[English] 日本語
Yorodumi
- PDB-5fmj: Bcl-xL with mouse Bak BH3 Q75L complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fmj
TitleBcl-xL with mouse Bak BH3 Q75L complex
Components
  • BAK1 PROTEIN
  • BCL-2-LIKE PROTEIN 1
KeywordsAPOPTOSIS / BCL-XL / BAK / BH3 DOMAIN / BCL-2 FAMILY
Function / homology
Function and homology information


Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / Pyroptosis / leukocyte homeostasis / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin ...Activation and oligomerization of BAK protein / Release of apoptotic factors from the mitochondria / Pyroptosis / leukocyte homeostasis / BH domain binding / B cell negative selection / BAK complex / negative regulation of endoplasmic reticulum calcium ion concentration / response to fungus / response to mycotoxin / limb morphogenesis / apoptotic process in bone marrow cell / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / The NLRP1 inflammasome / dendritic cell apoptotic process / SARS-CoV-1-mediated effects on programmed cell death / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / establishment or maintenance of transmembrane electrochemical gradient / 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 / B cell apoptotic process / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / myeloid cell homeostasis / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / porin activity / STAT5 activation downstream of FLT3 ITD mutants / thymocyte apoptotic process / hepatocyte apoptotic process / pore complex / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of developmental process / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / germ cell development / positive regulation of calcium ion transport into cytosol / BH3 domain binding / vagina development / B cell homeostasis / positive regulation of proteolysis / negative regulation of anoikis / homeostasis of number of cells / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / blood vessel remodeling / animal organ regeneration / 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 / heat shock protein binding / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / regulation of mitochondrial membrane potential / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of cytokinesis / epithelial cell proliferation / response to gamma radiation / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / establishment of localization in cell / response to hydrogen peroxide / cellular response to mechanical stimulus / cellular response to gamma radiation / mitochondrial membrane / RAS processing / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / synaptic vesicle membrane / protein-folding chaperone binding / channel activity / neuron apoptotic process / response to ethanol / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / regulation of apoptotic process / nuclear membrane / defense response to virus / in utero embryonic development
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-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 homologous antagonist/killer / Bcl-2-like protein 1 / BCL2-antagonist/killer 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsFairlie, W.D. / Lee, E.F. / Smith, B.J.
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 1.2Jan 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-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0246
Polymers21,7752
Non-polymers2484
Water1,58588
1
A: BCL-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules

A: BCL-2-LIKE PROTEIN 1
B: BAK1 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,04712
Polymers43,5514
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area9690 Å2
ΔGint-37.3 kcal/mol
Surface area16760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.789, 57.789, 268.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2008-

HOH

-
Components

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


Mass: 17917.959 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-26,83-209
Source method: isolated from a genetically manipulated source
Details: DELETION OF RESIDUES 27-82 / 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 BAK1 PROTEIN


Mass: 3857.354 Da / Num. of mol.: 1 / Fragment: BH3 DOMAIN, UNP RESIDUES 61-94 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q91WX5, UniProt: O08734*PLUS
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN A LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN ...CHAIN A LACKS THE LARGE LOOP BETWEEN RESIDUES 27-82 AND HAS THE C-TERMINAL TRANSMEMBRANE DOMAIN DELETED CHAIN B HAS Q75L MUTATION

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.58 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM THIOCYANATE, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.43→19.66 Å / Num. obs: 10808 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 19.2 % / Biso Wilson estimate: 47.28 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.6
Reflection shellResolution: 2.43→2.67 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.8 / % possible all: 98.3

-
Processing

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

2p1l


Resolution: 2.43→19.662 Å / SU ML: 0.24 / σ(F): 2.03 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 540 5 %
Rwork0.1799 --
obs0.1819 10808 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.43→19.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1413 0 16 88 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091471
X-RAY DIFFRACTIONf_angle_d0.9351980
X-RAY DIFFRACTIONf_dihedral_angle_d19.758869
X-RAY DIFFRACTIONf_chiral_restr0.048208
X-RAY DIFFRACTIONf_plane_restr0.005259
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4295-2.67350.29151290.22392438X-RAY DIFFRACTION99
2.6735-3.05910.27741320.20972517X-RAY DIFFRACTION100
3.0591-3.84940.25371350.18642570X-RAY DIFFRACTION100
3.8494-19.66280.17231440.1592743X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 4.5981 Å / Origin y: 23.6931 Å / Origin z: 12.5338 Å
111213212223313233
T0.1284 Å2-0.0265 Å2-0.0223 Å2-0.3604 Å2-0.0518 Å2--0.2616 Å2
L1.1293 °20.3036 °2-0.2865 °2-0.9913 °20.1338 °2--0.8224 °2
S0.0383 Å °0.1728 Å °-0.2436 Å °0.107 Å °-0.0417 Å °-0.0806 Å °0.0463 Å °0.1399 Å °-0.0068 Å °
Refinement TLS groupSelection details: CHAIN A OR CHAIN B

+
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