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- PDB-4bpk: Bcl-xL bound to alpha beta Puma BH3 peptide 5 -

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Basic information

Entry
Database: PDB / ID: 4bpk
TitleBcl-xL bound to alpha beta Puma BH3 peptide 5
Components
  • ALPHA BETA BH3-PEPTIDE
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / T cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of growth / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / T cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cysteine-type endopeptidase activity / fertilization / regulation of mitochondrial membrane permeability / positive regulation of thymocyte apoptotic process / negative regulation of protein localization to plasma membrane / regulation of growth / fibroblast apoptotic process / execution phase of apoptosis / Bcl-2 family protein complex / Activation of PUMA and translocation to mitochondria / NFE2L2 regulating tumorigenic genes / FOXO-mediated transcription of cell death genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to endoplasmic reticulum stress / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to ionizing radiation / determination of adult lifespan / apoptotic signaling pathway / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / activation of cysteine-type endopeptidase activity involved in apoptotic process / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular response to hypoxia / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / DNA damage response / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site / Apoptosis regulator, Bcl-2 family BH4 motif signature. / Apoptosis regulator, Bcl-2 protein, BH4 / Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2 family BH4 motif profile. / BH4 Bcl-2 homology region 4 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. / 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
Similarity search - Domain/homology
: / Bcl-2-like protein 1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å
AuthorsSmith, B.J. / Lee, E.F. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: Chembiochem / Year: 2013
Title: Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity for Bcl-2 Family Prosurvival Proteins.
Authors: Smith, B.J. / Lee, E.F. / Checco, J.W. / Evangelista, M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Data collection
Revision 2.0Jun 20, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 3.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / diffrn_source / entity_poly / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 3.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 4.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_conn_type / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 4.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 4.2May 15, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 1
C: ALPHA BETA BH3-PEPTIDE
D: ALPHA BETA BH3-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,47621
Polymers40,6664
Non-polymers1,81017
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-121.5 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.175, 72.133, 80.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein BCL-2-LIKE PROTEIN 1 / BCL2-L-1 / APOPTOSIS REGULATOR BCL-X / BCL-XL


Mass: 17830.881 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Details: BCL-XL WITHOUT C-TERMINAL DOMAIN OR LOOP BETWEEN ALPHA 1 AND ALPHA 2 HELICES
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide ALPHA BETA BH3-PEPTIDE


Mass: 2501.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9BXH1*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION MUTANT CONTAINING RESIDUES 1-40 AND 81-209 DELETION REMOVES 41-80 AND 210-233

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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: 1.79 Å3/Da / Density % sol: 55.6 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES, PH7.5 1M SODIUM ACETATE 50MM CADMIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.76→3 Å / Num. obs: 198352 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.74
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 9.35 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.39 / % possible all: 97.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 1.756→36.066 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 3620 5 %
Rwork0.2192 --
obs0.2209 38364 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.756→36.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 23 151 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012933
X-RAY DIFFRACTIONf_angle_d1.0583939
X-RAY DIFFRACTIONf_dihedral_angle_d16.031085
X-RAY DIFFRACTIONf_chiral_restr0.064399
X-RAY DIFFRACTIONf_plane_restr0.004520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7564-1.77950.37411120.35232272X-RAY DIFFRACTION85
1.7795-1.80390.32451420.33632668X-RAY DIFFRACTION98
1.8039-1.82970.34821360.31162618X-RAY DIFFRACTION99
1.8297-1.8570.36981420.28972651X-RAY DIFFRACTION100
1.857-1.8860.28231390.28582646X-RAY DIFFRACTION100
1.886-1.91690.25271430.26672711X-RAY DIFFRACTION100
1.9169-1.950.36711420.28342665X-RAY DIFFRACTION100
1.95-1.98540.32961390.27372666X-RAY DIFFRACTION100
1.9854-2.02360.30661370.26112652X-RAY DIFFRACTION100
2.0236-2.06490.32581480.25192701X-RAY DIFFRACTION100
2.0649-2.10980.24841380.24732696X-RAY DIFFRACTION100
2.1098-2.15890.28011360.25032666X-RAY DIFFRACTION100
2.1589-2.21290.27051360.22862657X-RAY DIFFRACTION100
2.2129-2.27270.29031420.23552646X-RAY DIFFRACTION100
2.2727-2.33960.23641380.22372684X-RAY DIFFRACTION100
2.3396-2.41510.27641440.21762711X-RAY DIFFRACTION100
2.4151-2.50140.2451400.21372652X-RAY DIFFRACTION100
2.5014-2.60150.26921430.22322681X-RAY DIFFRACTION100
2.6015-2.71980.23521440.21562673X-RAY DIFFRACTION100
2.7198-2.86320.27131450.21752680X-RAY DIFFRACTION100
2.8632-3.04250.27931410.20832640X-RAY DIFFRACTION100
3.0425-3.27720.28171370.21872688X-RAY DIFFRACTION100
3.2772-3.60680.22271460.20562696X-RAY DIFFRACTION100
3.6068-4.1280.24421370.17072633X-RAY DIFFRACTION100
4.128-5.19840.15821420.17762661X-RAY DIFFRACTION100
5.1984-36.07410.24771310.23722528X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 18.3088 Å / Origin y: -27.8496 Å / Origin z: -12.7689 Å
111213212223313233
T0.1376 Å20.0291 Å2-0.0422 Å2-0.3573 Å2-0.1274 Å2--0.1263 Å2
L4.1447 °2-4.4369 °20.8859 °2-9.5458 °2-2.0407 °2--1.1506 °2
S-0.2501 Å °-0.417 Å °0.4348 Å °0.4352 Å °0.3343 Å °-0.4398 Å °-0.1077 Å °-0.1191 Å °-0.0167 Å °
Refinement TLS groupSelection details: ALL

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