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- PDB-7yb7: anti-apoptotic protein BCL-2-M12 -

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Basic information

Entry
Database: PDB / ID: 7yb7
Titleanti-apoptotic protein BCL-2-M12
Components
  • Apoptosis regulator Bcl-2,Bcl-2-like protein 1
  • cp2 peptide
KeywordsAPOPTOSIS / BCL-2 / M12 mutants / anti-apoptotic / cyclic peptide
Function / homology
Function and homology information


channel inhibitor activity / 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 / melanin metabolic process ...channel inhibitor activity / 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 / melanin metabolic process / myeloid cell apoptotic process / cochlear nucleus development / osteoblast proliferation / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / 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 / SARS-CoV-1-mediated effects on programmed cell death / stem cell development / dendritic cell proliferation / lymphoid progenitor cell differentiation / positive regulation of mononuclear cell proliferation / T cell apoptotic process / melanocyte differentiation / 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 / negative regulation of dendritic cell apoptotic process / negative regulation of T cell apoptotic process / B cell apoptotic process / glomerulus development / regulation of nitrogen utilization / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of multicellular organism growth / metanephros development / Regulation of MITF-M-dependent genes involved in apoptosis / neuron maturation / focal adhesion assembly / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / oocyte development / negative regulation of execution phase of apoptosis / endoplasmic reticulum calcium ion homeostasis / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / response to UV-B / calcium ion transport into cytosol / response to iron ion / negative regulation of ossification / motor neuron apoptotic process / negative regulation of mitochondrial depolarization / axon regeneration / epithelial cell apoptotic process / Bcl-2 family protein complex / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / intrinsic apoptotic signaling pathway in response to oxidative stress / organ growth / negative regulation of B cell apoptotic process / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / apoptotic mitochondrial changes / digestive tract morphogenesis / response to cycloheximide / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / STAT5 activation downstream of FLT3 ITD mutants / B cell lineage commitment / cellular response to alkaloid / positive regulation of smooth muscle cell migration / negative regulation of G1/S transition of mitotic cell cycle / hepatocyte apoptotic process / pore complex / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of intrinsic apoptotic signaling pathway / T cell homeostasis / germ cell development / BH3 domain binding / B cell homeostasis / humoral immune response / B cell proliferation / negative regulation of apoptotic signaling pathway / negative regulation of anoikis / regulation of calcium ion transport / extrinsic apoptotic signaling pathway via death domain receptors / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling
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
Chem-IQ8 / Apoptosis regulator Bcl-2 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, F.W. / Liu, C. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2024
Title: Cyclic peptides discriminate BCL-2 and its clinical mutants from BCL-X L by engaging a single-residue discrepancy.
Authors: Li, F. / Liu, J. / Liu, C. / Liu, Z. / Peng, X. / Huang, Y. / Chen, X. / Sun, X. / Wang, S. / Chen, W. / Xiong, D. / Diao, X. / Wang, S. / Zhuang, J. / Wu, C. / Wu, D.
History
DepositionJun 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
B: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
C: cp2 peptide
D: cp2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6296
Polymers38,0464
Non-polymers5832
Water4,702261
1
A: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
C: cp2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3143
Polymers19,0232
Non-polymers2911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-2 kcal/mol
Surface area7900 Å2
MethodPISA
2
B: Apoptosis regulator Bcl-2,Bcl-2-like protein 1
D: cp2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3143
Polymers19,0232
Non-polymers2911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-2 kcal/mol
Surface area7930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.761, 104.788, 111.525
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 17593.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2, BCL2L1, BCL2L, BCLX / Production host: Escherichia coli (E. coli) / References: UniProt: P10415, UniProt: Q07817
#2: Protein/peptide cp2 peptide


Mass: 1429.575 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This is a cyclic peptide, with a special linker IQ8 connected with A and C.
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-IQ8 / N-(2-acetamidoethyl)-4-(4,5-dihydro-1,3-thiazol-2-yl)benzamide


Mass: 291.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 0.5 M Ammonium sulfate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 1.0 M Lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29689 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.023 / Rrim(I) all: 0.107 / Χ2: 1.044 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.25-2.2922.30.4327420.9870.9970.0930.4421.143100
2.29-2.3324.20.3927560.9850.9960.0810.4011.13100
2.33-2.3824.10.3467600.9880.9970.0720.3541.139100
2.38-2.42240.3427400.990.9970.0710.351.1100
2.42-2.4823.60.2997680.9890.9970.0630.3061.123100
2.48-2.5323.50.2687330.990.9980.0560.2741.16100
2.53-2.623.20.237570.9940.9980.0480.2351.151100
2.6-2.6722.60.227610.9940.9980.0470.2251.194100
2.67-2.7521.10.1857510.9920.9980.0410.191.247100
2.75-2.83230.1637690.9950.9990.0350.1671.143100
2.83-2.9423.70.1457600.9960.9990.030.1481.094100
2.94-3.0523.80.1337560.9970.9990.0280.1361.099100
3.05-3.1923.40.1277730.9960.9990.0270.131.098100
3.19-3.3623.10.117630.9970.9990.0230.1131.026100
3.36-3.5721.30.1057770.9960.9990.0230.1081.058100
3.57-3.85230.1027810.9970.9990.0210.1041.057100
3.85-4.2323.40.0967770.9970.9990.020.0980.971100
4.23-4.8522.50.0867900.9980.9990.0180.0880.847100
4.85-6.1210.0738190.9960.9990.0160.0750.602100
6.1-5020.10.0628860.99810.0150.0640.51899.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.52 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.256 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19375 1656 5.3 %RANDOM
Rwork0.17522 ---
obs0.17626 29689 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.972 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0 Å2
2--0.2 Å20 Å2
3----0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.2→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 0 261 2737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0132542
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182241
X-RAY DIFFRACTIONr_angle_refined_deg1.9611.6533437
X-RAY DIFFRACTIONr_angle_other_deg1.5531.6035119
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3765288
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83621.779163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78615392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2421520
X-RAY DIFFRACTIONr_chiral_restr0.0930.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6063.0251174
X-RAY DIFFRACTIONr_mcbond_other3.5933.0261173
X-RAY DIFFRACTIONr_mcangle_it5.1234.5041456
X-RAY DIFFRACTIONr_mcangle_other5.1214.5031457
X-RAY DIFFRACTIONr_scbond_it5.7973.6761364
X-RAY DIFFRACTIONr_scbond_other5.7963.6761364
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8535.2691980
X-RAY DIFFRACTIONr_long_range_B_refined11.22857.15810665
X-RAY DIFFRACTIONr_long_range_B_other11.25256.87410477
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A45870.09
12B45870.09
21C2980.12
22D2980.12
LS refinement shellResolution: 2.2→2.253 Å
RfactorNum. reflection% reflection
Rfree0.242 111 -
Rwork0.194 2105 -
obs--96.9 %

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