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- PDB-2voi: Structure of mouse A1 bound to the Bid BH3-domain -

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Basic information

Entry
Database: PDB / ID: 2voi
TitleStructure of mouse A1 bound to the Bid BH3-domain
Components
  • BCL-2-RELATED PROTEIN A1
  • BH3-INTERACTING DOMAIN DEATH AGONIST P13
KeywordsAPOPTOSIS / PROTEIN-PROTEIN COMPLEX / BH3 / BCL-2 / MEMBRANE / PRO-SURVIVAL / MITOCHONDRION / PHOSPHOPROTEIN
Function / homology
Function and homology information


positive regulation of autophagy in response to ER overload / Activation, myristolyation of BID and translocation to mitochondria / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of fibroblast apoptotic process ...positive regulation of autophagy in response to ER overload / Activation, myristolyation of BID and translocation to mitochondria / Activation, translocation and oligomerization of BAX / Activation and oligomerization of BAK protein / Activation of BAD and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mitochondrial outer membrane permeabilization / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of fibroblast apoptotic process / positive regulation of natural killer cell mediated cytotoxicity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / programmed cell death / establishment of protein localization to membrane / regulation of mitochondrial membrane permeability involved in apoptotic process / mitochondrial fusion / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of mitochondrial membrane potential / negative regulation of B cell apoptotic process / : / hepatocyte apoptotic process / positive regulation of release of cytochrome c from mitochondria / mitochondrial ATP synthesis coupled electron transport / apoptotic mitochondrial changes / B cell homeostasis / regulation of G1/S transition of mitotic cell cycle / extrinsic apoptotic signaling pathway / signal transduction in response to DNA damage / positive regulation of intrinsic apoptotic signaling pathway / supramolecular fiber organization / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / mitochondrial membrane / intrinsic apoptotic signaling pathway in response to DNA damage / regulation of cell population proliferation / channel activity / protein-containing complex assembly / regulation of apoptotic process / mitochondrial outer membrane / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / mitochondrion / membrane / cytoplasm / cytosol
Similarity search - Function
BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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 ...BH3-interacting domain death agonist / BH3 interacting domain (BID) / 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
BH3-interacting domain death agonist / Bcl-2-related protein A1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Refinement description / 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: BH3-INTERACTING DOMAIN DEATH AGONIST P13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8993
Polymers21,8642
Non-polymers351
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-18 kcal/mol
Surface area10800 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.737, 80.808, 32.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1150-

CL

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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 BH3-INTERACTING DOMAIN DEATH AGONIST P13 / BH3-INTERACTING DOMAIN DEATH AGONIST / P13 BID


Mass: 3941.365 Da / Num. of mol.: 1 / Fragment: BH3-DOMAIN, RESIDUES 76-109 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: P70444
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.84 Å3/Da / Density % sol: 33 % / Description: NONE
Crystal growDetails: 0.1 M CITRIC ACID, KOH (PH 4.2), 18% PEG 2000, 0.4 M LICL

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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: 2.1→28.54 Å / Num. obs: 9930 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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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: 2.1→26.94 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.326 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 478 4.8 %RANDOM
Rwork0.207 ---
obs0.209 9451 99.8 %-
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: 52.29 Å2
Baniso -1Baniso -2Baniso -3
1-1.07 Å20 Å20 Å2
2--0.91 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 1 25 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221409
X-RAY DIFFRACTIONr_bond_other_d0.0010.021245
X-RAY DIFFRACTIONr_angle_refined_deg1.1611.9191902
X-RAY DIFFRACTIONr_angle_other_deg0.80732888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8215172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.67325.20573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.772155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021584
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02290
X-RAY DIFFRACTIONr_nbd_refined0.2040.2343
X-RAY DIFFRACTIONr_nbd_other0.160.21165
X-RAY DIFFRACTIONr_nbtor_refined0.1850.2695
X-RAY DIFFRACTIONr_nbtor_other0.0850.2770
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1290.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6161.5892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97921375
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3163596
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9324.5527
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 36
Rwork0.268 687
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)
16.16911.64590.93155.3849-0.82776.59430.1641-0.0295-0.13040.53190.0374-0.09020.56580.2615-0.2015-0.16730.0337-0.0336-0.2272-0.0357-0.253422.6193-11.6063-8.9445
235.5986-17.5640.599923.00645.759910.95260.28250.105-2.10081.18310.14480.69312.08790.1821-0.42730.3445-0.1877-0.1393-0.20030.0142-0.039214.6521-22.57-13.8768
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION2B78 - 101

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