[English] 日本語
Yorodumi
- PDB-5vwz: Bak in complex with Bim-h3Pc -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vwz
TitleBak in complex with Bim-h3Pc
Components
  • Bcl-2 homologous antagonist/killer
  • Bcl-2-like protein 11
KeywordsAPOPTOSIS / Bcl-2 Family / Inhibitor
Function / homology
Function and homology information


BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway ...BIM-BCL-xl complex / BIM-BCL-2 complex / regulation of developmental pigmentation / Activation and oligomerization of BAK protein / RUNX3 regulates BCL2L11 (BIM) transcription / BH domain binding / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell negative selection / BAK complex / positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Activation of BIM and translocation to mitochondria / negative regulation of endoplasmic reticulum calcium ion concentration / developmental pigmentation / response to fungus / positive regulation of fibroblast apoptotic process / apoptotic process involved in embryonic digit morphogenesis / response to mycotoxin / limb morphogenesis / Release of apoptotic factors from the mitochondria / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / endocrine pancreas development / ear development / establishment or maintenance of transmembrane electrochemical gradient / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / meiosis I / positive regulation of T cell apoptotic process / regulation of organ growth / mammary gland development / tube formation / B cell apoptotic process / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / calcium ion transport into cytosol / fibroblast apoptotic process / response to UV-C / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / cellular response to glucocorticoid stimulus / NRAGE signals death through JNK / porin activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / thymocyte apoptotic process / pore complex / FOXO-mediated transcription of cell death genes / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / T cell homeostasis / vagina development / positive regulation of calcium ion transport into cytosol / B cell homeostasis / positive regulation of proteolysis / blood vessel remodeling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / animal organ regeneration / cellular response to unfolded protein / Pyroptosis / positive regulation of intrinsic apoptotic signaling pathway / spleen development / positive regulation of cell cycle / heat shock protein binding / extrinsic apoptotic signaling pathway in absence of ligand / FLT3 Signaling / endomembrane system / intrinsic apoptotic signaling pathway / response to endoplasmic reticulum stress / release of cytochrome c from mitochondria / thymus development / cell-matrix adhesion / epithelial cell proliferation / post-embryonic development / regulation of mitochondrial membrane potential / response to gamma radiation / positive regulation of protein-containing complex assembly / kidney development / apoptotic signaling pathway / establishment of localization in cell / response to hydrogen peroxide / cellular response to mechanical stimulus / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / Signaling by BRAF and RAF1 fusions / positive regulation of neuron apoptotic process / protein-folding chaperone binding / channel activity / spermatogenesis / regulation of apoptotic process / response to ethanol / microtubule binding / in utero embryonic development / transmembrane transporter binding / mitochondrial outer membrane / regulation of cell cycle / positive regulation of apoptotic process
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 / Blc2-like / Apoptosis Regulator Bcl-x / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...Apoptosis, Bim N-terminal / Bcl-2-like protein 11 / : / Bim protein N-terminus / Bcl-x interacting, BH3 domain / Bcl-x interacting, BH3 domain / Blc2-like / Apoptosis Regulator Bcl-x / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-1PG / AMMONIUM ION / Bcl-2-like protein 11 / Bcl-2 homologous antagonist/killer
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.622 Å
AuthorsBrouwer, J.M. / Colman, P.M. / Czabotar, P.E.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1079706 Australia
National Health and Medical Research Council (NHMRC, Australia)1058331 Australia
National Health and Medical Research Council (NHMRC, Australia)1113133 Australia
CitationJournal: Mol. Cell / Year: 2017
Title: Conversion of Bim-BH3 from Activator to Inhibitor of Bak through Structure-Based Design.
Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / ...Authors: Brouwer, J.M. / Lan, P. / Cowan, A.D. / Bernardini, J.P. / Birkinshaw, R.W. / van Delft, M.F. / Sleebs, B.E. / Robin, A.Y. / Wardak, A. / Tan, I.K. / Reljic, B. / Lee, E.F. / Fairlie, W.D. / Call, M.J. / Smith, B.J. / Dewson, G. / Lessene, G. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2 homologous antagonist/killer
B: Bcl-2-like protein 11
C: Bcl-2 homologous antagonist/killer
D: Bcl-2-like protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2637
Polymers44,7404
Non-polymers5233
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.237, 56.668, 79.291
Angle α, β, γ (deg.)90.00, 103.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Bcl-2 homologous antagonist/killer / Apoptosis regulator BAK / Bcl-2-like protein 7 / Bcl2-L-7


Mass: 19037.320 Da / Num. of mol.: 2 / Fragment: UNP residues 23-186 / Mutation: C166S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAK1, BAK, BCL2L7, CDN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16611
#2: Protein/peptide Bcl-2-like protein 11 / Bcl2-L-11 / Bcl2-interacting mediator of cell death


Mass: 3332.727 Da / Num. of mol.: 2 / Fragment: UNP residues 141-166 / Mutation: W147R, Y163T / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O43521
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#4: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.17 %
Crystal growTemperature: 281 K / Method: vapor diffusion
Details: 10 % PEG 20000, 20 % PEG MME 550, 38 mM Imidazole pH 6.5, 20 mM ammonium acetate, 20 mM potassium sodium tartrate, 20 mM sodium formate, 62 mM sodium MES pH 6.5, 20 mM trisodium citrate, and 20 mM sodium oxamate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.622→38.58 Å / Num. obs: 41869 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1174 / Net I/σ(I): 15.1

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata processing
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.622→38.579 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.2
RfactorNum. reflection% reflection
Rfree0.1906 1996 4.77 %
Rwork0.154 --
obs0.1558 41867 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.622→38.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3096 0 31 390 3517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063307
X-RAY DIFFRACTIONf_angle_d1.1324482
X-RAY DIFFRACTIONf_dihedral_angle_d22.1791942
X-RAY DIFFRACTIONf_chiral_restr0.048457
X-RAY DIFFRACTIONf_plane_restr0.006601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.622-1.66260.28431420.22272842X-RAY DIFFRACTION99
1.6626-1.70750.29391470.21172799X-RAY DIFFRACTION100
1.7075-1.75780.23331440.21122807X-RAY DIFFRACTION100
1.7578-1.81450.22221430.18982847X-RAY DIFFRACTION100
1.8145-1.87930.25911430.18412822X-RAY DIFFRACTION100
1.8793-1.95460.23371400.17922864X-RAY DIFFRACTION100
1.9546-2.04350.19121440.16052811X-RAY DIFFRACTION100
2.0435-2.15130.19131410.15282849X-RAY DIFFRACTION100
2.1513-2.2860.18481400.14682860X-RAY DIFFRACTION100
2.286-2.46250.20511410.14672834X-RAY DIFFRACTION100
2.4625-2.71030.16921410.14842875X-RAY DIFFRACTION100
2.7103-3.10230.17751410.14632850X-RAY DIFFRACTION100
3.1023-3.9080.16611400.12842875X-RAY DIFFRACTION100
3.908-38.590.14621490.13222936X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1597-0.2157-0.01582.1560.33013.39890.0521-0.0860.09740.03530.02070.2313-0.1303-0.1462-0.08220.0022-0.01090.01990.08420.00470.1355-8.9232-50.79293.9929
20.8613-1.39772.00112.2644-3.2785.75270.0118-1.1269-1.23821.3497-0.496-0.27390.67490.01770.51560.6801-0.07870.0860.4210.22960.4677-5.9163-51.635324.1923
32.96180.5931.10720.33240.03670.591-0.0375-0.23320.13180.2229-0.03010.4078-0.1011-0.16260.0556-0.01030.00790.05510.1337-0.00350.2263-13.1147-50.30057.7924
41.90632.36560.34075.3367-1.26083.07390.3164-0.26010.06490.6974-0.3051-0.1059-0.12320.0838-0.01340.13350.0062-0.01010.0986-0.00950.10325.9454-56.195615.144
50.72150.00550.23661.35490.11931.30960.01450.0112-0.0171-0.0168-0.0287-0.0115-0.04260.0233-0.01490.01350.00250.01180.08150.00510.08360.1771-54.8361.7993
65.60551.1178-0.01871.93280.37172.14230.1334-0.1872-0.1093-0.0047-0.1379-0.29110.1515-0.0650.00010.040.02090.02630.07580.02130.13972.9764-65.5378.3332
72.6881-0.04711.10343.00110.5891.77520.1938-0.0991-0.2162-0.1446-0.04670.39030.4306-0.3855-0.13650.1822-0.0301-0.01720.12370.02670.1984-1.5384-78.321134.4191
83.2017-0.5991-1.28743.2745-1.21744.54790.05560.2182-0.0262-0.2147-0.03030.10720.1521-0.1788-0.06090.1306-0.0472-0.05720.0411-0.01880.07354.3061-70.988827.5112
91.6285-0.40240.13983.10340.62382.96450.04160.07140.0221-0.1729-0.0032-0.10690.18050.0201-0.0160.13570.00530.00310.07030.02810.052511.3878-73.322931.1297
102.5123-0.2685-0.52283.93471.17594.10320.0639-0.2250.08240.33640.0042-0.054-0.1075-0.0883-0.050.1709-0.00350.00350.11530.01930.05167.8572-72.744442.9873
117.9512-2.045-4.24795.25781.31656.59010.0204-0.070.1895-0.1612-0.0768-0.1634-0.15580.28530.02040.1234-0.0225-0.04060.07950.02840.076110.0437-61.904930.4237
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 21 through 48 )
2X-RAY DIFFRACTION2chain 'A' and (resid 49 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 82 )
4X-RAY DIFFRACTION4chain 'A' and (resid 83 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 186 )
6X-RAY DIFFRACTION6chain 'B' and (resid 141 through 166 )
7X-RAY DIFFRACTION7chain 'C' and (resid 21 through 69 )
8X-RAY DIFFRACTION8chain 'C' and (resid 70 through 106 )
9X-RAY DIFFRACTION9chain 'C' and (resid 107 through 150 )
10X-RAY DIFFRACTION10chain 'C' and (resid 151 through 184 )
11X-RAY DIFFRACTION11chain 'D' and (resid 141 through 166 )

+
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