[English] 日本語
Yorodumi
- PDB-3pl7: Crystal structure of Bcl-xL in complex with the BaxBH3 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3pl7
TitleCrystal structure of Bcl-xL in complex with the BaxBH3 domain
Components
  • Apoptosis regulator BAX
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS/APOPTOSIS REGULATOR / Bcl-2 family fold / Regulation of apoptosis / Bax / mitochondria / APOPTOSIS-APOPTOSIS REGULATOR complex
Function / homology
Function and homology information


T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / 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 / Activation, translocation and oligomerization of BAX ...T cell homeostatic proliferation / release of matrix enzymes from mitochondria / positive regulation of developmental pigmentation / BAX complex / protein insertion into mitochondrial membrane / 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 / Activation, translocation and oligomerization of BAX / spermatid differentiation / Sertoli cell proliferation / NTRK3 as a dependence receptor / positive regulation of apoptotic DNA fragmentation / development of secondary sexual characteristics / positive regulation of B cell apoptotic process / positive regulation of mitochondrial membrane permeability involved in apoptotic process / B cell homeostatic proliferation / glycosphingolipid metabolic process / retinal cell programmed cell death / B cell negative selection / BAK complex / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / negative regulation of endoplasmic reticulum calcium ion concentration / apoptotic process involved in embryonic digit morphogenesis / mitochondrial permeability transition pore complex / Release of apoptotic factors from the mitochondria / apoptotic process in bone marrow cell / mitochondrial fragmentation involved in apoptotic process / apoptotic process involved in blood vessel morphogenesis / post-embryonic camera-type eye morphogenesis / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / Transcriptional regulation by RUNX2 / establishment or maintenance of transmembrane electrochemical gradient / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / apoptotic process involved in mammary gland involution / positive regulation of apoptotic process involved in mammary gland involution / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / 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 / endoplasmic reticulum calcium ion homeostasis / regulation of mitochondrial membrane permeability / positive regulation of epithelial cell apoptotic process / fertilization / regulation of growth / calcium ion transport into cytosol / epithelial cell apoptotic process / mitochondrial fusion / Bcl-2 family protein complex / myeloid cell homeostasis / motor neuron apoptotic process / NFE2L2 regulating tumorigenic genes / execution phase of apoptosis / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / thymocyte apoptotic process / hepatocyte apoptotic process / pore complex / hypothalamus development / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / positive regulation of IRE1-mediated unfolded protein response / negative regulation of intrinsic apoptotic signaling pathway / odontogenesis of dentin-containing tooth / positive regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / apoptotic mitochondrial changes / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / germ cell development / BH3 domain binding / vagina development / negative regulation of mitochondrial membrane potential / intrinsic apoptotic signaling pathway by p53 class mediator / B cell homeostasis / positive regulation of calcium ion transport into cytosol / negative regulation of anoikis / negative regulation of apoptotic signaling pathway / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / extrinsic apoptotic signaling pathway via death domain receptors / blood vessel remodeling / cellular response to unfolded protein / Pyroptosis / 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 / response to axon injury / negative regulation of fibroblast proliferation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein binding / ovarian follicle development / positive regulation of intrinsic apoptotic signaling pathway
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 / Blc2-like / Apoptosis Regulator Bcl-x ...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 / 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
Apoptosis regulator BAX / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.613 Å
AuthorsCzabotar, P.E. / Colman, P.M.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Mutation to Bax beyond the BH3 domain disrupts interactions with pro-survival proteins and promotes apoptosis
Authors: Czabotar, P.E. / Lee, E.F. / Thompson, G.V. / Wardak, A.Z. / Fairlie, W.D. / Colman, P.M.
History
DepositionNov 14, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2-like protein 1
C: Apoptosis regulator BAX
B: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)45,4473
Polymers45,4473
Non-polymers00
Water68538
1
A: Bcl-2-like protein 1
C: Apoptosis regulator BAX


Theoretical massNumber of molelcules
Total (without water)24,6422
Polymers24,6422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area8720 Å2
MethodPISA
2
B: Bcl-2-like protein 1


Theoretical massNumber of molelcules
Total (without water)20,8051
Polymers20,8051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.246, 99.050, 113.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

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


Mass: 20804.918 Da / Num. of mol.: 2 / Fragment: Bcl-xL, UNP residues 1-209 / Mutation: deletion of residues 45-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Protein/peptide Apoptosis regulator BAX / Bcl-2-like protein 4 / Bcl2-L-4


Mass: 3837.381 Da / Num. of mol.: 1 / Fragment: BH3 domain, UNP residues 48-81 / Source method: obtained synthetically / Details: Synthesized peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07812
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 13% Peg 6000, 0.2M CaCl2, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95661 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2008
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95661 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 12250 / Num. obs: 12238 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.5 % / Biso Wilson estimate: 38.92 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 26.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.6-2.6914.60.5916.111981100
2.69-2.814.70.5056.9611981100
2.8-2.9314.60.3629.1511981100
2.93-3.0814.70.28111.411991100
3.08-3.2814.70.19215.512131100
3.28-3.5314.70.1221.912361100
3.53-3.8814.60.08528.712151100
3.88-4.4514.50.06236.812271100
4.45-5.614.30.547.512411100
5.6-5013.40.042501313199.5

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YXJ

2yxj


Resolution: 2.613→33.544 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.33 / σ(F): 1.34 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2495 587 4.81 %Random
Rwork0.1857 ---
obs0.1888 12214 99.33 %-
all-12296 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.391 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 243.03 Å2 / Biso min: 6.92 Å2
Baniso -1Baniso -2Baniso -3
1-5.1489 Å20 Å2-0 Å2
2--4.2409 Å2-0 Å2
3----9.3898 Å2
Refinement stepCycle: LAST / Resolution: 2.613→33.544 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 0 38 2540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082557
X-RAY DIFFRACTIONf_angle_d1.0213451
X-RAY DIFFRACTIONf_dihedral_angle_d16.496913
X-RAY DIFFRACTIONf_chiral_restr0.068361
X-RAY DIFFRACTIONf_plane_restr0.004446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6131-2.8760.33111430.23142794X-RAY DIFFRACTION97
2.876-3.29180.2961490.19032881X-RAY DIFFRACTION100
3.2918-4.14610.22181450.16742928X-RAY DIFFRACTION100
4.1461-33.54670.22661500.18463024X-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)
11.9104-0.77760.74840.6732-0.45911.1627-0.1326-0.1407-0.10520.03070.14080.1564-0.0328-0.2933-0.00630.0499-0.0385-0.02760.1029-0.02320.068512.389119.556110.8671
21.2337-0.5833-0.16130.3908-0.18022.1693-0.0710.0558-0.0807-0.07360.0127-0.06810.43630.2870.0610.11370.04040.03370.0474-0.03350.103942.89510.258115.2796
31.636-0.8353-0.21534.96070.40.4723-0.26260.05260.2554-0.02290.3903-0.47470.06620.0715-0.13560.1924-0.02550.01960.214-0.0190.200926.711217.101212.4711
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

+
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