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- PDB-7ya5: Crystal structure analysis of cp1 bound BCL2/G101V -

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Basic information

Entry
Database: PDB / ID: 7ya5
TitleCrystal structure analysis of cp1 bound BCL2/G101V
Components
  • Apoptosis regulator Bcl-2
  • cp1 peptide
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation ...negative regulation of cellular pH reduction / negative regulation of retinal cell programmed cell death / pigment granule organization / channel inhibitor activity / CD8-positive, alpha-beta T cell lineage commitment / BAD-BCL-2 complex / regulation of glycoprotein biosynthetic process / melanin metabolic process / positive regulation of skeletal muscle fiber development / positive regulation of melanocyte differentiation / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / positive regulation of neuron maturation / negative regulation of osteoblast proliferation / gland morphogenesis / renal system process / regulation of cell-matrix adhesion / T cell apoptotic process / stem cell development / negative regulation of calcium ion transport into cytosol / melanocyte differentiation / The NLRP1 inflammasome / dendritic cell apoptotic process / ear development / lymphoid progenitor cell differentiation / negative regulation of myeloid cell apoptotic process / negative regulation of epithelial cell apoptotic process / regulation of nitrogen utilization / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / B cell apoptotic process / negative regulation of T cell apoptotic process / glomerulus development / negative regulation of dendritic cell apoptotic process / oocyte development / positive regulation of multicellular organism growth / metanephros development / neuron maturation / regulation of viral genome replication / negative regulation of motor neuron apoptotic process / focal adhesion assembly / endoplasmic reticulum calcium ion homeostasis / negative regulation of ossification / negative regulation of B cell apoptotic process / response to UV-B / regulation of mitochondrial membrane permeability / response to iron ion / calcium ion transport into cytosol / channel activity / negative regulation of mitochondrial depolarization / motor neuron apoptotic process / axon regeneration / epithelial cell apoptotic process / smooth muscle cell migration / intrinsic apoptotic signaling pathway in response to oxidative stress / NFE2L2 regulating tumorigenic genes / organ growth / digestive tract morphogenesis / branching involved in ureteric bud morphogenesis / hair follicle morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / : / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / B cell lineage commitment / pore complex / positive regulation of smooth muscle cell migration / B cell proliferation / T cell homeostasis / BH3 domain binding / regulation of calcium ion transport / B cell homeostasis / negative regulation of apoptotic signaling pathway / humoral immune response / negative regulation of anoikis / extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / Activation of BAD and translocation to mitochondria / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / behavioral fear response / cellular response to glucose starvation / skeletal muscle fiber development / negative regulation of intrinsic apoptotic signaling pathway / ovarian follicle development / positive regulation of B cell proliferation / response to glucocorticoid / homeostasis of number of cells within a tissue / extrinsic apoptotic signaling pathway in absence of ligand / spleen development / reactive oxygen species metabolic process / negative regulation of autophagy / negative regulation of cell migration / ossification / axonogenesis / release of cytochrome c from mitochondria / post-embryonic development
Similarity search - Function
Apoptosis regulator, Bcl-2 / 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 / 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 (B-Cell lymphoma); contains BH1, BH2 regions / Bcl-2 family / Bcl-2, Bcl-2 homology region 1-3 / Bcl2-like / Apoptosis regulator proteins, Bcl-2 family / BCL2-like apoptosis inhibitors family profile. / Bcl-2-like superfamily
Similarity search - Domain/homology
Chem-JFF / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLi, F.W. / Liu, C. / Wu, C.L. / 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 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Apoptosis regulator Bcl-2
B: cp1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2493
Polymers20,7612
Non-polymers4881
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.726, 50.054, 48.693
Angle α, β, γ (deg.)90.000, 107.580, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19399.637 Da / Num. of mol.: 1 / Mutation: G101V
Source method: isolated from a genetically manipulated source
Details: N-terminal 1-34 and C-terminal 92-207 residues from database UNP P10415 linked with linker residues DVEENRTEAPEGTESE
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10415
#2: Protein/peptide cp1 peptide


Mass: 1361.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-JFF / (2R)-3-[2-(aminomethyl)-3-azanyl-1-[4-[2-(2-chloranylethanoylamino)ethylcarbamoyl]phenyl]prop-1-enyl]sulfanyl-2-(carboxyamino)propanoic acid


Mass: 487.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26ClN5O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: Calcium acetate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 21, 2021 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 13695 / % possible obs: 92.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.059 / Rrim(I) all: 0.106 / Χ2: 0.937 / Net I/σ(I): 6.7 / Num. measured all: 39933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.85-1.882.50.3425220.8660.2390.420.86971.9
1.88-1.922.50.3915370.8660.2740.480.9574.2
1.92-1.952.60.375900.8930.2610.4551.00778.6
1.95-1.992.70.3035900.9110.2140.3730.94979.9
1.99-2.042.70.296180.9130.2030.3560.94986.4
2.04-2.082.70.2716570.9190.1910.3340.98186.9
2.08-2.142.80.2446440.9350.1710.30.99389
2.14-2.192.60.1916840.9620.1380.2370.92191.9
2.19-2.2630.1997410.9610.1350.2420.93197.4
2.26-2.333.10.197260.9670.1270.230.90699.2
2.33-2.413.20.1637330.9770.1090.1970.8699.3
2.41-2.513.10.1537300.9760.10.1840.97298.5
2.51-2.633.20.1367170.9810.0890.1630.96598
2.63-2.7630.1137380.9840.0780.1380.97998.1
2.76-2.942.90.097350.9880.0630.1110.91598.3
2.94-3.163.20.0837510.990.0540.0990.86999.9
3.16-3.483.20.0787430.9870.0520.0940.94798.8
3.48-3.9930.0677200.9890.0460.0820.8898
3.99-5.0230.0657550.9870.0440.0790.9198.8
5.02-5030.0737640.990.0490.0891.03297.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→29.22 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 3.567 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2435 584 5.1 %RANDOM
Rwork0.1907 ---
obs0.1934 10965 77.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.95 Å2 / Biso mean: 26.543 Å2 / Biso min: 13.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20.77 Å2
2---1.47 Å20 Å2
3---1.89 Å2
Refinement stepCycle: final / Resolution: 1.85→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 111 108 1381
Biso mean--21.46 38.24 -
Num. residues----139
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131309
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181150
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.7611773
X-RAY DIFFRACTIONr_angle_other_deg1.4681.6862619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32620.3781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23215191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9761513
X-RAY DIFFRACTIONr_chiral_restr0.080.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02367
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 20 -
Rwork0.215 456 -
all-476 -
obs--43.99 %

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