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- PDB-3fdm: alpha/beta foldamer in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 3fdm
Titlealpha/beta foldamer in complex with Bcl-xL
Components
  • Apoptosis regulator Bcl-XBcl-2-like protein 1
  • alpha/beta-peptide foldamer
KeywordsAPOPTOSIS / protein-peptide complex / helical bundle / foldamer / Alternative splicing / Membrane / Mitochondrion / Nucleus / Transmembrane
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / 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 dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / negative regulation of protein localization to plasma membrane / regulation of mitochondrial membrane permeability / 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 / apoptotic mitochondrial changes / germ cell development / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / 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 / 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 / defense response to virus / neuron apoptotic process / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / mitochondrial inner membrane / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / identical protein binding / cytosol / cytoplasm
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 / Blc2-like / Apoptosis Regulator Bcl-x ...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 / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J. / Czabotar, P.E. / Colman, P.M. / Sadowsky, J.D. / Peterson-Kaufman, K.J. / Gellman, S.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: High-Resolution Structural Characterization of a Helical alpha/beta-Peptide Foldamer Bound to the Anti-Apoptotic Protein Bcl-x(L)
Authors: Lee, E.F. / Sadowsky, J.D. / Smith, B.J. / Czabotar, P.E. / Peterson-Kaufman, K.J. / Colman, P.M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Aug 16, 2017Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-X
B: Apoptosis regulator Bcl-X
C: Apoptosis regulator Bcl-X
D: alpha/beta-peptide foldamer
E: alpha/beta-peptide foldamer
F: alpha/beta-peptide foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,67817
Polymers58,9956
Non-polymers68311
Water5,188288
1
A: Apoptosis regulator Bcl-X
B: Apoptosis regulator Bcl-X
D: alpha/beta-peptide foldamer
E: alpha/beta-peptide foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,01315
Polymers39,3304
Non-polymers68311
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9890 Å2
ΔGint-12 kcal/mol
Surface area15420 Å2
MethodPISA
2
C: Apoptosis regulator Bcl-X
F: alpha/beta-peptide foldamer

C: Apoptosis regulator Bcl-X
F: alpha/beta-peptide foldamer


Theoretical massNumber of molelcules
Total (without water)39,3304
Polymers39,3304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8080 Å2
ΔGint-48 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.161, 92.281, 165.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Apoptosis regulator Bcl-X / Bcl-2-like protein 1 / Bcl-xL / Bcl-2-like 1 protein


Mass: 17917.959 Da / Num. of mol.: 3 / Fragment: residue 1-209, Deletion of amino acids 27 to 82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Bcl-x / Plasmid: pGEX-6P3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q07817
#2: Protein/peptide alpha/beta-peptide foldamer


Mass: 1747.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: Chemically synthesized / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBCL-XL WITH AMINO ACIDS 27 TO 82 DELETED AND A C-TERMINAL TRUNCATION OF THE LAST 24 RESIDUES

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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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2M Lithium Nitrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 23, 2008 / Details: AXCO Capillary optic
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. all: 26633 / Num. obs: 25355 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 38.6
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 13.1 / Num. unique all: 2611 / % possible all: 90.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L without Beclin BH3 ligand

2p1l


Resolution: 2.26→47.14 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.17 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.311 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23483 1299 5.1 %RANDOM
Rwork0.17233 ---
all0.17561 25236 --
obs0.17561 24020 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.26→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 44 288 4223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214018
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9525411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83123.702208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.74615636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1031531
X-RAY DIFFRACTIONr_chiral_restr0.1150.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023051
X-RAY DIFFRACTIONr_mcbond_it0.7941.52383
X-RAY DIFFRACTIONr_mcangle_it1.50923795
X-RAY DIFFRACTIONr_scbond_it2.41931635
X-RAY DIFFRACTIONr_scangle_it3.8344.51615
LS refinement shellResolution: 2.262→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 81 -
Rwork0.159 1639 -
obs--90.29 %

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