[English] 日本語
Yorodumi
- PDB-9li8: Crystal structure of Bcl-xL in complex with HRK BH3 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9li8
TitleCrystal structure of Bcl-xL in complex with HRK BH3 peptide
Components
  • Activator of apoptosis harakiri
  • Bcl-2-like protein 1
KeywordsAPOPTOSIS / Bcl-2 family / mitochondrial apoptosis / BH3-only proteins
Function / homology
Function and homology information


cellular response to potassium ion starvation / apoptotic process in bone marrow cell / 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 / 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 ...cellular response to potassium ion starvation / apoptotic process in bone marrow cell / 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 / 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 / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / 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 / BH3 domain binding / negative regulation of anoikis / 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 / 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 / cellular response to amino acid stimulus / positive regulation of protein-containing complex assembly / cellular response to gamma radiation / RAS processing / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / synaptic vesicle membrane / positive regulation of neuron apoptotic process / channel activity / neuron apoptotic process / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / nuclear membrane / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / apoptotic process / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Activator of apoptosis harakiri / Activator of apoptosis harakiri / 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 ...Activator of apoptosis harakiri / Activator of apoptosis harakiri / 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
Activator of apoptosis harakiri / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsWei, H. / Guo, M. / Wang, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82470176, 82273496 and 31900880 China
CitationJournal: To Be Published
Title: Molecular mechanisms underlying HRK interaction with BCL-XL and BCL-2 reveal specificity determinants for selective BH3 mimetics
Authors: Wei, H. / Wang, J. / Guo, M. / Dai, S.
History
DepositionJan 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bcl-2-like protein 1
B: Activator of apoptosis harakiri


Theoretical massNumber of molelcules
Total (without water)27,2752
Polymers27,2752
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15 kcal/mol
Surface area8150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.873, 63.606, 78.862
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

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


Mass: 24458.824 Da / Num. of mol.: 1
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 Activator of apoptosis harakiri / BH3-interacting domain-containing protein 3 / Neuronal death protein DP5


Mass: 2816.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O00198
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21.02 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5 and 25% w/v Polyethylene glycol 3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Oct 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.32→49.51 Å / Num. obs: 7726 / % possible obs: 98.73 % / Redundancy: 10.8 % / Biso Wilson estimate: 30.48 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 10.5
Reflection shellResolution: 2.321→2.404 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.82 / Num. unique obs: 686 / % possible all: 90.75

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→49.51 Å / SU ML: 0.2757 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.7006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2638 773 10.01 %
Rwork0.2213 6949 -
obs0.2256 7722 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.23 Å2
Refinement stepCycle: LAST / Resolution: 2.32→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1374 0 0 49 1423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251409
X-RAY DIFFRACTIONf_angle_d0.5181908
X-RAY DIFFRACTIONf_chiral_restr0.033205
X-RAY DIFFRACTIONf_plane_restr0.0042244
X-RAY DIFFRACTIONf_dihedral_angle_d3.7468189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.470.32471190.27371069X-RAY DIFFRACTION94.06
2.47-2.660.32471270.26441150X-RAY DIFFRACTION99.69
2.66-2.920.2861280.241138X-RAY DIFFRACTION99.76
2.92-3.350.28751290.24031171X-RAY DIFFRACTION99.77
3.35-4.220.23481310.19421175X-RAY DIFFRACTION99.47
4.22-490.23371390.20111246X-RAY DIFFRACTION99.64
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)
14.53858528241-0.8850778563080.1062018560262.598506551473.469035750065.409872002240.03875461941270.08729370524720.413069268004-0.2839971299540.289777057790.520191817924-0.906872540527-2.35314195013-0.2984076221750.3322338240410.2072939838040.01927865832060.7377755195720.03777986503960.287315815203-10.9870023529-9.9306343453114.7368776781
20.747361482454-0.09130221706040.1316281489350.42859228943-0.9544715022954.210894144570.310767365905-0.3668911214940.2720303905370.2047098428420.7552718695840.17846435607-0.0347549727459-1.60133007245-0.5032026716610.2679449286180.1603113773860.02610535132881.35813827203-0.1479930018670.696036426655-15.6353232806-9.9905561691922.8476383354
34.80911268748-0.4143429761250.281076823314.40695244431-0.6902990043667.37381820492-0.2783364171850.651588413591-0.468292780681-0.117504182751-0.007923998110360.4834460901670.89492697378-2.152141164650.0621158712840.286846877999-0.1275579046980.1055134016640.604045914611-0.09405635236430.26772127166-8.93548563598-21.253026372412.2895642034
40.369308969849-0.108284479286-0.1146740889593.024889311091.377497190180.5962058948480.0653606523143-1.23993196953-0.4937690721711.7423016954-0.0376908101166-0.3664306545921.50459383402-0.3026221085020.2273393842620.9499335102380.01782625199520.07110536922790.6104407976090.07028135861670.438322464299-0.186616447798-21.245589840227.1361767727
53.566674738860.910619948059-1.239416917253.540194583150.3932188434467.055659526430.03833174873090.1804010893820.1033566204-0.03227744874920.0467963536286-0.159291884058-0.746024961956-0.0828775372611-0.07997727491360.1934032754410.0005009178888930.0001499560618910.1590030238150.01066126234440.222317510011-0.154881874313-11.381737562515.1014813734
64.012316107170.542792361701-2.195301974463.41133387290.8525276556575.03031711172-0.349916893830.194258202137-0.510121894166-0.266579151629-0.311882896577-0.4833508386790.7599853000080.9604146325610.6433390694410.590136991078-0.287164476339-0.03986292700140.7475392867980.05565559534050.323560906992-11.3929439399-28.42087035745.69802068699
77.032072955340.2531029351263.150634704993.5982992440.4929234526476.847422536930.5531520590620.43212173639-1.105636712920.1739337155470.29636691518-0.319003819420.4936644586830.376467081724-0.3128477308580.2336194215530.0486282848867-0.01595592142730.2132731558560.02393451588050.4101132729483.99070662015-23.62963875611.9123830397
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 19 )AA2 - 191 - 18
22chain 'A' and (resid 20 through 82 )AA20 - 8219 - 27
33chain 'A' and (resid 83 through 104 )AA83 - 10428 - 49
44chain 'A' and (resid 105 through 115 )AA105 - 11550 - 60
55chain 'A' and (resid 116 through 195 )AA116 - 19561 - 140
66chain 'A' and (resid 196 through 205 )AA196 - 205141 - 150
77chain 'B' and (resid 27 through 51 )BB27 - 511 - 25

+
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