[English] 日本語
Yorodumi
- PDB-8vxn: Human Bcl-2/Bcl-xL Chimera Fused to Maltose-Binding Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vxn
TitleHuman Bcl-2/Bcl-xL Chimera Fused to Maltose-Binding Protein
ComponentsMaltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera
KeywordsAPOPTOSIS / Bcl-2 / MBP Fusion / Bcl-xL Chimera
Function / homology
Function and homology information


BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...BCL-2 complex / BAD-BCL-2 complex / channel inhibitor activity / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of viral genome replication / pigmentation / 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 / Bcl-2 family protein complex / negative regulation of mitochondrial depolarization / NFE2L2 regulating tumorigenic genes / pore complex / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / humoral immune response / detection of maltose stimulus / regulation of calcium ion transport / negative regulation of apoptotic signaling pathway / carbohydrate transport / negative regulation of anoikis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway in absence of ligand / 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 / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / carbohydrate transmembrane transporter activity / maltose binding / neuron apoptotic process / negative regulation of protein localization to plasma membrane / maltose transport / maltodextrin transmembrane transport / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / response to cytokine / B cell receptor signaling pathway / regulation of mitochondrial membrane potential / negative regulation of autophagy / ATP-binding cassette (ABC) transporter complex / protein phosphatase 2A binding / regulation of cytokinesis / response to nicotine / intrinsic apoptotic signaling pathway in response to DNA damage / cell chemotaxis / female pregnancy / myelin sheath / endocytosis / response to radiation / response to toxic substance / protein polyubiquitination / RAS processing / synaptic vesicle membrane / positive regulation of cell growth / negative regulation of neuron apoptotic process / outer membrane-bounded periplasmic space / nuclear membrane / defense response to virus / channel activity / protease binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor binding / Estrogen-dependent gene expression / sequence-specific DNA binding / molecular adaptor activity / mitochondrial outer membrane / periplasmic space / mitochondrial inner membrane / response to xenobiotic stimulus / positive regulation of apoptotic process / apoptotic process / mitochondrial matrix / protein heterodimerization activity / ubiquitin protein ligase binding / centrosome / positive regulation of cell population proliferation / DNA damage response / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum membrane / endoplasmic reticulum / protein-containing complex / mitochondrion / membrane / identical protein binding
Similarity search - Function
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 / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsBaird, J. / Holliday, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Anal.Chem. / Year: 2025
Title: Hydrogen/Deuterium Exchange and Protein Oxidative Footprinting with Mass Spectrometry Collectively Discriminate the Binding of Small-Molecule Therapeutics to Bcl-2.
Authors: Sun, Y. / Houde, D. / Iacob, R.E. / Baird, J. / Swift, R.V. / Holliday, M. / Shi, X. / Sidoli, S. / Brenowitz, M.
History
DepositionFeb 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 12, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera


Theoretical massNumber of molelcules
Total (without water)61,2611
Polymers61,2611
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.070, 88.950, 140.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein fused to apoptosis regulator Bcl-2/Bcl-xL chimera / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Bcl2-L-1 / Apoptosis regulator Bcl-X


Mass: 61260.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: For the alignment, MBP (UNP P0AEX9, 27-392) spans residues 19-384 (w/ surface entropy reduction mutations at 100, 101, 190, 191, and 257) and is fused to a Bcl-2/Bcl-xL chimera via a linker ...Details: For the alignment, MBP (UNP P0AEX9, 27-392) spans residues 19-384 (w/ surface entropy reduction mutations at 100, 101, 190, 191, and 257) and is fused to a Bcl-2/Bcl-xL chimera via a linker sequence (AARAAA) spanning 385-390. Bcl-2 (UNP P10415, 10-207) has the unstructured loop spanning 35-91 deleted and replaced with Bcl-xL (UNP Q07817, 29-44) for residues 35-50 of the Bcl-2/Bcl-xL chimera, so Bcl-2 spans 391-415 and 432-547, while Bcl-xL spans 416-431. For the 3D model, MBP (-362-3), linker (4-9), Bcl-2 (10-34 and 92-207), and Bcl-xL (35-50). GLU91 of the final model corresponds to residue 50 (Bcl-xL) of the loop replacement (35-50).
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Strain: K12 / Gene: malE, b4034, JW3994, BCL2, BCL2L1, BCL2L, BCLX / Plasmid: pET-24b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: P10415, UniProt: Q07817
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris (pH 8.0), 29% PEG 3350, 200 mM sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.005→75.222 Å / Num. obs: 29956 / % possible obs: 93 % / Redundancy: 6.3 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Net I/σ(I): 13
Reflection shellResolution: 2.005→2.04 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1591 / CC1/2: 0.852 / Rpim(I) all: 0.338 / Rrim(I) all: 0.89 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROC1.1.7data reduction
PHASERphasing
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→55.24 Å / SU ML: 0.263 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2635 1366 4.94 %
Rwork0.2036 26294 -
obs0.2064 27660 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.65 Å2
Refinement stepCycle: LAST / Resolution: 2.09→55.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3962 0 0 134 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00344063
X-RAY DIFFRACTIONf_angle_d0.55285515
X-RAY DIFFRACTIONf_chiral_restr0.0422588
X-RAY DIFFRACTIONf_plane_restr0.0042715
X-RAY DIFFRACTIONf_dihedral_angle_d18.38711463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.160.31611410.2532662X-RAY DIFFRACTION99.89
2.16-2.250.31461390.23832439X-RAY DIFFRACTION99.5
2.25-2.350.26821320.23842560X-RAY DIFFRACTION99.52
2.35-2.480.3111430.2332682X-RAY DIFFRACTION99.93
2.48-2.630.31281360.2312678X-RAY DIFFRACTION99.68
2.63-2.840.32561370.23082349X-RAY DIFFRACTION87.81
2.84-3.120.26071290.2272697X-RAY DIFFRACTION99.96
3.12-3.570.27881480.21542705X-RAY DIFFRACTION99.72
3.57-4.50.23771300.17712603X-RAY DIFFRACTION94.37
4.5-55.240.21741310.17542919X-RAY DIFFRACTION99.58
Refinement TLS params.Method: refined / Origin x: 7.22774740958 Å / Origin y: 7.93514182339 Å / Origin z: 18.8073890097 Å
111213212223313233
T0.228353617105 Å20.0035323713978 Å2-0.00268828251064 Å2-0.231020692311 Å20.00139084662161 Å2--0.343904067555 Å2
L0.401909917451 °2-0.0196645391381 °2-0.134219251289 °2-1.66888136407 °20.208048341306 °2--0.871473788956 °2
S0.00311026977735 Å °0.0795049574767 Å °0.00504390472296 Å °-0.11872531933 Å °0.00382850063159 Å °0.0287908235961 Å °0.126035477624 Å °-0.010106503496 Å °-0.00614320680228 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