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- PDB-4a1w: Crystal structure of alpha-beta foldamer 4c in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 4a1w
TitleCrystal structure of alpha-beta foldamer 4c in complex with Bcl-xL
Components
  • ALPHA-BETA-FOLDAMER 2C
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS/INHIBITOR / APOPTOSIS-INHIBITOR COMPLEX / MIMICRY
Function / homology
Function and homology information


dynorphin receptor activity / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...dynorphin receptor activity / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / neuropeptide binding / regulation of growth / Bcl-2 family protein complex / BH domain binding / NFE2L2 regulating tumorigenic genes / response to cycloheximide / negative regulation of release of cytochrome c from mitochondria / STAT5 activation downstream of FLT3 ITD mutants / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / ectopic germ cell programmed cell death / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / neuropeptide signaling pathway / negative regulation of protein localization to plasma membrane / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / extrinsic apoptotic signaling pathway in absence of ligand / ovarian follicle development / sensory perception of pain / release of cytochrome c from mitochondria / negative regulation of autophagy / response to cytokine / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / endocytosis / RAS processing / male gonad development / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to virus / nuclear membrane / in utero embryonic development / neuron apoptotic process / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / neuron projection / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Kappa opioid receptor / Opioid receptor / 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 ...Kappa opioid receptor / Opioid receptor / 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-2 family / BCL (B-Cell lymphoma); contains BH1, BH2 regions / Bcl2-like / Bcl-2, Bcl-2 homology region 1-3 / BCL2-like apoptosis inhibitors family profile. / Apoptosis regulator proteins, Bcl-2 family / Bcl-2-like superfamily / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
ALPHA-BETA-FOLDAMER 2C / Kappa-type opioid receptor / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 Å
AuthorsBoersma, M.D. / Haase, H.S. / Kaufman, K.J. / Horne, W.S. / Lee, E.F. / Clarke, O.B. / Smith, B.J. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Evaluation of Diverse Alpha/Beta-Backbone Patterns for Functional Alpha-Helix Mimicry: Analogues of the Bim Bh3 Domain.
Authors: Boersma, M.D. / Haase, H.S. / Peterson-Kaufman, K.J. / Lee, E.F. / Clarke, O.B. / Colman, P.M. / Smith, B.J. / Horne, W.S. / Fairlie, W.D. / Gellman, S.H.
History
DepositionSep 20, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Jun 20, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_unobs_or_zero_occ_atoms / struct_conn
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: 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 2.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / 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_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / 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 / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 1
C: BCL-2-LIKE PROTEIN 1
D: BCL-2-LIKE PROTEIN 1
P: ALPHA-BETA-FOLDAMER 2C
Q: ALPHA-BETA-FOLDAMER 2C
R: ALPHA-BETA-FOLDAMER 2C
S: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)80,9828
Polymers80,9828
Non-polymers00
Water4,612256
1
A: BCL-2-LIKE PROTEIN 1
D: BCL-2-LIKE PROTEIN 1
P: ALPHA-BETA-FOLDAMER 2C
S: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)40,4914
Polymers40,4914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8320 Å2
ΔGint-43.2 kcal/mol
Surface area14960 Å2
MethodPISA
2
B: BCL-2-LIKE PROTEIN 1
C: BCL-2-LIKE PROTEIN 1
Q: ALPHA-BETA-FOLDAMER 2C
R: ALPHA-BETA-FOLDAMER 2C


Theoretical massNumber of molelcules
Total (without water)40,4914
Polymers40,4914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-41.4 kcal/mol
Surface area15590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.213, 106.290, 100.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2001-

HOH

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Components

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


Mass: 17917.959 Da / Num. of mol.: 4
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-FOLDAMER 2C


Type: Peptide-like / Class: Inhibitor / Mass: 2327.661 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: ALPHA-BETA-FOLDAMER 2C, UniProt: O43521*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsAMIDE (NH2): TERMINAL AMIDE 3-AMINO-4-(P-TOLYL)BUTANOIC ACID (BTY): BETA PEPTIDE 3-AMINO-4- ...AMIDE (NH2): TERMINAL AMIDE 3-AMINO-4-(P-TOLYL)BUTANOIC ACID (BTY): BETA PEPTIDE 3-AMINO-4-METHYLHEXANOIC ACID (BIL): BETA PEPTIDE 3-AMINO-4-PHENYLBUTANOIC ACID (BFE): BETA PEPTIDE 3-AMINO-4-(1H-INDOL-3-YL)BUTANOIC ACID (W3B): BETA PEPTIDE 3-AMINOPROPANOIC ACID (BGL): BETA PEPTIDE
Sequence detailsDELETION OF AMINO ACID RESIDUES 27-82 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: 2.67 Å3/Da / Density % sol: 53.98 %
Description: MOLECULAR REPLACEMENT WAS PERFORMED USING THE STRUCTURE OF BCL-XL FROM THE PDB ENTRY 3FDL, WITH THE PEPTIDE REMOVED, AS A SEARCH MODEL
Crystal growpH: 7.5
Details: 25% (W/V) PEG 3350, 0.2 M LITHIUM SULFATE, 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: 0.95373
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30333 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 6.55 % / Biso Wilson estimate: 37.36 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 14.99
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.17 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FDL

3fdl


Resolution: 2.497→64.027 Å / SU ML: 0.85 / σ(F): 1.99 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1522 5 %
Rwork0.1972 --
obs0.2004 30333 99.37 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.098 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.992 Å20 Å20 Å2
2---9.6346 Å20 Å2
3----8.3575 Å2
Refinement stepCycle: LAST / Resolution: 2.497→64.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5207 0 0 256 5463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085386
X-RAY DIFFRACTIONf_angle_d1.1557291
X-RAY DIFFRACTIONf_dihedral_angle_d18.1031972
X-RAY DIFFRACTIONf_chiral_restr0.082745
X-RAY DIFFRACTIONf_plane_restr0.004938
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4967-2.57730.35381310.27852453X-RAY DIFFRACTION94
2.5773-2.66940.34471370.25852591X-RAY DIFFRACTION100
2.6694-2.77630.29581380.25372590X-RAY DIFFRACTION100
2.7763-2.90260.33131360.22952583X-RAY DIFFRACTION100
2.9026-3.05570.33531400.20762626X-RAY DIFFRACTION100
3.0557-3.24710.27661360.20232592X-RAY DIFFRACTION100
3.2471-3.49780.29261380.2122631X-RAY DIFFRACTION100
3.4978-3.84980.23691380.18772616X-RAY DIFFRACTION100
3.8498-4.40670.22331400.15512653X-RAY DIFFRACTION100
4.4067-5.55150.23071410.15822681X-RAY DIFFRACTION100
5.5515-64.04790.22561470.20052795X-RAY DIFFRACTION99

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