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- PDB-5uup: Human Bfl-1 covalently cross-linked to an electrophilic variant o... -

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Basic information

Entry
Database: PDB / ID: 5uup
TitleHuman Bfl-1 covalently cross-linked to an electrophilic variant of a Bfl-1-specific selected peptide
Components
  • Bcl-2-related protein A1
  • Bfl-1-specific selected peptide
KeywordsAPOPTOSIS / Apoptosis Regulatory Proteins / Electrophile / 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: 1.726 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 1.4Nov 6, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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)20,1504
Polymers19,9582
Non-polymers1922
Water2,162120
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-33 kcal/mol
Surface area9100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.395, 43.493, 47.068
Angle α, β, γ (deg.)90.000, 114.780, 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: 2514.777 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.: 120 / 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 Å3/Da / Density % sol: 38.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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: 1.726→100 Å / Num. obs: 15904 / % possible obs: 94.2 % / Redundancy: 5 % / Biso Wilson estimate: 20.46 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.035 / Rrim(I) all: 0.083 / Χ2: 0.969 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.762.60.3030.8770.1850.3570.65251.5
1.76-1.792.80.2960.9120.1720.3450.77568.4
1.79-1.833.30.280.9020.1570.3230.67883.3
1.83-1.863.80.280.9290.1490.3190.72392.6
1.86-1.94.20.2510.9580.1280.2830.72896.1
1.9-1.954.50.230.9750.1140.2570.78899.2
1.95-24.80.2190.9640.1050.2440.92499.3
2-2.054.80.1860.9750.090.2080.86898.1
2.05-2.115.10.1670.9780.0780.1850.98899.2
2.11-2.185.50.1520.9860.0680.1671.01299.6
2.18-2.265.60.1370.9810.0630.1511.016100
2.26-2.355.50.1270.9880.0570.1391.01999.9
2.35-2.455.50.1150.9890.0520.1271.01299.6
2.45-2.585.30.10.9920.0460.110.95499.1
2.58-2.755.90.0890.9920.0390.0980.96899.8
2.75-2.965.80.0790.9950.0350.0870.97999.8
2.96-3.265.40.070.9950.0330.0781.06599.2
3.26-3.735.80.0580.9960.0260.0641.11999.2
3.73-4.75.60.0480.9970.0220.0531.13699.4
4.7-1005.50.0480.9960.0230.0531.13499

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZEQ

4zeq


Resolution: 1.726→39.399 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 22.96
RfactorNum. reflection% reflection
Rfree0.206 1603 10.09 %
Rwork0.1802 --
obs0.1827 15887 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.71 Å2 / Biso mean: 31.5701 Å2 / Biso min: 9.31 Å2
Refinement stepCycle: final / Resolution: 1.726→39.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 10 120 1534
Biso mean--81.07 34.85 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031460
X-RAY DIFFRACTIONf_angle_d0.4841973
X-RAY DIFFRACTIONf_chiral_restr0.041214
X-RAY DIFFRACTIONf_plane_restr0.003258
X-RAY DIFFRACTIONf_dihedral_angle_d9.867879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7263-1.7820.336880.315777586357
1.782-1.84570.35321390.27351153129285
1.8457-1.91960.26711470.231320146796
1.9196-2.0070.2451490.20791365151499
2.007-2.11280.25771490.1961372152199
2.1128-2.24520.19531600.179513501510100
2.2452-2.41850.21091550.1713871542100
2.4185-2.66180.19451470.17141375152299
2.6618-3.04690.2021570.174113851542100
3.0469-3.83820.18511560.16331385154199
3.8382-39.4090.17321560.16661417157399

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