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- PDB-6vo4: Crystal Structure Analysis of BFL1 -

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Basic information

Entry
Database: PDB / ID: 6vo4
TitleCrystal Structure Analysis of BFL1
ComponentsBcl-2-related protein A1
KeywordsAPOPTOSIS / BFL-1/A1 / BCL-2 family / disulfide tethering / small molecule / inhibitor
Function / homology
Function and homology information


channel activity / 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 / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of apoptotic process ...channel activity / 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 / mitochondrial outer membrane / positive regulation of apoptotic process / protein heterodimerization activity / negative regulation of apoptotic process / protein homodimerization activity / cytosol / cytoplasm
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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 ...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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cell Chem Biol / Year: 2020
Title: Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering.
Authors: Harvey, E.P. / Hauseman, Z.J. / Cohen, D.T. / Rettenmaier, T.J. / Lee, S. / Huhn, A.J. / Wales, T.E. / Seo, H.S. / Luccarelli, J. / Newman, C.E. / Guerra, R.M. / Bird, G.H. / Dhe-Paganon, S. ...Authors: Harvey, E.P. / Hauseman, Z.J. / Cohen, D.T. / Rettenmaier, T.J. / Lee, S. / Huhn, A.J. / Wales, T.E. / Seo, H.S. / Luccarelli, J. / Newman, C.E. / Guerra, R.M. / Bird, G.H. / Dhe-Paganon, S. / Engen, J.R. / Wells, J.A. / Walensky, L.D.
History
DepositionJan 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 11, 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


Theoretical massNumber of molelcules
Total (without water)18,5961
Polymers18,5961
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.550, 43.240, 43.490
Angle α, β, γ (deg.)90.000, 104.900, 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: 18596.062 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 1.93 Å3/Da / Density % sol: 36.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.5M Sodium formate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.74→38.22 Å / Num. obs: 13579 / % possible obs: 92.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 36.743 Å2 / Rpim(I) all: 0.035 / Rrim(I) all: 0.063 / Net I/σ(I): 11.2 / Num. measured all: 43051
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.74-1.773.40.721906531.0681.9992.9
4.72-38.233.130.720906680.0240.04287.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
xia2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WHH

5whh


Resolution: 1.74→38.22 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.27
RfactorNum. reflection% reflection
Rfree0.2831 686 5.07 %
Rwork0.2386 --
obs0.2409 13520 91.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.55 Å2 / Biso mean: 60.0618 Å2 / Biso min: 30.87 Å2
Refinement stepCycle: final / Resolution: 1.74→38.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1069 0 0 20 1089
Biso mean---58.45 -
Num. residues----138
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.74-1.870.50861330.42672521265491
1.87-2.060.33241160.31262636275295
2.06-2.360.31821500.25082627277795
2.36-2.970.32561450.27822539268492
2.98-38.220.24531420.20442511265388
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)
15.0192-3.43121.7095.2076-1.08567.6480.09160.13920.55920.27810.1956-0.9802-1.47610.5374-0.38160.5944-0.07810.01080.2756-0.04450.4565.769512.5565-11.5575
24.06651.19833.48625.46661.12856.7246-0.14310.7389-0.7175-0.47340.44060.27780.99050.669-0.19490.7358-0.11340.02230.30190.02230.37620.34534.1026-19.7762
37.32494.7221.28723.51211.9292.7962-0.69581.7084-0.404-1.6171.3354-0.6525-1.0595-2.407-0.0291.03-0.05690.11480.94830.13810.6667-12.768719.1734-24.3573
43.5085-1.0517-1.2247.7029-4.25365.35220.14320.22690.40850.35930.64311.1054-0.5892-1.5242-0.62880.51110.08170.040.5440.05810.3895-8.396312.1952-14.9209
53.0964-0.47830.00351.6511.41394.53550.3508-0.02990.08540.1988-0.50960.4795-0.509-0.28470.09920.57180.06290.1460.3255-0.00270.3433-4.54279.9147-4.4658
68.506-3.7508-4.1868.54385.35553.84410.3879-0.06490.22580.65320.1131-0.4930.39610.2875-0.36090.8335-0.00060.00290.36920.00390.36374.2185-3.2404-7.6571
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 31 )A4 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 51 )A32 - 51
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 63 )A52 - 63
4X-RAY DIFFRACTION4chain 'A' and (resid 64 through 114 )A64 - 114
5X-RAY DIFFRACTION5chain 'A' and (resid 115 through 137 )A115 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 150 )A138 - 150

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