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- PDB-2voh: Structure of mouse A1 bound to the Bak BH3-domain -

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Basic information

Entry
Database: PDB / ID: 2voh
TitleStructure of mouse A1 bound to the Bak BH3-domain
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
  • BCL-2-RELATED PROTEIN A1
KeywordsAPOPTOSIS / BH3 / BCL-2 / MEMBRANE / PRO-SURVIVAL / TRANSMEMBRANE / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / leukocyte homeostasis / Pyroptosis / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / establishment or maintenance of transmembrane electrochemical gradient / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / myeloid cell homeostasis / negative regulation of B cell apoptotic process / porin activity / thymocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / pore complex / positive regulation of release of cytochrome c from mitochondria / vagina development / B cell homeostasis / positive regulation of calcium ion transport into cytosol / positive regulation of proteolysis / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / epithelial cell proliferation / response to gamma radiation / regulation of mitochondrial membrane potential / response to hydrogen peroxide / positive regulation of protein-containing complex assembly / establishment of localization in cell / cellular response to mechanical stimulus / mitochondrial membrane / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / response to ethanol / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process / response to xenobiotic stimulus / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of apoptotic process / protein-containing complex binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / metal ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Bcl-2-related protein A1 / 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-2 family ...Bcl-2-related protein A1 / 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-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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Bcl-2 homologous antagonist/killer / Bcl-2-related protein A1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmits, C. / Czabotar, P.E. / Hinds, M.G. / Day, C.L.
CitationJournal: Structure / Year: 2008
Title: Structural Plasticity Underpins Promiscuous Binding of the Prosurvival Protein A1.
Authors: Smits, C. / Czabotar, P.E. / Hinds, M.G. / Day, C.L.
History
DepositionFeb 17, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2-RELATED PROTEIN A1
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1284
Polymers20,8402
Non-polymers2882
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-16 kcal/mol
Surface area11230 Å2
MethodPQS
Unit cell
Length a, b, c (Å)44.239, 33.255, 58.508
Angle α, β, γ (deg.)90.00, 104.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BCL-2-RELATED PROTEIN A1 / PROTEIN BFL-1 / HEMOPOIETIC-SPECIFIC EARLY RESPONSE PROTEIN / A1-A


Mass: 17922.418 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-152 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX 6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PSJS 1240 / References: UniProt: Q07440
#2: Protein/peptide BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK


Mass: 2917.218 Da / Num. of mol.: 1 / Fragment: BH3-DOMAIN, RESIDUES 64-89
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HOMOSERINE LACTONE DUE TO CNBR CLEAVAGE.
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET31B BAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O08734
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 104 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS 113 TO SER

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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 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CITRATE (PH 5.6), 0.3 M (NH4)2SO4, 0.6 M LI2SO4

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30.61 Å / Num. obs: 12891 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VOF

2vof


Resolution: 1.9→30.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.387 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 632 4.9 %RANDOM
Rwork0.182 ---
obs0.185 12258 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å21.07 Å2
2--0.22 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1432 0 18 122 1572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221486
X-RAY DIFFRACTIONr_bond_other_d0.0010.021334
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9482006
X-RAY DIFFRACTIONr_angle_other_deg0.80133103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1995179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56424.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91215259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.632158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02306
X-RAY DIFFRACTIONr_nbd_refined0.210.2363
X-RAY DIFFRACTIONr_nbd_other0.1610.21321
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2741
X-RAY DIFFRACTIONr_nbtor_other0.0810.2814
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.294
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2010.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7251.5964
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01421426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7793655
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5574.5579
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.363 47
Rwork0.256 871
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)
12.25090.00430.37881.38160.42262.41860.0191-0.0841-0.18020.011-0.05690.05120.2082-0.06970.0378-0.1218-0.00380.0084-0.14780.0019-0.1329-3.20784.096117.2521
25.86364.2074.14028.99255.8567.322-0.09020.3201-0.0502-0.38040.2545-0.4195-0.13770.3363-0.1643-0.1050.01360.0329-0.1320.0327-0.15062.403411.83295.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 150
2X-RAY DIFFRACTION2B64 - 87

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