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- PDB-2vof: Structure of mouse A1 bound to the Puma BH3-domain -

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Basic information

Entry
Database: PDB / ID: 2vof
TitleStructure of mouse A1 bound to the Puma BH3-domain
Components
  • BCL-2-BINDING COMPONENT 3
  • BCL-2-RELATED PROTEIN A1
KeywordsAPOPTOSIS / BH3 / BCL-2 / PRO-SURVIVAL / MITOCHONDRION / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


positive regulation of lymphocyte apoptotic process / lymphocyte apoptotic process / positive regulation of establishment of protein localization to mitochondrion / positive regulation of fibroblast apoptotic process / T cell apoptotic process / B cell apoptotic process / positive regulation of T cell apoptotic process / mitochondrial envelope / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process ...positive regulation of lymphocyte apoptotic process / lymphocyte apoptotic process / positive regulation of establishment of protein localization to mitochondrion / positive regulation of fibroblast apoptotic process / T cell apoptotic process / B cell apoptotic process / positive regulation of T cell apoptotic process / mitochondrial envelope / positive regulation of thymocyte apoptotic process / fibroblast apoptotic process / negative regulation of B cell apoptotic process / execution phase of apoptosis / positive regulation of release of cytochrome c from mitochondria / B cell homeostasis / intrinsic apoptotic signaling pathway by p53 class mediator / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / cellular response to ionizing radiation / determination of adult lifespan / positive regulation of protein-containing complex assembly / apoptotic signaling pathway / negative regulation of cell growth / positive regulation of neuron apoptotic process / cellular response to hypoxia / DNA damage response / negative regulation of apoptotic process / mitochondrion / cytoplasm
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of 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-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of 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-binding component 3
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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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-BINDING COMPONENT 3
C: BCL-2-RELATED PROTEIN A1
D: BCL-2-BINDING COMPONENT 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6786
Polymers42,6074
Non-polymers712
Water3,171176
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-39 kcal/mol
Surface area19430 Å2
MethodPQS
2
A: BCL-2-RELATED PROTEIN A1
B: BCL-2-BINDING COMPONENT 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3393
Polymers21,3032
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BCL-2-RELATED PROTEIN A1
D: BCL-2-BINDING COMPONENT 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3393
Polymers21,3032
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.640, 60.683, 59.986
Angle α, β, γ (deg.)90.00, 109.53, 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: 18110.000 Da / Num. of mol.: 2 / 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-BINDING COMPONENT 3 / P53 UP-REGULATED MODULATOR OF APOPTOSIS


Mass: 3193.467 Da / Num. of mol.: 2 / Fragment: BH3-DOMAIN, RESIDUES 130-155 / Mutation: YES
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 PUMA TR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99ML1
#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.: 176 / 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 ...ENGINEERED RESIDUE IN CHAIN A, PRO 104 TO LYS ENGINEERED RESIDUE IN CHAIN A, CYS 113 TO SER ENGINEERED RESIDUE IN CHAIN B, MET 144 TO ILE ENGINEERED RESIDUE IN CHAIN C, PRO 104 TO LYS ENGINEERED RESIDUE IN CHAIN C, CYS 113 TO SER ENGINEERED RESIDUE IN CHAIN D, MET 144 TO ILE
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE
Crystal growDetails: 0.1 M CITRIC ACID.KOH (PH 4.35), 15% PEG 20,000, 0.4 M LICL, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9782
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.8→56.52 Å / Num. obs: 29292 / % possible obs: 94 % / Observed criterion σ(I): 1 / Redundancy: 6.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 28.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 9.6 / % possible all: 93.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
MLPHAREphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.8→43.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.139 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1460 5 %RANDOM
Rwork0.183 ---
obs0.184 27830 93.7 %-
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: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-1.78 Å2
2--0.11 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 2 176 2893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222778
X-RAY DIFFRACTIONr_bond_other_d0.0010.022486
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.9243745
X-RAY DIFFRACTIONr_angle_other_deg0.80935747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4435335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12724.552145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06515473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6551515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023109
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.220.2651
X-RAY DIFFRACTIONr_nbd_other0.1640.22500
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21410
X-RAY DIFFRACTIONr_nbtor_other0.0810.21530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2124
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1790.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9041.51745
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20822669
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00131217
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8434.51075
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 111
Rwork0.181 2046
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)
12.1848-0.21010.24582.1557-0.2783.8516-0.0866-0.07290.11360.05430.03110.0959-0.0986-0.22280.0555-0.1534-0.01290.0385-0.225-0.009-0.1331-20.253-0.789-10.556
27.94288.6987-1.349915.1699-4.44995.0343-0.09620.1112-0.02080.02970.10.04190.1026-0.1209-0.0038-0.1624-0.02410.0137-0.20650.0043-0.212-25.708-4.546-22.964
30.95990.12410.34352.0959-0.23241.98020.0029-0.0129-0.0417-0.0725-0.06220.16910.0105-0.15270.0594-0.16710.03760.0364-0.2105-0.0147-0.1053-33.115-0.285-44.673
410.34245.9486-6.084812.3885-6.380911.45240.1427-0.24290.06110.2046-0.3348-0.682-0.18210.40960.1921-0.16640.0186-0.0209-0.26280.0126-0.123-23.532-3.75-34.714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 150
2X-RAY DIFFRACTION2B131 - 153
3X-RAY DIFFRACTION3C-3 - 149
4X-RAY DIFFRACTION4D132 - 153

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