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- PDB-7y99: Crystal Structure Analysis of cp2 bound BCLxl -

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Basic information

Entry
Database: PDB / ID: 7y99
TitleCrystal Structure Analysis of cp2 bound BCLxl
Components
  • Bcl-2-like protein 1
  • CP2 peptide
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 ...The NLRP1 inflammasome / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / RAS processing / apoptotic process in bone marrow cell / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / 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 / fertilization / regulation of growth / regulation of mitochondrial membrane permeability / Bcl-2 family protein complex / response to cycloheximide / cellular response to alkaloid / hepatocyte apoptotic process / negative regulation of release of cytochrome c from mitochondria / negative regulation of reproductive process / negative regulation of developmental process / germ cell development / BH3 domain binding / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ovarian follicle development / extrinsic apoptotic signaling pathway in absence of ligand / response to cytokine / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / mitochondrion organization / cellular response to amino acid stimulus / mitochondrial membrane / response to radiation / cellular response to gamma radiation / response to virus / synaptic vesicle membrane / intrinsic apoptotic signaling pathway in response to DNA damage / male gonad development / neuron apoptotic process / spermatogenesis / nuclear membrane / defense response to virus / negative regulation of neuron apoptotic process / in utero embryonic development / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of apoptotic process / apoptotic process / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / mitochondrion / identical protein binding / membrane / cytosol
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 / Apoptosis regulator, Bcl-2, BH3 motif, conserved site / Apoptosis regulator, Bcl-2 family BH3 motif signature. ...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 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 24, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.2Feb 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 1.3Oct 9, 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: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9113
Polymers17,6202
Non-polymers2911
Water1,49583
1
A: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules

A: Bcl-2-like protein 1
B: CP2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8226
Polymers35,2394
Non-polymers5832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7220 Å2
ΔGint-36 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.433, 100.478, 51.326
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16190.101 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bcl2l1, Bcl2l, Bclx / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64373
#2: Protein/peptide CP2 peptide


Mass: 1429.575 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Molecule 2 is a cyclic peptide, IQ8 is a special linker 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.: 1 / Source method: obtained synthetically / Formula: C14H17N3O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: Ammonium acetate, BIS-TRIS, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14253 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 0.975 / CC star: 0.994 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.045 / Rrim(I) all: 0.159 / Χ2: 0.961 / Net I/σ(I): 7.9 / Num. measured all: 179227
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9312.80.4926670.9560.9890.1410.5120.99399.9
1.93-1.9712.90.4097100.9660.9910.1180.4260.931100
1.97-2.0112.80.386860.9710.9930.1090.3950.957100
2.01-2.0512.60.3217150.9760.9940.0930.3340.94100
2.05-2.0912.60.2917190.980.9950.0850.3031.041100
2.09-2.14120.2586930.980.9950.0760.2690.956100
2.14-2.1911.20.2386930.9790.9950.0740.251.013100
2.19-2.25130.2187150.9860.9960.0630.2281.053100
2.25-2.3213.20.2077020.9860.9960.0590.2160.971100
2.32-2.39130.1947060.9840.9960.0560.2020.953100
2.39-2.4813.10.1817080.9840.9960.0520.1890.957100
2.48-2.5812.80.1697120.9880.9970.0490.1760.921100
2.58-2.712.60.167020.9890.9970.0470.1670.92699.7
2.7-2.8411.50.1517230.9870.9970.0460.1580.97299.9
2.84-3.0213.30.1457150.9890.9970.0410.1510.924100
3.02-3.2513.20.1417160.9920.9980.040.1470.909100
3.25-3.5812.90.1377280.9880.9970.0390.1420.909100
3.58-4.0911.70.1377210.9880.9970.0410.1430.97899.7
4.09-5.1612.70.1327390.990.9980.0390.1380.93699.9
5.16-5011.50.1447830.9540.9880.0450.1521.00299.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data scaling
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.49 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.756 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19217 697 5 %RANDOM
Rwork0.17446 ---
obs0.17538 13311 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å2-0 Å2-0 Å2
2---0.11 Å2-0 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.9→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 0 83 1330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131281
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181144
X-RAY DIFFRACTIONr_angle_refined_deg1.8451.6531734
X-RAY DIFFRACTIONr_angle_other_deg1.5551.6012620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3635148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57922.07877
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58315199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.579159
X-RAY DIFFRACTIONr_chiral_restr0.0910.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02338
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_it2.381.895599
X-RAY DIFFRACTIONr_mcbond_other2.2441.89598
X-RAY DIFFRACTIONr_mcangle_it3.3342.817746
X-RAY DIFFRACTIONr_mcangle_other3.3322.82747
X-RAY DIFFRACTIONr_scbond_it3.4322.322681
X-RAY DIFFRACTIONr_scbond_other3.3912.321681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3163.332989
X-RAY DIFFRACTIONr_long_range_B_refined7.36135.0715140
X-RAY DIFFRACTIONr_long_range_B_other7.32934.9465100
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 38 -
Rwork0.206 831 -
obs--86.04 %

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