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- PDB-5uul: Human Bfl-1 in complex with PUMA BH3 -

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Basic information

Entry
Database: PDB / ID: 5uul
TitleHuman Bfl-1 in complex with PUMA BH3
Components
  • Bcl-2-binding component 3
  • Bcl-2-related protein A1
KeywordsAPOPTOSIS / Apoptosis Regulatory Proteins / Protein Binding / Protein Structure / Proto-Oncogene / BCL2A1 / BCL2 related protein A1
Function / homology
Function and homology information


positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / positive regulation of establishment of protein localization to mitochondrion / negative regulation of growth / positive regulation of cysteine-type endopeptidase activity / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Regulation of MITF-M-dependent genes involved in apoptosis / fibroblast apoptotic process / positive regulation of thymocyte apoptotic process ...positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / positive regulation of establishment of protein localization to mitochondrion / negative regulation of growth / positive regulation of cysteine-type endopeptidase activity / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / Regulation of MITF-M-dependent genes involved in apoptosis / fibroblast apoptotic process / positive regulation of thymocyte apoptotic process / mitochondrial fusion / FOXO-mediated transcription of cell death genes / BH domain binding / Activation of PUMA and translocation to mitochondria / execution phase of apoptosis / positive regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / 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 / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / apoptotic signaling pathway / determination of adult lifespan / cellular response to ionizing radiation / positive regulation of protein-containing complex assembly / : / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / channel activity / cellular response to hypoxia / mitochondrial outer membrane / DNA damage response / negative regulation of apoptotic process / mitochondrion / cytosol / 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 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-related protein A1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsJenson, J.M. / Grant, R.A. / Keating, A.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM110048 United States
CitationJournal: Elife / Year: 2017
Title: Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1.
Authors: Jenson, J.M. / Ryan, J.A. / Grant, R.A. / Letai, A. / Keating, A.E.
History
DepositionFeb 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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-binding component 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3583
Polymers20,2622
Non-polymers961
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-32 kcal/mol
Surface area9330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.213, 43.428, 47.384
Angle α, β, γ (deg.)90.000, 114.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bcl-2-related protein A1 / Bcl-2-like protein 5 / Bcl2-L-5 / Hemopoietic-specific early response protein / Protein BFL-1 / Protein GRS


Mass: 17442.889 Da / Num. of mol.: 1 / Fragment: UNP residues 1-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2A1, BCL2L5, BFL1, GRS, HBPA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16548
#2: Protein/peptide Bcl-2-binding component 3 / JFY-1 / p53 up-regulated modulator of apoptosis


Mass: 2819.144 Da / Num. of mol.: 1 / Fragment: UNP residues 132-154 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9BXH1
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 147 / 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 Å3/Da / Density % sol: 38.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M ammonium sulfate, 0.1 M MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 35909 / % possible obs: 97.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 13.07 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.066 / Χ2: 0.86 / Net I/σ(I): 8.6 / Num. measured all: 208187
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.3530.280.9210.1660.3280.60276.1
1.35-1.383.30.2720.9260.1530.3150.62686.8
1.38-1.44.20.2640.9510.1340.2980.61897.2
1.4-1.435.10.2450.9650.1140.2710.67399.1
1.43-1.465.40.2220.9770.1010.2440.68399.8
1.46-1.55.60.1950.9790.0880.2140.76299.7
1.5-1.545.60.1680.9820.0760.1850.75299.8
1.54-1.585.40.1450.9850.0670.1610.76899.8
1.58-1.625.80.1350.9890.0610.1490.76399.7
1.62-1.686.20.1310.9910.0560.1430.79999.9
1.68-1.746.20.1250.9930.0530.1370.81299.8
1.74-1.816.20.1230.9930.0530.1340.76999.2
1.81-1.895.80.1190.9910.0530.1310.81299.2
1.89-1.996.70.1030.9940.0430.1120.85599.7
1.99-2.116.80.090.9960.0360.0970.91499.5
2.11-2.276.70.0720.9970.0290.0780.91599.3
2.27-2.56.40.060.9970.0260.0660.88999.5
2.5-2.877.10.050.9980.020.0540.85299.7
2.87-3.616.50.0430.9970.0190.0471.03598.8
3.61-506.80.0480.9960.020.0511.61999.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZEQ

4zeq


Resolution: 1.33→43.154 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 15.51
RfactorNum. reflection% reflection
Rfree0.1552 2013 5.61 %
Rwork0.1325 --
obs0.1338 35887 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.72 Å2 / Biso mean: 22.825 Å2 / Biso min: 7.73 Å2
Refinement stepCycle: final / Resolution: 1.33→43.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1427 0 5 147 1579
Biso mean--78.84 36.46 -
Num. residues----177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061544
X-RAY DIFFRACTIONf_angle_d0.7782102
X-RAY DIFFRACTIONf_chiral_restr0.07224
X-RAY DIFFRACTIONf_plane_restr0.005277
X-RAY DIFFRACTIONf_dihedral_angle_d12.08609
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3301-1.36340.23851070.16921872197975
1.3634-1.40020.17581350.14392317245294
1.4002-1.44140.1891540.11982418257299
1.4414-1.4880.16071360.112324872623100
1.488-1.54110.15581480.109824572605100
1.5411-1.60280.15891480.098124762624100
1.6028-1.67580.13851460.099724552601100
1.6758-1.76410.14971540.10524682622100
1.7641-1.87470.17251400.11062466260699
1.8747-2.01940.14151460.11252458260499
2.0194-2.22260.13151480.11712474262299
2.2226-2.54420.13931470.122525142661100
2.5442-3.20530.14171500.15242472262299
3.2053-43.17660.17251540.15912540269499

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