_gen_planes353HARMONIC5
X-RAY DIFFRACTIONt_it2392HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2745SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2392HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3232HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion1.85
X-RAY DIFFRACTIONt_other_torsion19.81
LS refinement shellResolution: 2.9→3.24 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2749 203 9.67 %
Rwork0.2359 1896 -
all0.2397 2099 -
obs--98.71 %
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)
12.02820.8889-1.23920.5437-0.01681.9901-0.1405-0.35670.05160.18310.05770.0137-0.11520.08120.0828-0.21370.054-0.054-0.18420.00850.2751-24.9817-8.747210.6266
22.90221.0629-1.61510.7558-0.28032.66010.1084-0.6921-0.09460.2681-0.2213-0.19480.1820.130.113-0.17460.0324-0.0587-0.0551-0.01690.0293-33.3415-19.231121.2862
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A21 - 182
2X-RAY DIFFRACTION2{ B|* }B22 - 182

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