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- PDB-6rjp: Bfl-1 in complex with alpha helical peptide -

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Basic information

Entry
Database: PDB / ID: 6rjp
TitleBfl-1 in complex with alpha helical peptide
Components
  • Bcl-2-like protein 11
  • Bcl-2-related protein A1
KeywordsPEPTIDE BINDING PROTEIN / protein-protein interactions / stapled alpha helix / covalent inhibitor / Bcl2-2 family proteins
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / RUNX3 regulates BCL2L11 (BIM) transcription / positive regulation of mitochondrial membrane permeability involved in apoptotic process / Activation of BIM and translocation to mitochondria / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / developmental pigmentation / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / ear development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / mammary gland development / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / tube formation / Regulation of MITF-M-dependent genes involved in apoptosis / mitochondrial fusion / cellular response to glucocorticoid stimulus / Bcl-2 family protein complex / myeloid cell homeostasis / NRAGE signals death through JNK / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / odontogenesis of dentin-containing tooth / B cell homeostasis / Nuclear events stimulated by ALK signaling in cancer / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / FLT3 Signaling / endomembrane system / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / thymus development / cell-matrix adhesion / post-embryonic development / kidney development / positive regulation of protein-containing complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / channel activity / microtubule binding / regulation of apoptotic process / spermatogenesis / in utero embryonic development / mitochondrial outer membrane / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / protein kinase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Bcl-2-related protein A1 / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH1 motif, conserved site ...Bcl-2-related protein A1 / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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-like protein 11 / Bcl-2-related protein A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsBaggio, C. / Gambini, L. / Udompholkul, P. / Salem, A.F. / Hakansson, M. / Jossart, J. / Perry, J. / Pellecchia, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 CA168517 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 NS107479 United States
CitationJournal: Chem.Biol.Drug Des. / Year: 2020
Title: N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists.
Authors: Baggio, C. / Udompholkul, P. / Gambini, L. / Jossart, J. / Salem, A.F. / Hakansson, M. / Perry, J.J.P. / Pellecchia, M.
History
DepositionApr 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / software / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Bcl-2-related protein A1
C: Bcl-2-like protein 11
D: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)43,2274
Polymers43,2274
Non-polymers00
Water18010
1
A: Bcl-2-related protein A1
C: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)21,6132
Polymers21,6132
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-11 kcal/mol
Surface area8400 Å2
MethodPISA
2
B: Bcl-2-related protein A1
D: Bcl-2-like protein 11


Theoretical massNumber of molelcules
Total (without water)21,6132
Polymers21,6132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-13 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.749, 113.749, 79.148
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21D
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LV8LV8TYRTYRCC1 - 171 - 17
21LV8LV8TYRTYRDD1 - 171 - 17
12SERSERGLUGLUAA0 - 14922 - 171
22SERSERGLUGLUBB0 - 14922 - 171

NCS ensembles :
ID
1
2

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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: 19718.299 Da / Num. of mol.: 2
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 Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 1895.125 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is modified amino acids. Made to get a tethered peptide produced with covalent bonds.
Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.42 Å3/Da / Density % sol: 64.05 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1 M sodium acetate pH 4.6 16% (w/v) PEG smear high

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.975312 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975312 Å / Relative weight: 1
ReflectionResolution: 2.57→61.7 Å / Num. obs: 10669 / % possible obs: 55.5 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.027 / Rrim(I) all: 0.051 / Net I/σ(I): 13.3
Reflection shellResolution: 2.57→2.94 Å / Rmerge(I) obs: 0.685 / Num. unique obs: 533 / CC1/2: 0.692 / Rpim(I) all: 0.359 / Rrim(I) all: 0.776

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Processing

Software
NameClassification
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VM6

2vm6


Resolution: 2.57→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 36.987 / SU ML: 0.325 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 555 5.2 %RANDOM
Rwork0.1992 ---
obs0.2025 10097 55.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 274.33 Å2 / Biso mean: 118.462 Å2 / Biso min: 40.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å2-0.47 Å20 Å2
2---0.94 Å20 Å2
3---3.06 Å2
Refinement stepCycle: final / Resolution: 2.57→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 10 2704
Biso mean---71.66 -
Num. residues----334
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C4560.24
12D4560.24
21A48330.12
22B48330.12
LS refinement shellResolution: 2.57→2.636 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 1 -
Rwork0.274 48 -
all-49 -
obs--3.54 %
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)
13.3571.6047-0.21283.3179-1.19852.89460.12750.22350.04990.30690.04580.41940.06990.1976-0.17330.279-0.0350.07940.07260.00170.077445.473-32.594.868
22.65983.56231.85927.39712.75091.3324-0.57920.6746-0.6626-0.58951.0747-1.5485-0.41710.5193-0.49550.4179-0.41520.11190.467-0.20270.550332.664-55.383-4.576
36.88021.26060.10673.168-1.84133.01610.6352-1.09560.12991.1671-0.57410.5014-0.77520.5009-0.06110.9756-0.31370.19410.4415-0.05930.113449.139-25.0816.11
49.4755-0.64533.00775.4468-3.61783.20080.04321.8416-0.9138-0.0495-0.2336-0.8232-0.22310.80070.19040.7978-0.49450.27780.969-0.53610.74928.3-63.099-16.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION2B0 - 149
3X-RAY DIFFRACTION3C1 - 17
4X-RAY DIFFRACTION4D1 - 17

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