[English] 日本語
Yorodumi
- PDB-5agw: Bcl-2 alpha beta-1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / : / meiosis I / RUNX3 regulates BCL2L11 (BIM) transcription / channel inhibitor activity / positive regulation of fibroblast apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / The NLRP1 inflammasome ...BIM-BCL-xl complex / BIM-BCL-2 complex / : / meiosis I / RUNX3 regulates BCL2L11 (BIM) transcription / channel inhibitor activity / positive regulation of fibroblast apoptotic process / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / The NLRP1 inflammasome / SARS-CoV-1-mediated effects on programmed cell death / 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 / hair follicle morphogenesis / pigmentation / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / Regulation of MITF-M-dependent genes involved in apoptosis / regulation of mitochondrial membrane permeability / B cell proliferation / apoptotic mitochondrial changes / response to iron ion / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of release of cytochrome c from mitochondria / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / FOXO-mediated transcription of cell death genes / humoral immune response / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of IRE1-mediated unfolded protein response / pore complex / regulation of calcium ion transport / positive regulation of release of cytochrome c from mitochondria / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of B cell proliferation / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of protein localization to plasma membrane / neuron apoptotic process / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / endomembrane system / FLT3 Signaling / B cell receptor signaling pathway / negative regulation of autophagy / regulation of mitochondrial membrane potential / response to endoplasmic reticulum stress / protein phosphatase 2A binding / regulation of cytokinesis / response to nicotine / intrinsic apoptotic signaling pathway in response to DNA damage / female pregnancy / myelin sheath / positive regulation of protein-containing complex assembly / response to radiation / response to toxic substance / endocytosis / autophagy / protein polyubiquitination / RAS processing / Signaling by BRAF and RAF1 fusions / synaptic vesicle membrane / positive regulation of cell growth / negative regulation of neuron apoptotic process / nuclear membrane / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / defense response to virus / Estrogen-dependent gene expression / sequence-specific DNA binding / microtubule binding / molecular adaptor activity / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / mitochondrial matrix / protein heterodimerization activity / ubiquitin protein ligase binding / apoptotic process / centrosome
Similarity search - Function
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-2 / Apoptosis regulator, Bcl-X / Apoptosis regulator, Bcl-2/ BclX / Apoptosis regulator, Bcl-2, BH4 motif, conserved site ...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-2 / 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
Revision 2.2Feb 12, 2025Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more