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- PDB-2yj1: Puma BH3 foldamer in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 2yj1
TitlePuma BH3 foldamer in complex with Bcl-xL
Components
  • ALPHA-BETA-PUMA BH3 FOLDAMER
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / MEMBRANE PROTEIN / FOLDAMER / BH3 DOMAIN / AUTOPHAGY
Function / homology
Function and homology information


apoptotic process in bone marrow cell / 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 ...apoptotic process in bone marrow cell / 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 / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic 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 / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / 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 / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
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-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
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLee, E.F. / Smith, B.J. / Horne, W.S. / Mayer, K.N. / Evangelista, M. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: Chembiochem / Year: 2011
Title: Structural Basis of Bcl-Xl Recognition by a Bh3-Mimetic Alpha-Beta-Peptide Generated Via Sequence-Based Design
Authors: Lee, E.F. / Smith, B.J. / Horne, W.S. / Mayer, K.N. / Evangelista, M. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionMay 18, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / diffrn_source / entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2May 15, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: ALPHA-BETA-PUMA BH3 FOLDAMER
C: BCL-2-LIKE PROTEIN 1
D: ALPHA-BETA-PUMA BH3 FOLDAMER


Theoretical massNumber of molelcules
Total (without water)41,0704
Polymers41,0704
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-56.8 kcal/mol
Surface area15070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.918, 71.382, 75.605
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: 17917.959 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide ALPHA-BETA-PUMA BH3 FOLDAMER


Mass: 2616.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL AMINO ACID RESIDUES GPLGS ARE A RESULT OF A CLONING ARTIFACT, DELETION OF AMINO ACID ...N-TERMINAL AMINO ACID RESIDUES GPLGS ARE A RESULT OF A CLONING ARTIFACT, DELETION OF AMINO ACID RESIDUES 27 TO 82 AND 210 TO 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: 1.99 Å3/Da / Density % sol: 38.15 % / Description: NONE
Crystal growpH: 7.5
Details: 0.05 M CADMIUM SULPHATE 1.0 M SODIUM ACETATE 0.1 M HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953692
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953692 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 15846 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 29.22 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 14.2
Reflection shellResolution: 2.24→2.32 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERFOR MRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 2.24→45.439 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 787 5 %
Rwork0.1904 --
obs0.1936 15803 99.33 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.64 Å2 / ksol: 0.441 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.655 Å20 Å20 Å2
2--0.5477 Å20 Å2
3---3.1073 Å2
Refinement stepCycle: LAST / Resolution: 2.24→45.439 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 0 68 2761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082758
X-RAY DIFFRACTIONf_angle_d1.1643725
X-RAY DIFFRACTIONf_dihedral_angle_d19.6421047
X-RAY DIFFRACTIONf_chiral_restr0.08384
X-RAY DIFFRACTIONf_plane_restr0.004484
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2392-2.37950.2931300.19742404X-RAY DIFFRACTION97
2.3795-2.56320.2821250.19542468X-RAY DIFFRACTION100
2.5632-2.82110.26351390.18632483X-RAY DIFFRACTION100
2.8211-3.22920.26761450.18192476X-RAY DIFFRACTION100
3.2292-4.0680.20371290.15832526X-RAY DIFFRACTION100
4.068-45.44840.25991190.21652659X-RAY DIFFRACTION99

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