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- PDB-6mbb: Human Bfl-1 in complex with the designed peptide dF1 -

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Basic information

Entry
Database: PDB / ID: 6mbb
TitleHuman Bfl-1 in complex with the designed peptide dF1
Components
  • Bcl-2-related protein A1
  • dF1
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: 1.59 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: Structure / Year: 2019
Title: Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.
Authors: Frappier, V. / Jenson, J.M. / Zhou, J. / Grigoryan, G. / Keating, A.E.
History
DepositionAug 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Bcl-2-related protein A1
B: dF1


Theoretical massNumber of molelcules
Total (without water)19,9672
Polymers19,9672
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-19 kcal/mol
Surface area9000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.223, 42.920, 47.718
Angle α, β, γ (deg.)90.000, 115.960, 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 dF1


Mass: 2523.858 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 38.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 1.8 M ammonium sulfate, 0.1 M MES pH 6.5

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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 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 19614 / % possible obs: 91.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 1.018 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.59-1.624.30.3596960.9070.1690.3990.53765.2
1.62-1.655.10.3249640.9460.1440.3560.52390.8
1.65-1.685.70.2989690.9630.1270.3240.50992.5
1.68-1.715.90.27710090.9720.1160.3010.51293.3
1.71-1.756.20.25210020.9730.1050.2730.52593.9
1.75-1.796.30.22510140.9760.0930.2440.55894
1.79-1.846.30.1979860.9830.0820.2140.54894.3
1.84-1.896.30.1689510.9870.070.1820.60789.2
1.89-1.946.90.14310040.990.0570.1550.63495.2
1.94-26.90.13110230.9910.0520.1410.73495.3
2-2.076.90.11310120.9930.0450.1220.79395.7
2.07-2.166.90.110080.9940.040.1070.89693.5
2.16-2.266.60.0969260.9910.0390.1041.10486.7
2.26-2.3870.08310200.9950.0330.091.08795.9
2.38-2.527.10.08210300.9940.0330.0891.295.3
2.52-2.7270.0769980.9950.030.0821.393.4
2.72-2.996.90.0739670.9960.0290.0791.48890
2.99-3.437.20.06510450.9960.0260.0711.78395.5
3.43-4.3270.0619520.9960.0250.0662.08387.4
4.32-506.90.05610380.9950.0240.0612.01393.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 1.59→42.904 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.82
RfactorNum. reflection% reflection
Rfree0.1957 1970 10.05 %
Rwork0.1651 --
obs0.1683 19599 91.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.61 Å2 / Biso mean: 30.2207 Å2 / Biso min: 10.77 Å2
Refinement stepCycle: final / Resolution: 1.59→42.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 0 128 1533
Biso mean---40.15 -
Num. residues----176
Refinement TLS params.Method: refined / Origin x: -9.1582 Å / Origin y: 7.1999 Å / Origin z: -7.8542 Å
111213212223313233
T0.1261 Å20.0038 Å20.0022 Å2-0.1448 Å2-0.0092 Å2--0.1299 Å2
L0.9615 °20.4891 °20.0619 °2-1.6959 °2-0.1891 °2--0.5935 °2
S0.0202 Å °0.0242 Å °0.0603 Å °-0.0543 Å °-0.0338 Å °0.0929 Å °-0.0341 Å °0.0365 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 151
2X-RAY DIFFRACTION1allB1 - 24
3X-RAY DIFFRACTION1allS1 - 141

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