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- PDB-5agw: Bcl-2 alpha beta-1 complex -

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Basic information

Entry
Database: PDB / ID: 5agw
TitleBcl-2 alpha beta-1 complex
Components
  • APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
  • BCL-2-LIKE PROTEIN 11
KeywordsAPOPTOSIS / BCL-2 / FOLDAMER / BIM
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / regulation of developmental pigmentation / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process ...BIM-BCL-xl complex / BIM-BCL-2 complex / negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / regulation of developmental pigmentation / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / positive regulation of skeletal muscle fiber development / melanin metabolic process / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / RUNX3 regulates BCL2L11 (BIM) transcription / cochlear nucleus development / osteoblast proliferation / positive regulation of mitochondrial membrane permeability involved in apoptotic process / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / Activation of BIM and translocation to mitochondria / negative regulation of osteoblast proliferation / 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 / gland morphogenesis / renal system process / apoptotic process in bone marrow cell / regulation of cell-matrix adhesion / negative regulation of calcium ion transport into cytosol / stem cell development / The NLRP1 inflammasome / ear development / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / lymphoid progenitor cell differentiation / T cell apoptotic process / dendritic cell proliferation / melanocyte differentiation / positive regulation of mononuclear cell proliferation / negative regulation of myeloid cell apoptotic process / meiosis I / negative regulation of epithelial cell apoptotic process / mammary gland development / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / glomerulus development / negative regulation of execution phase of apoptosis / regulation of nitrogen utilization / tube formation / positive regulation of T cell apoptotic process / oocyte development / regulation of organ growth / Regulation of MITF-M-dependent genes involved in apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / neuron maturation / positive regulation of multicellular organism growth / metanephros development / negative regulation of motor neuron apoptotic process / focal adhesion assembly / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / fertilization / negative regulation of ossification / negative regulation of B cell apoptotic process / regulation of growth / regulation of mitochondrial membrane permeability / response to UV-B / response to iron ion / calcium ion transport into cytosol / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / Bcl-2 family protein complex / axon regeneration / cellular response to glucocorticoid stimulus / epithelial cell apoptotic process / smooth muscle cell migration / myeloid cell homeostasis / FOXO-mediated transcription of cell death genes / BH domain binding / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / branching involved in ureteric bud morphogenesis / digestive tract morphogenesis / hair follicle morphogenesis / response to cycloheximide / negative regulation of G1/S transition of mitotic cell cycle / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / NRAGE signals death through JNK / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / thymocyte apoptotic process / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants
Similarity search - Function
Apoptosis regulator, Bcl-2 / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site ...Apoptosis regulator, Bcl-2 / Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / 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 / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Bcl-2-like protein 11 / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.695 Å
AuthorsSmith, B.J. / F Lee, E. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Alpha Beta Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity on Living Cells
Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / ...Authors: Checco, J.W. / Lee, E.F. / Evangelista, M. / Sleebs, N. / Rodgers, K. / Pettikiriarachchi, A. / Kershaw, N. / Eddinger, G.A. / Belair, D.G. / Wilson, J.L. / Eller, C.H. / Raines, R.T. / Murphy, W.L. / Smith, B.J. / Gellman, S.H. / Fairlie, W.D.
History
DepositionFeb 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 2.1May 1, 2024Group: 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: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
C: BCL-2-LIKE PROTEIN 11
D: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)44,1374
Polymers44,1374
Non-polymers00
Water1086
1
B: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
C: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)22,0692
Polymers22,0692
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14.7 kcal/mol
Surface area7680 Å2
MethodPISA
2
A: APOPTOSIS REGULATOR BCL-2, BCL-2-LIKE PROTEIN 1, APOPTOSIS REGULATOR BCL-2
D: BCL-2-LIKE PROTEIN 11


Theoretical massNumber of molelcules
Total (without water)22,0692
Polymers22,0692
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-14.8 kcal/mol
Surface area8360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.673, 87.673, 107.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 19357.557 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-34,29-44,92-207
Source method: isolated from a genetically manipulated source
Details: CONTAINS RESIDUES 1-34,92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide BCL-2-LIKE PROTEIN 11 / BCL2-L-11 / BCL2-INTERACTING MEDIATOR OF CELL DEATH


Mass: 2711.190 Da / Num. of mol.: 2 / Fragment: RESIDUES 148-166 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-6P-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43521
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS RESIDUES 1-34, 92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED ...CONTAINS RESIDUES 1-34, 92-207 OF BCL-2 AND THE UNSTRUCTURED LOOP BETWEEN RESIDUES 35-91 REPLACED IS WITH RESIDUES 35-50 OF BCL-XL RESIDUES 2,6,16 ARE CYCLIC BETA AMINO ACIDS RESIDUES 9,13 ARE PENETENYL S5 AMINO ACIDS THAT ARE CROSS-LINKED

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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: 2.4 Å3/Da / Density % sol: 48.73 % / Description: NONE
Crystal growpH: 7 / Details: 0.02M CACL2, 0.1M MOPS PH7.0, 10% 2-PROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.7→33.97 Å / Num. obs: 12081 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 79.51 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.29
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 9.3 % / Mean I/σ(I) obs: 1.08 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED BCL-2 BECLIN BH3 COMPLEX

Resolution: 2.695→33.969 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 31.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 603 5 %
Rwork0.2015 --
obs0.2051 12074 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.695→33.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 6 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092634
X-RAY DIFFRACTIONf_angle_d1.2743589
X-RAY DIFFRACTIONf_dihedral_angle_d24.161933
X-RAY DIFFRACTIONf_chiral_restr0.05373
X-RAY DIFFRACTIONf_plane_restr0.005456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6946-2.96560.38641450.3052764X-RAY DIFFRACTION99
2.9656-3.39440.32611490.25722824X-RAY DIFFRACTION100
3.3944-4.27530.26931500.19222863X-RAY DIFFRACTION100
4.2753-33.97130.2451590.17973020X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 5.976 Å / Origin y: 11.0786 Å / Origin z: -18.711 Å
111213212223313233
T0.5839 Å20.0399 Å2-0.0175 Å2-0.5244 Å20.1209 Å2--0.4974 Å2
L6.8231 °2-2.5406 °2-2.2251 °2-2.8216 °20.8283 °2--3.8444 °2
S-0.5842 Å °-0.6413 Å °-0.2248 Å °0.2147 Å °0.209 Å °-0.2223 Å °0.2106 Å °0.5912 Å °0.3604 Å °
Refinement TLS groupSelection details: ALL

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