[English] 日本語
Yorodumi
- PDB-8svk: Crystal structure of Bax D71N core domain BH3-groove dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8svk
TitleCrystal structure of Bax D71N core domain BH3-groove dimer
ComponentsApoptosis regulator BAX
KeywordsAPOPTOSIS / BAX / BCL2
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / protein insertion into mitochondrial membrane / BAX complex / B cell receptor apoptotic signaling pathway / positive regulation of reproductive process / positive regulation of motor neuron apoptotic process / regulation of mammary gland epithelial cell proliferation / spermatid differentiation / Activation, translocation and oligomerization of BAX / positive regulation of B cell apoptotic process / development of secondary sexual characteristics / NTRK3 as a dependence receptor / Sertoli cell proliferation / positive regulation of apoptotic DNA fragmentation / B cell homeostatic proliferation / glycosphingolipid metabolic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / retinal cell programmed cell death / B cell negative selection / BAK complex / apoptotic process involved in blood vessel morphogenesis / mitochondrial fragmentation involved in apoptotic process / negative regulation of endoplasmic reticulum calcium ion concentration / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / apoptotic process involved in embryonic digit morphogenesis / Release of apoptotic factors from the mitochondria / mitochondrial permeability transition pore complex / post-embryonic camera-type eye morphogenesis / establishment or maintenance of transmembrane electrochemical gradient / apoptotic process involved in mammary gland involution / Transcriptional regulation by RUNX2 / positive regulation of apoptotic process involved in mammary gland involution / regulation of nitrogen utilization / B cell apoptotic process / positive regulation of endoplasmic reticulum unfolded protein response / endoplasmic reticulum calcium ion homeostasis / fertilization / positive regulation of epithelial cell apoptotic process / calcium ion transport into cytosol / motor neuron apoptotic process / channel activity / mitochondrial fusion / Bcl-2 family protein complex / epithelial cell apoptotic process / myeloid cell homeostasis / BH domain binding / execution phase of apoptosis / hypothalamus development / positive regulation of calcium ion transport into cytosol / thymocyte apoptotic process / pore complex / odontogenesis of dentin-containing tooth / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / germ cell development / positive regulation of IRE1-mediated unfolded protein response / positive regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / vagina development / B cell homeostasis / negative regulation of mitochondrial membrane potential / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway by p53 class mediator / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / response to axon injury / blood vessel remodeling / ectopic germ cell programmed cell death / cellular response to unfolded protein / Pyroptosis / supramolecular fiber organization / negative regulation of fibroblast proliferation / extrinsic apoptotic signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / release of sequestered calcium ion into cytosol / extrinsic apoptotic signaling pathway in absence of ligand / homeostasis of number of cells within a tissue / response to salt stress / Hsp70 protein binding / intrinsic apoptotic signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / negative regulation of protein binding / kidney development / response to gamma radiation / apoptotic signaling pathway / neuron migration / positive regulation of protein-containing complex assembly / response to toxic substance / cellular response to virus / cerebral cortex development / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to UV / positive regulation of neuron apoptotic process
Similarity search - Function
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, 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
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Apoptosis regulator BAX
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMiller, M.S. / Czabotar, P.E. / Colman, P.M.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: Febs J. / Year: 2024
Title: Sequence differences between BAX and BAK core domains manifest as differences in their interactions with lipids.
Authors: Miller, M.S. / Cowan, A.D. / Brouwer, J.M. / Smyth, S.T. / Peng, L. / Wardak, A.Z. / Uren, R.T. / Luo, C. / Roy, M.J. / Shah, S. / Tan, Z. / Reid, G.E. / Colman, P.M. / Czabotar, P.E.
History
DepositionMay 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,94412
Polymers35,8854
Non-polymers1,0598
Water36020
1
A: Apoptosis regulator BAX
B: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4556
Polymers17,9422
Non-polymers5134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-28 kcal/mol
Surface area9180 Å2
MethodPISA
2
C: Apoptosis regulator BAX
D: Apoptosis regulator BAX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4896
Polymers17,9422
Non-polymers5474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-29 kcal/mol
Surface area8520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.393, 67.393, 140.822
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-313-

HOH

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 8971.242 Da / Num. of mol.: 4 / Mutation: C62S, D71N, C126S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BAX, BCL2L4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07812

-
Non-polymers , 5 types, 28 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium citrate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953651 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953651 Å / Relative weight: 1
ReflectionResolution: 2.25→44.93 Å / Num. obs: 18223 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.155 / Rrim(I) all: 0.164 / Net I/σ(I): 11.43
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.25-2.392.70728670.3682.8481
2.39-2.551.60727260.6371.6911
2.55-2.750.9925260.8221.0451
2.75-3.020.56523600.9290.5951
3.02-3.370.28921490.9810.3051
3.37-3.890.13818900.9950.1451
3.89-4.750.0716250.9980.0741
4.75-6.690.06813020.9980.0711
6.69-44.930.0377810.0321

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→44.93 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 912 5.01 %
Rwork0.2543 --
obs0.2559 18217 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2313 0 69 20 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022419
X-RAY DIFFRACTIONf_angle_d0.4523223
X-RAY DIFFRACTIONf_dihedral_angle_d14.308898
X-RAY DIFFRACTIONf_chiral_restr0.031354
X-RAY DIFFRACTIONf_plane_restr0.003406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.35691270.33732399X-RAY DIFFRACTION100
2.37-2.520.37161270.33212424X-RAY DIFFRACTION100
2.52-2.710.30181300.28252456X-RAY DIFFRACTION100
2.71-2.980.3361280.28492427X-RAY DIFFRACTION100
2.98-3.420.31611300.27972474X-RAY DIFFRACTION100
3.42-4.30.26021310.22882489X-RAY DIFFRACTION100
4.3-44.930.26161390.23172636X-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)
14.4232-3.7004-2.72364.39095.94110.0304-0.3986-0.5260.7838-0.59361.1215-0.9462-0.37370.8804-0.50010.69290.04950.13050.5657-0.12070.723218.4008-16.088644.3517
27.6805-3.2557-3.30544.85974.97538.48350.0164-0.1718-0.00450.5789-0.1816-0.0394-0.15150.4933-0.41870.49050.1582-0.01530.47360.11360.784123.1611-26.855838.516
35.9113.7662-1.62726.15-1.6423.5741-0.0459-0.0939-1.17220.3647-0.0852-1.02180.38550.44620.14330.26610.05780.01430.51580.0290.531314.8961-25.00333.9033
46.19913.82890.10935.0966-2.44043.35130.05181.34940.4218-0.610.14991.3595-0.3608-0.6524-0.49110.52560.0493-0.04080.4839-0.00340.6151-14.5738.7664.4406
52.60273.1712-0.30798.4275-1.62212.66840.1845-0.526-0.3318-0.63470.75391.20870.8702-1.4018-0.78920.4514-0.0016-0.04450.80140.12890.8784-24.9576-3.93817.4777
67.0813-0.5752-1.32253.2842.1785.5154-0.7429-1.2288-1.50731.3348-0.21980.03971.20160.75480.34110.66490.0020.08530.5550.21951.0042-13.8826-8.997426.791
77.8546-1.06713.39445.3599-3.03756.2634-0.66571.3635-1.26571.00333.16610.12511.12822.55440.39370.69470.3326-0.16740.68680.07320.8948-6.2805-11.09111.6073
84.5621-2.0041-1.39222.59741.24778.125-0.0904-0.71140.8667-0.17030.4949-0.2312-0.33940.80490.38170.4298-0.038-0.17810.4369-0.00380.6167-14.0680.234820.3956
94.5351-0.1162-8.44745.0485-0.72177.3428-0.63710.2535-1.0577-0.34650.38220.67041.7058-0.28970.44780.4766-0.0047-0.07830.49860.00590.7709-16.675-8.897311.3848
103.97460.9295-0.27213.38352.88393.078-0.30311.6459-0.4537-1.67390.2264-0.74460.430.1027-0.12940.65130.04410.05440.5077-0.05240.5583-4.53324.47281.6513
119.7666-6.85164.99131.9635-9.76088.9041-1.34825.92884.4460.1724-1.8631-8.2437-1.23322.17092.88381.32420.16350.0921.6370.77232.6333.441616.38194.4507
123.3749-1.2396-0.67223.10340.6874.91490.67330.49990.8214-0.8379-1.0282-0.5278-0.69420.05650.27130.7654-0.0680.03940.51730.10931.1708-8.383518.49128.8369
134.6484-0.60662.68355.2388-2.41742.6043-0.401-3.49211.93092.93130.62132.5691-2.6394-1.6817-0.58430.69090.3154-0.16070.307-0.30771.2249-21.378114.919411.2538
142.12790.54710.24042.39411.51714.120.2148-0.30050.06880.02130.0467-0.33070.2320.2501-0.13820.4751-0.0311-0.06430.34820.00790.575-5.24068.847413.3886
155.76472.64914.9014.6158-0.48246.47891.0165-2.3127-1.69281.25220.24920.03180.6391-1.3182-0.84610.65820.12720.07840.50250.05790.780110.4616-28.233441.544
164.71770.6593.743.16541.58674.81060.7388-1.81490.1140.3371-1.02441.48121.7986-3.76520.26170.6089-0.1034-0.05840.70750.24561.481-4.9157-31.961430.2715
175.75670.91690.93632.90550.76679.96140.27970.2183-0.5926-0.24430.13451.1663-0.1678-1.51-0.06530.54850.0711-0.04610.93620.31380.7463-5.512-20.125321.2522
185.34632.72624.76887.34820.14667.2375-0.15780.0363-0.23530.24250.31070.3164-0.01440.0546-0.0170.17120.02450.08860.35510.10340.4613.15-22.554625.9489
196.7815-0.62981.18286.23256.54936.6176-0.2407-0.37950.49660.7185-0.16721.73340.0163-2.03870.8970.4978-0.01010.11050.74840.20190.7642-3.9646-21.053633.9362
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 72 through 86 )
2X-RAY DIFFRACTION2chain 'D' and (resid 87 through 100 )
3X-RAY DIFFRACTION3chain 'D' and (resid 101 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 72 )
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 81 )
6X-RAY DIFFRACTION6chain 'A' and (resid 82 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 106 )
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 54 through 73 )
10X-RAY DIFFRACTION10chain 'B' and (resid 74 through 82 )
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 87 )
12X-RAY DIFFRACTION12chain 'B' and (resid 88 through 100 )
13X-RAY DIFFRACTION13chain 'B' and (resid 101 through 106 )
14X-RAY DIFFRACTION14chain 'B' and (resid 107 through 126 )
15X-RAY DIFFRACTION15chain 'C' and (resid 54 through 72 )
16X-RAY DIFFRACTION16chain 'C' and (resid 73 through 81 )
17X-RAY DIFFRACTION17chain 'C' and (resid 82 through 101 )
18X-RAY DIFFRACTION18chain 'C' and (resid 102 through 127 )
19X-RAY DIFFRACTION19chain 'D' and (resid 53 through 71 )

+
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://pdbjlc1.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