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- PDB-5uuk: Human Bfl-1 in complex with a Bfl-1-specific selected peptide -

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Basic information

Entry
Database: PDB / ID: 5uuk
TitleHuman Bfl-1 in complex with a Bfl-1-specific selected peptide
Components
  • Bcl-2-related protein A1
  • Bfl-1-specific selected peptide
KeywordsAPOPTOSIS / Apoptosis Regulatory Proteins / Peptide Library / Protein Binding / Protein Structure / Proto-Oncogene / Specificity / BCL2A1 / BCL2 related protein A1 / Peptide Inhibitor
Function / homology
Function and homology information


Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process ...Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / release of cytochrome c from mitochondria / intrinsic apoptotic signaling pathway in response to DNA damage / channel activity / mitochondrial outer membrane / positive regulation of apoptotic process / negative regulation of apoptotic process / cytoplasm / cytosol
Similarity search - Function
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-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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Bfl-1-specific selected peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2874
Polymers20,0952
Non-polymers1922
Water2,594144
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-35 kcal/mol
Surface area9230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.249, 43.326, 45.744
Angle α, β, γ (deg.)90.000, 110.900, 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 Bfl-1-specific selected peptide


Mass: 2651.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
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: 2.01 Å3/Da / Density % sol: 38.74 %
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: 1.199→100 Å / Num. obs: 47346 / % possible obs: 95.4 % / Redundancy: 10.2 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.022 / Rrim(I) all: 0.075 / Χ2: 1.785 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.2-1.225.50.4830.8910.1960.5240.95488.5
1.22-1.2470.4940.9070.1790.5271.00390.8
1.24-1.278.20.4950.9360.1640.5230.9991.7
1.27-1.298.70.4790.9510.1550.5041.0293.2
1.29-1.329.20.4560.9570.1440.4790.99293.6
1.32-1.359.50.4360.9660.1390.4580.95594.1
1.35-1.399.90.380.970.120.3991.01195
1.39-1.4210.30.3330.9750.1040.3491.0795.1
1.42-1.4611.10.2920.9830.0870.3051.17795
1.46-1.5111.20.2350.9870.070.2451.3195.7
1.51-1.57110.1980.9890.060.2071.4795.8
1.57-1.63110.1680.990.0520.1761.55996.4
1.63-1.711.40.1480.9930.0450.1541.60896.6
1.7-1.7911.20.1280.9950.0390.1341.84696.7
1.79-1.911.70.1170.9950.0350.1222.10497.6
1.9-2.0511.30.0990.9960.030.1042.50397.5
2.05-2.2611.70.0820.9970.0250.0862.82498.3
2.26-2.5911.10.0710.9980.0220.0752.88298.2
2.59-3.2611.30.0630.9980.0190.0663.05499
3.26-10010.60.0590.9970.0190.0623.29198.6

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Processing

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

4zeq


Resolution: 1.199→42.735 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 17.44
RfactorNum. reflection% reflection
Rfree0.1629 1994 4.21 %
Rwork0.1435 --
obs0.1443 47318 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 148.81 Å2 / Biso mean: 28.7707 Å2 / Biso min: 13.05 Å2
Refinement stepCycle: final / Resolution: 1.199→42.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 10 144 1558
Biso mean--53.26 39.4 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081492
X-RAY DIFFRACTIONf_angle_d0.9022026
X-RAY DIFFRACTIONf_chiral_restr0.075216
X-RAY DIFFRACTIONf_plane_restr0.006265
X-RAY DIFFRACTIONf_dihedral_angle_d13.797563
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 (%)
1.1988-1.22880.22941270.20562937306487
1.2288-1.2620.20361390.17683088322792
1.262-1.29920.17841440.16093132327693
1.2992-1.34110.17321430.15483196333994
1.3411-1.3890.20631420.14143200334295
1.389-1.44470.14541420.13893213335595
1.4447-1.51040.15151400.12163222336296
1.5104-1.59010.16071400.11383262340296
1.5901-1.68970.14921460.12223280342697
1.6897-1.82010.15591440.12813299344397
1.8201-2.00330.17951470.13433315346298
2.0033-2.29320.16961380.12913368350698
2.2932-2.88910.14951470.14483366351399
2.8891-42.76230.16281550.1563446360199

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