[English] 日本語
Yorodumi
- PDB-4yk9: Complex structure of BCL-XL and mutated BIM BH3 domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yk9
TitleComplex structure of BCL-XL and mutated BIM BH3 domain
Components
  • BH3BIM
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS / BCL-XL / BIM / BH3 / complex
Function / homology
Function and homology information


The NLRP1 inflammasome / apoptotic process in bone marrow cell / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / fertilization / regulation of growth ...The NLRP1 inflammasome / apoptotic process in bone marrow cell / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / synaptic vesicle recycling via endosome / positive regulation of synaptic vesicle exocytosis / positive regulation of synaptic vesicle clustering / RAS processing / BH domain binding / fertilization / regulation of growth / positive regulation of synaptic vesicle endocytosis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / germ cell development / hepatocyte apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cellular response to alkaloid / regulation of mitochondrial membrane permeability / response to cycloheximide / Bcl-2 family protein complex / negative regulation of release of cytochrome c from mitochondria / clathrin binding / negative regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of ATP biosynthetic process / negative regulation of anoikis / extrinsic apoptotic signaling pathway in absence of ligand / BH3 domain binding / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of synaptic vesicle endocytosis / neuron apoptotic process / negative regulation of protein localization to plasma membrane / response to ischemia / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / release of cytochrome c from mitochondria / response to cytokine / regulation of long-term synaptic depression / male gonad development / in utero embryonic development / clathrin-coated pit / MDM2/MDM4 family protein binding / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / regulation of cytokinesis / mitochondrion organization / intrinsic apoptotic signaling pathway in response to DNA damage / cellular response to gamma radiation / response to radiation / response to virus / cell population proliferation / mitochondrial membrane / synaptic vesicle membrane / negative regulation of neuron apoptotic process / synaptic vesicle / presynapse / nuclear membrane / channel activity / GTPase binding / spermatogenesis / defense response to virus / regulation of apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / protein-containing complex binding / endoplasmic reticulum / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
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
ACETATE ION / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHa, N.C. / Kim, J.S.
Citation
Journal: To be published
Title: Complex structure of BCL-XL and mutated BIM BH3 domain
Authors: Ha, N.C. / Kim, J.S.
#1: Journal: Immunity / Year: 2003
Title: The structure of a Bcl-xL/Bim fragment complex: implications for Bim function.
Authors: Liu, X. / Dai, S. / Zhu, Y. / Marrack, P. / Kappler, J.W.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2-like protein 1
B: BH3BIM
F: Bcl-2-like protein 1
G: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,47310
Polymers49,1904
Non-polymers2836
Water2,108117
1
A: Bcl-2-like protein 1
B: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7846
Polymers24,5952
Non-polymers1894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-36 kcal/mol
Surface area8040 Å2
MethodPISA
2
F: Bcl-2-like protein 1
G: BH3BIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6894
Polymers24,5952
Non-polymers942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-24 kcal/mol
Surface area7940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.738, 81.738, 42.568
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

-
Components

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


Mass: 21925.014 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 2-196
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Production host: Escherichia coli (E. coli) / References: UniProt: Q64373
#2: Protein/peptide BH3BIM


Mass: 2669.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.3 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate (pH 4.6), 0.01 M calcium chloride and 15% v/v 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 37932 / % possible obs: 99.2 % / Redundancy: 6.4 % / Net I/σ(I): 2.08

-
Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data processing
Cootmodel building
MOLREPphasing
RefinementResolution: 1.7→19.633 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 24.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1745 5.01 %
Rwork0.1923 --
obs0.1941 34825 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→19.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2680 0 15 117 2812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072767
X-RAY DIFFRACTIONf_angle_d1.1773747
X-RAY DIFFRACTIONf_dihedral_angle_d16.797998
X-RAY DIFFRACTIONf_chiral_restr0.072376
X-RAY DIFFRACTIONf_plane_restr0.004489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.37891460.34672674X-RAY DIFFRACTION98
1.75-1.80640.33851350.3092806X-RAY DIFFRACTION99
1.8064-1.8710.29031370.28162743X-RAY DIFFRACTION99
1.871-1.94580.29331360.24152768X-RAY DIFFRACTION99
1.9458-2.03430.28231540.22142750X-RAY DIFFRACTION100
2.0343-2.14140.26741510.20322775X-RAY DIFFRACTION100
2.1414-2.27540.21161610.16622722X-RAY DIFFRACTION100
2.2754-2.45080.19851250.1712772X-RAY DIFFRACTION100
2.4508-2.69680.22641410.17362784X-RAY DIFFRACTION100
2.6968-3.08580.22871530.17032762X-RAY DIFFRACTION100
3.0858-3.88280.18311650.15762767X-RAY DIFFRACTION100
3.8828-19.63410.17741410.16432757X-RAY DIFFRACTION100

+
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