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- PDB-7y8d: Crystal structure of cp1 bound BCLxl -

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Basic information

Entry
Database: PDB / ID: 7y8d
TitleCrystal structure of cp1 bound BCLxl
Components
  • Bcl-2-like protein 1
  • cp1 peptide
KeywordsAPOPTOSIS / anti-apoptosis protein
Function / homology
Function and homology information


apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / 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 ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / 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 intrinsic apoptotic signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / germ cell development / apoptotic mitochondrial changes / 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / channel activity / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / nuclear membrane / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / cytoplasm / 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-JFF / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, F.W. / Liu, C. / Wu, C.L. / Wu, D.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) 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 23, 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 1.2Oct 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: cp1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0883
Polymers17,6002
Non-polymers4881
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-2 kcal/mol
Surface area9310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.803, 99.366, 51.359
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 16238.185 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: ecological metagenomes (others) / References: UniProt: Q07817
#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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M HEPES pH7.5, 2.0M Ammonium formate

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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: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 19, 2020 / Details: mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12248 / % possible obs: 98.2 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Χ2: 0.959 / Net I/σ(I): 7.1 / Num. measured all: 156882
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0311.70.6635970.9070.1970.6930.95595.7
2.03-2.0711.50.5625990.910.1710.5891.00296.9
2.07-2.1111.80.5195910.9360.1550.5431.01298.5
2.11-2.1511.60.3925940.9570.1190.4110.99496.3
2.15-2.211.90.3775950.9570.1120.3941.00999.2
2.2-2.2513.60.3216010.9830.0890.3340.99596.9
2.25-2.3113.60.2976100.9860.0820.309199.2
2.31-2.3713.70.2575860.9870.0710.2670.99297.7
2.37-2.4413.50.2146190.9940.060.2230.96798.3
2.44-2.5213.50.1846010.9930.0520.1910.96399.5
2.52-2.6113.30.1556050.9960.0440.1610.97197.9
2.61-2.7112.80.1266230.9960.0360.1310.95498.6
2.71-2.8411.90.16060.9950.030.1040.95898.5
2.84-2.9913.70.0846160.9980.0230.0870.9599
2.99-3.1713.90.0676180.9990.0180.0690.97398.9
3.17-3.4213.50.0536150.9990.0150.0550.95698.9
3.42-3.7613.20.0426390.9990.0120.0430.96799.4
3.76-4.3112.10.0336090.9990.010.0350.90397
4.31-5.4313.40.0316460.9990.0090.0330.91999.5
5.43-50120.02967810.0080.030.76998.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF2

Resolution: 2→49.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.089 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 570 4.9 %RANDOM
Rwork0.1875 ---
obs0.1903 11034 93.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.36 Å2 / Biso mean: 29.24 Å2 / Biso min: 11.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å20 Å2
2---0.29 Å2-0 Å2
3----0.55 Å2
Refinement stepCycle: final / Resolution: 2→49.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 111 73 1323
Biso mean--34.35 38.54 -
Num. residues----140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131286
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181141
X-RAY DIFFRACTIONr_angle_refined_deg1.911.7561744
X-RAY DIFFRACTIONr_angle_other_deg1.4371.6822608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.7622.25471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06615188
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.284158
X-RAY DIFFRACTIONr_chiral_restr0.0710.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021471
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02348
LS refinement shellResolution: 2→2.05 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.272 25 -
Rwork0.217 593 -
obs--68.14 %

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