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- PDB-6e3i: Human Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F4 -

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Basic information

Entry
Database: PDB / ID: 6e3i
TitleHuman Bfl-1 in complex with the Bfl-1-specific designed peptide srt.F4
Components
  • Bcl-2-related protein A1
  • peptide srt.F4
KeywordsAPOPTOSIS / anti-apoptotic Bcl-2 / inhibitor / design
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.481 Å
AuthorsJenson, J.M. / 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: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Peptide design by optimization on a data-parameterized protein interaction landscape.
Authors: Jenson, J.M. / Xue, V. / Stretz, L. / Mandal, T. / Reich, L.L. / Keating, A.E.
History
DepositionJul 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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: peptide srt.F4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8783
Polymers19,7822
Non-polymers961
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-25 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.220, 42.947, 46.762
Angle α, β, γ (deg.)90.000, 114.730, 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
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 peptide srt.F4


Mass: 2338.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.99 Å3/Da / Density % sol: 38.28 %
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: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 23986 / % possible obs: 92.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.88 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.03 / Rrim(I) all: 0.069 / Χ2: 1.249 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.512.70.3447370.8560.2180.4110.69157.4
1.51-1.533.20.3159580.920.1790.3650.71574.5
1.53-1.563.60.30710270.8980.1710.3540.68980.5
1.56-1.593.90.27411400.9480.1460.3130.73288.6
1.59-1.6340.26711900.9370.1420.3040.79792
1.63-1.674.20.23712270.9430.1250.270.80494.2
1.67-1.714.20.21912320.960.1150.2490.85896
1.71-1.754.50.20212380.9580.1030.2280.95297.3
1.75-1.814.80.18312890.9690.090.2050.93598.2
1.81-1.864.90.16212760.9710.080.1821.08598.8
1.86-1.934.80.14412550.980.0720.1621.16598.1
1.93-2.014.70.12212690.9820.0610.1371.31898.6
2.01-2.14.50.10812480.9850.0540.1211.596.3
2.1-2.2150.09812760.9860.0480.111.64198.8
2.21-2.3550.09312760.9880.0450.1041.84198
2.35-2.534.80.07812800.9910.0380.0871.63897.6
2.53-2.794.70.07112460.9910.0350.081.69696.7
2.79-3.1950.05812920.9940.0280.0651.52598.4
3.19-4.024.80.04812480.9970.0240.0541.54294.8
4.02-504.90.0412820.9980.0190.0441.38494.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 1.481→39.255 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.11
RfactorNum. reflection% reflection
Rfree0.1729 2003 8.36 %
Rwork0.1391 --
obs0.142 23967 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.11 Å2 / Biso mean: 31.9675 Å2 / Biso min: 14.88 Å2
Refinement stepCycle: final / Resolution: 1.481→39.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1394 0 5 108 1507
Biso mean--47.73 40.6 -
Num. residues----175
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 (%)
1.4808-1.51780.2474920.1869932102456
1.5178-1.55890.26071040.15331330143477
1.5589-1.60470.20041470.13981480162789
1.6047-1.65650.18911450.13361578172393
1.6565-1.71580.19871460.14121629177596
1.7158-1.78440.18041520.14011637178998
1.7844-1.86570.22431510.14171696184799
1.8657-1.9640.20331520.13111680183298
1.964-2.08710.16791520.12371640179297
2.0871-2.24820.16361560.11831686184299
2.2482-2.47440.14331480.12131658180698
2.4744-2.83240.17671500.13321673182397
2.8324-3.56810.17611590.14241682184197
3.5681-39.26910.15891490.15481663181294

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