[English] 日本語
Yorodumi
- PDB-4bpk: Bcl-xL bound to alpha beta Puma BH3 peptide 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bpk
TitleBcl-xL bound to alpha beta Puma BH3 peptide 5
Components
  • ALPHA BETA BH3-PEPTIDE
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / T cell apoptotic process ...positive regulation of establishment of protein localization to mitochondrion / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of fibroblast apoptotic process / apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / T cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / positive regulation of thymocyte apoptotic process / regulation of growth / fibroblast apoptotic process / Activation of PUMA and translocation to mitochondria / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / execution phase of apoptosis / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / FOXO-mediated transcription of cell death genes / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / apoptotic mitochondrial changes / BH3 domain binding / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway / negative regulation of autophagy / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to ionizing radiation / determination of adult lifespan / cellular response to amino acid stimulus / apoptotic signaling pathway / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / positive regulation of neuron apoptotic process / channel activity / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / nuclear membrane / defense response to virus / cellular response to hypoxia / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / DNA damage response / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 ...Bcl-2-binding component 3 / Bcl-2-binding component 3, p53 upregulated modulator of apoptosis / 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 1 / Bcl-2-binding component 3, isoforms 1/2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.756 Å
AuthorsSmith, B.J. / Lee, E.F. / Checco, J.W. / Gellman, S.H. / Fairlie, W.D.
CitationJournal: Chembiochem / Year: 2013
Title: Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity for Bcl-2 Family Prosurvival Proteins.
Authors: Smith, B.J. / Lee, E.F. / Checco, J.W. / Evangelista, M. / Gellman, S.H. / Fairlie, W.D.
History
DepositionMay 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Data collection
Revision 2.0Jun 20, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 3.0Apr 24, 2019Group: Data collection / Polymer sequence
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / 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 3.1Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 4.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_conn_type / struct_site
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 / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 4.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 4.2May 15, 2024Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-2-LIKE PROTEIN 1
B: BCL-2-LIKE PROTEIN 1
C: ALPHA BETA BH3-PEPTIDE
D: ALPHA BETA BH3-PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,47621
Polymers40,6664
Non-polymers1,81017
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10810 Å2
ΔGint-121.5 kcal/mol
Surface area14890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.175, 72.133, 80.579
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 17830.881 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Details: BCL-XL WITHOUT C-TERMINAL DOMAIN OR LOOP BETWEEN ALPHA 1 AND ALPHA 2 HELICES
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein/peptide ALPHA BETA BH3-PEPTIDE


Mass: 2501.887 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9BXH1*PLUS
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION MUTANT CONTAINING RESIDUES 1-40 AND 81-209 DELETION REMOVES 41-80 AND 210-233

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.79 Å3/Da / Density % sol: 55.6 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1M HEPES, PH7.5 1M SODIUM ACETATE 50MM CADMIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.76→3 Å / Num. obs: 198352 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.74
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 9.35 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.39 / % possible all: 97.4

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 1.756→36.066 Å / SU ML: 0.26 / σ(F): 1.99 / Phase error: 27.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2522 3620 5 %
Rwork0.2192 --
obs0.2209 38364 99.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.756→36.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 23 151 2779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012933
X-RAY DIFFRACTIONf_angle_d1.0583939
X-RAY DIFFRACTIONf_dihedral_angle_d16.031085
X-RAY DIFFRACTIONf_chiral_restr0.064399
X-RAY DIFFRACTIONf_plane_restr0.004520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7564-1.77950.37411120.35232272X-RAY DIFFRACTION85
1.7795-1.80390.32451420.33632668X-RAY DIFFRACTION98
1.8039-1.82970.34821360.31162618X-RAY DIFFRACTION99
1.8297-1.8570.36981420.28972651X-RAY DIFFRACTION100
1.857-1.8860.28231390.28582646X-RAY DIFFRACTION100
1.886-1.91690.25271430.26672711X-RAY DIFFRACTION100
1.9169-1.950.36711420.28342665X-RAY DIFFRACTION100
1.95-1.98540.32961390.27372666X-RAY DIFFRACTION100
1.9854-2.02360.30661370.26112652X-RAY DIFFRACTION100
2.0236-2.06490.32581480.25192701X-RAY DIFFRACTION100
2.0649-2.10980.24841380.24732696X-RAY DIFFRACTION100
2.1098-2.15890.28011360.25032666X-RAY DIFFRACTION100
2.1589-2.21290.27051360.22862657X-RAY DIFFRACTION100
2.2129-2.27270.29031420.23552646X-RAY DIFFRACTION100
2.2727-2.33960.23641380.22372684X-RAY DIFFRACTION100
2.3396-2.41510.27641440.21762711X-RAY DIFFRACTION100
2.4151-2.50140.2451400.21372652X-RAY DIFFRACTION100
2.5014-2.60150.26921430.22322681X-RAY DIFFRACTION100
2.6015-2.71980.23521440.21562673X-RAY DIFFRACTION100
2.7198-2.86320.27131450.21752680X-RAY DIFFRACTION100
2.8632-3.04250.27931410.20832640X-RAY DIFFRACTION100
3.0425-3.27720.28171370.21872688X-RAY DIFFRACTION100
3.2772-3.60680.22271460.20562696X-RAY DIFFRACTION100
3.6068-4.1280.24421370.17072633X-RAY DIFFRACTION100
4.128-5.19840.15821420.17762661X-RAY DIFFRACTION100
5.1984-36.07410.24771310.23722528X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 18.3088 Å / Origin y: -27.8496 Å / Origin z: -12.7689 Å
111213212223313233
T0.1376 Å20.0291 Å2-0.0422 Å2-0.3573 Å2-0.1274 Å2--0.1263 Å2
L4.1447 °2-4.4369 °20.8859 °2-9.5458 °2-2.0407 °2--1.1506 °2
S-0.2501 Å °-0.417 Å °0.4348 Å °0.4352 Å °0.3343 Å °-0.4398 Å °-0.1077 Å °-0.1191 Å °-0.0167 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