[English] 日本語
Yorodumi
- PDB-9o14: Crystal Structure of BCL-2 in complex with a stapled BAD BH3 pept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9o14
TitleCrystal Structure of BCL-2 in complex with a stapled BAD BH3 peptide BAD SAHB 4.2
Components
  • Apoptosis regulator Bcl-2,Bcl-2-like protein 1
  • stapled BAD BH3 peptide BAD SAHB 4.2
KeywordsAPOPTOSIS / Apoptosis regulator / stapled peptide
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / positive regulation of skeletal muscle fiber development / regulation of glycoprotein biosynthetic process / positive regulation of melanocyte differentiation / channel inhibitor activity / melanin metabolic process / positive regulation of neuron maturation / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / gland morphogenesis / apoptotic process in bone marrow cell / renal system process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / negative regulation of calcium ion transport into cytosol / dendritic cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / lymphoid progenitor cell differentiation / melanocyte differentiation / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / regulation of nitrogen utilization / negative regulation of dendritic cell apoptotic process / glomerulus development / focal adhesion assembly / regulation of transmembrane transporter activity / negative regulation of T cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / oocyte development / metanephros development / B cell apoptotic process / neuron maturation / Regulation of MITF-M-dependent genes involved in apoptosis / negative regulation of motor neuron apoptotic process / positive regulation of multicellular organism growth / regulation of viral genome replication / 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 / fertilization / regulation of growth / calcium ion transport into cytosol / response to UV-B / negative regulation of ossification / response to iron ion / axon regeneration / epithelial cell apoptotic process / negative regulation of mitochondrial depolarization / Bcl-2 family protein complex / motor neuron apoptotic process / positive regulation of smooth muscle cell migration / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / negative regulation of B cell apoptotic process / organ growth / branching involved in ureteric bud morphogenesis / hair follicle morphogenesis / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / digestive tract morphogenesis / B cell lineage commitment / hepatocyte apoptotic process / negative regulation of G1/S transition of mitotic cell cycle / pore complex / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / apoptotic mitochondrial changes / germ cell development / BH3 domain binding / T cell homeostasis / B cell homeostasis / regulation of calcium ion transport / B cell proliferation / humoral immune response / negative regulation of anoikis / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hematopoietic stem cell differentiation
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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 / 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
NICKEL (II) ION / NITRILOTRIACETIC ACID / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsSeo, H.-S. / DeAngelo, T.M. / Bird, G.H. / Walensky, L.D. / Dhe-Paganon, S.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into chemoresistance mutants of BCL-2 and their targeting by stapled BAD BH3 helices
Authors: DeAngelo, T.M. / Adhikary, U. / Korshavn, K.J. / Seo, H.S. / Brotzen-Smith, C.R. / Camara, C.M. / Dhe-Paganon, S. / Bird, G.H. / Wales, T.E. / Walensky, L.D.
History
DepositionApr 3, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: stapled BAD BH3 peptide BAD SAHB 4.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4475
Polymers22,1392
Non-polymers3093
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-28 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.920, 58.530, 61.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 19357.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide stapled BAD BH3 peptide BAD SAHB 4.2


Mass: 2781.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NTA / NITRILOTRIACETIC ACID


Mass: 191.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 15.0% PEG-3350 and 150 mM CsCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.73→38.84 Å / Num. obs: 20222 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.049 / Rrim(I) all: 0.133 / Net I/σ(I): 9 / Num. measured all: 146346
Reflection shellResolution: 1.73→1.76 Å / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 2.053 / Num. measured all: 6910 / Num. unique obs: 976 / CC1/2: 0.3 / Rpim(I) all: 1.01 / Rrim(I) all: 2.699 / Net I/σ(I) obs: 0.8

-
Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
xia2data scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→32.85 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 1017 5.04 %
Rwork0.1948 --
obs0.1962 20172 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→32.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 15 104 1483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031410
X-RAY DIFFRACTIONf_angle_d0.6411900
X-RAY DIFFRACTIONf_dihedral_angle_d14.44510
X-RAY DIFFRACTIONf_chiral_restr0.038187
X-RAY DIFFRACTIONf_plane_restr0.005246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.820.33291170.29792706X-RAY DIFFRACTION100
1.82-1.940.27861640.25242665X-RAY DIFFRACTION100
1.94-2.080.28251410.21132709X-RAY DIFFRACTION100
2.08-2.290.22341390.1872716X-RAY DIFFRACTION100
2.29-2.630.19281480.18282721X-RAY DIFFRACTION100
2.63-3.310.2571400.19622770X-RAY DIFFRACTION100
3.31-32.850.19441680.1822868X-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)
11.1863-0.4481-0.9532.1791-1.1061.83650.0245-0.0253-0.3801-0.1575-0.05810.13230.7404-0.2860.00070.2662-0.0258-0.00640.25940.02740.2915-2.235-3.2025.67
20.988-0.35210.10370.81480.16641.73880.3686-0.3841-0.39070.3396-0.3201-0.30760.6792-0.11970.00630.29640.02610.00980.29920.04970.32239.694-4.1254.363
30.3588-0.3576-0.00990.361-0.04090.51750.52870.0901-0.3080.1631-0.6802-0.2228-0.75240.21330.00270.4108-0.0009-0.03330.3690.04090.322611.9319.515.028
40.67150.14910.55920.4477-0.20870.960.11980.10470.50490.1418-0.06630.1808-0.4409-0.38660.00630.24970.00380.02540.2819-0.02990.279-0.08116.5758.808
51.6459-0.39340.20590.93130.07731.07130.0209-0.0108-0.0090.0950.0593-0.0569-0.0249-0.0722-0.00030.22890.01280.00960.1964-0.00520.23365.7887.9594.474
63.0051-0.4003-1.86542.7210.67193.23390.01160.002-0.0664-0.08780.0452-0.10930.08760.1489-0.00030.1835-0.0051-0.01360.2073-0.0080.18382.2964.079-1.562
71.34030.8586-0.37740.9325-0.95991.45520.0011-0.05720.0793-0.0339-0.0681-0.4056-0.0830.23530.00010.2457-0.0153-0.01870.30560.01320.260714.29812.8685.309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 9:32 )A9 - 32
2X-RAY DIFFRACTION2( CHAIN A AND RESID 92:107 )A92 - 107
3X-RAY DIFFRACTION3( CHAIN A AND RESID 108:117 )A108 - 117
4X-RAY DIFFRACTION4( CHAIN A AND RESID 118:137 )A118 - 137
5X-RAY DIFFRACTION5( CHAIN A AND RESID 138:163 )A138 - 163
6X-RAY DIFFRACTION6( CHAIN A AND RESID 164:206 )A164 - 206
7X-RAY DIFFRACTION7( CHAIN B AND RESID 303:323 )B303 - 323

+
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