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- PDB-2vog: Structure of mouse A1 bound to the Bmf BH3-domain -

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Basic information

Entry
Database: PDB / ID: 2vog
TitleStructure of mouse A1 bound to the Bmf BH3-domain
Components
  • BCL-2-MODIFYING FACTOR
  • BCL-2-RELATED PROTEIN A1
KeywordsAPOPTOSIS / PROTEIN-PROTEIN COMPLEX / BH3 / BCL-2 / PRO-SURVIVAL
Function / homology
Function and homology information


Activation of BMF and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of autophagic cell death / B cell apoptotic process / myosin complex / anoikis / negative regulation of B cell apoptotic process / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of apoptotic signaling pathway ...Activation of BMF and translocation to mitochondria / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of autophagic cell death / B cell apoptotic process / myosin complex / anoikis / negative regulation of B cell apoptotic process / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / negative regulation of apoptotic signaling pathway / negative regulation of autophagy / cellular response to starvation / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to UV / actin cytoskeleton / positive regulation of apoptotic process / negative regulation of apoptotic process / cytoplasm
Similarity search - Function
Bcl-2-modifying factor / Bcl-2-modifying factor, apoptosis / Bcl-2-related protein A1 / Blc2-like / Apoptosis Regulator Bcl-x / 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-modifying factor / Bcl-2-modifying factor, apoptosis / Bcl-2-related protein A1 / Blc2-like / Apoptosis Regulator Bcl-x / 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
Bcl-2-related protein A1 / Bcl-2-modifying factor
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

Downloads & links

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Assembly

Deposited unit
A: BCL-2-RELATED PROTEIN A1
B: BCL-2-MODIFYING FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2694
Polymers21,1982
Non-polymers712
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-19 kcal/mol
Surface area10050 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.654, 68.050, 32.136
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-1151-

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 BCL-2-MODIFYING FACTOR


Mass: 3275.765 Da / Num. of mol.: 1 / Fragment: BH3-DOMAIN, RESIDUES 126-152
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 BMF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91ZE9
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 1.72 Å3/Da / Density % sol: 29 % / Description: NONE
Crystal growDetails: 18% PEG 2000, 0.88 M LICL, 0.1 M CITRIC ACID, KOH (PH 4.35)

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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→23.81 Å / Num. obs: 12089 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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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→23.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.251 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 577 4.8 %RANDOM
Rwork0.191 ---
obs0.193 11512 99.9 %-
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: 26.59 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.9→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 2 49 1394
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221368
X-RAY DIFFRACTIONr_bond_other_d0.0010.021230
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.9221842
X-RAY DIFFRACTIONr_angle_other_deg0.86232852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8315164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81624.9371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53715243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.617156
X-RAY DIFFRACTIONr_chiral_restr0.0890.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02285
X-RAY DIFFRACTIONr_nbd_refined0.2280.2313
X-RAY DIFFRACTIONr_nbd_other0.1610.21181
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2694
X-RAY DIFFRACTIONr_nbtor_other0.080.2740
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0720.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0711.5905
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40221319
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4433597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5584.5523
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
Rfree0.362 30
Rwork0.243 825
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)
12.28720.1288-0.7783.00480.27173.0509-0.01580.06420.0034-0.1223-0.0445-0.01960.0204-0.00890.0603-0.1643-0.0281-0.0139-0.1223-0.0035-0.207245.9637.36423.46
217.5825-19.29132.579530.2732-2.3074.0118-0.1634-0.08910.96050.22390.1691-1.4402-0.43750.4482-0.0056-0.0858-0.10620.0064-0.0333-0.041-0.149255.68617.0728.08
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 149
2X-RAY DIFFRACTION2B4 - 25

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