[English] 日本語
Yorodumi
- PDB-5fmk: Bcl-xL with Bak BH3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fmk
TitleBcl-xL with Bak BH3 complex
Components
  • BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
  • BCL-XL
KeywordsAPOPTOSIS / BCL-XL / BAK / BH3 DOMAIN / BCL-2 FAMILY
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria ...Activation and oligomerization of BAK protein / response to mycotoxin / B cell negative selection / BAK complex / BH domain binding / apoptotic process involved in blood vessel morphogenesis / response to fungus / negative regulation of endoplasmic reticulum calcium ion concentration / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process in bone marrow cell / post-embryonic camera-type eye morphogenesis / SARS-CoV-1-mediated effects on programmed cell death / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / establishment or maintenance of transmembrane electrochemical gradient / positive regulation of mononuclear cell proliferation / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / activation of cysteine-type endopeptidase activity / endoplasmic reticulum calcium ion homeostasis / positive regulation of endoplasmic reticulum unfolded protein response / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / calcium ion transport into cytosol / response to UV-C / fibroblast apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / NFE2L2 regulating tumorigenic genes / positive regulation of calcium ion transport into cytosol / response to cycloheximide / porin activity / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / pore complex / thymocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / vagina development / positive regulation of proteolysis / B cell homeostasis / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to unfolded protein / ectopic germ cell programmed cell death / blood vessel remodeling / Pyroptosis / animal organ regeneration / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of 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 / heat shock protein binding / negative regulation of autophagy / intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / establishment of localization in cell / response to gamma radiation / apoptotic signaling pathway / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / response to hydrogen peroxide / response to organic cyclic compound / cellular response to gamma radiation / synaptic vesicle membrane / cellular response to mechanical stimulus / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / protein-folding chaperone binding / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling
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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...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 (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
Similarity search - Domain/homology
Bcl-2-like protein 1 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.731 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J. / Czabotar, P.E. / Colman, P.M.
CitationJournal: Genes Dev. / Year: 2016
Title: Physiological Restraint of Bak by Bcl-Xl is Essential for Cell Survival.
Authors: Lee, E.F. / Grabow, S. / Chappaz, S. / Dewson, G. / Hockings, C. / Kluck, R.M. / Gray, D.H. / Witkowski, M.T. / Evangelista, M. / Pettikiriarachchi, A. / Bouillet, P. / Lane, R.M. / ...Authors: Lee, E.F. / Grabow, S. / Chappaz, S. / Dewson, G. / Hockings, C. / Kluck, R.M. / Gray, D.H. / Witkowski, M.T. / Evangelista, M. / Pettikiriarachchi, A. / Bouillet, P. / Lane, R.M. / Czabotar, P.E. / Colman, P.M. / Smith, B.J. / Kile, B.T. / Fairlie, W.D.
History
DepositionNov 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Nov 8, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1446
Polymers21,7752
Non-polymers3684
Water2,198122
1
A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules

A: BCL-XL
B: BCL-2 HOMOLOGOUS ANTAGONIST/KILLER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,28712
Polymers43,5514
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area9860 Å2
ΔGint-58.1 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.668, 55.459, 61.053
Angle α, β, γ (deg.)90.00, 127.12, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 17933.959 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
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 BCL-2 HOMOLOGOUS ANTAGONIST/KILLER / APOPTOSIS REGULATOR BAK / BCL-2-LIKE PROTEIN 7 / BCL2-L-7 / BAK


Mass: 3841.312 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, UNP RESIDUES 63-96 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q16611
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN ...SEQUENCE LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN DELETED SEQUENCE OF PEPTIDES ON COVERS THE BH3 DOMAIN AND SURROUNDING RESIDUES

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.91 % / Description: NONE
Crystal growpH: 6.5
Details: 0.16M CALCIUM ACETATE, 0.08M SODIUM CACODYLATE, PH6.5, 20% GLYCEROL, 14.4% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364
DetectorType: ADSC Q210R / Detector: CCD / Date: Feb 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 1.73→19.4 Å / Num. obs: 21521 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 35.2
Reflection shellResolution: 1.73→1.81 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.73 / % possible all: 95.4

-
Processing

Software
NameVersionClassification
REFMAC5.4refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P1L

2p1l


Resolution: 1.731→19.401 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1856 1105 5.1 %RANDOM
Rwork0.1575 ---
obs0.159 21521 99.38 %-
Solvent computationShrinkage radii: 0.9 Å
Refinement stepCycle: LAST / Resolution: 1.731→19.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1365 0 24 122 1511
Refinement TLS params.Method: refined / Origin x: 13.216 Å / Origin y: -11.6307 Å / Origin z: -11.1698 Å
111213212223313233
T0.1067 Å2-0.02 Å20.0039 Å2-0.0972 Å2-0 Å2--0.1378 Å2
L0.6741 °2-0.195 °2-0.3678 °2-0.9503 °20.2357 °2--2.3104 °2
S-0.0287 Å °0.0736 Å °0.0151 Å °-0.0275 Å °-0.0581 Å °-0.0514 Å °0.0009 Å °-0.113 Å °0.0819 Å °

+
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://pdbjlvh1.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