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- PDB-7y90: Crystal Structure Analysis of cp1 bound BCL2 -

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Basic information

Entry
Database: PDB / ID: 7y90
TitleCrystal Structure Analysis of cp1 bound BCL2
Components
  • Apoptosis regulator Bcl-2
  • cp1 peptide
KeywordsAPOPTOSIS / BCL2 / cp1 / complex
Function / homology
Function and homology information


: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / 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 ...: / negative regulation of retinal cell programmed cell death / pigment granule organization / BCL-2 complex / 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 / positive regulation of neuron maturation / channel inhibitor activity / myeloid cell apoptotic process / osteoblast proliferation / cochlear nucleus development / mesenchymal cell development / retinal cell programmed cell death / negative regulation of osteoblast proliferation / stem cell development / renal system process / gland morphogenesis / dendritic cell apoptotic process / regulation of cell-matrix adhesion / The NLRP1 inflammasome / ear development / negative regulation of calcium ion transport into cytosol / T cell apoptotic process / negative regulation of myeloid cell apoptotic process / lymphoid progenitor cell differentiation / melanocyte differentiation / 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 / regulation of nitrogen utilization / negative regulation of T cell apoptotic process / B cell apoptotic process / focal adhesion assembly / glomerulus development / metanephros development / neuron maturation / negative regulation of motor neuron apoptotic process / regulation of viral genome replication / endoplasmic reticulum calcium ion homeostasis / positive regulation of multicellular organism growth / Regulation of MITF-M-dependent genes involved in apoptosis / calcium ion transport into cytosol / oocyte development / epithelial cell apoptotic process / regulation of mitochondrial membrane permeability / negative regulation of ossification / response to UV-B / response to iron ion / motor neuron apoptotic process / axon regeneration / negative regulation of mitochondrial depolarization / organ growth / smooth muscle cell migration / NFE2L2 regulating tumorigenic genes / negative regulation of B cell apoptotic process / intrinsic apoptotic signaling pathway in response to oxidative stress / hair follicle morphogenesis / branching involved in ureteric bud morphogenesis / positive regulation of smooth muscle cell migration / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / digestive tract morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / B cell lineage commitment / pore complex / negative regulation of intrinsic apoptotic signaling pathway / B cell homeostasis / T cell homeostasis / regulation of calcium ion transport / humoral immune response / B cell proliferation / negative regulation of anoikis / BH3 domain binding / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / negative regulation of apoptotic signaling pathway / extrinsic apoptotic signaling pathway via death domain receptors / Activation of BAD and translocation to mitochondria / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / hematopoietic stem cell differentiation / ovarian follicle development / behavioral fear response / cellular response to glucose starvation / spleen development / skeletal muscle fiber development / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of B cell proliferation / response to cytokine / axonogenesis / reactive oxygen species metabolic process / homeostasis of number of cells within a tissue / release of cytochrome c from mitochondria / ossification / protein phosphatase 2A binding / response to glucocorticoid / thymus development / negative regulation of cell migration
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-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 / Apoptosis regulator Bcl-2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLi, F.W.
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 1.0Nov 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 23, 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
B: cp1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2773
Polymers20,7892
Non-polymers4881
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-1 kcal/mol
Surface area7630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.602, 99.611, 52.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

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Components

#1: Protein Apoptosis regulator Bcl-2


Mass: 19427.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2 / Production host: Escherichia phage EcSzw_1 (virus) / 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.: 87 / 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: 2.21 Å3/Da / Density % sol: 44.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M Bis-Tris pH6.5, 2.0M Ammonium Sulfate

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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: Nov 8, 2020
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 10380 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.983 / CC star: 0.996 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.031 / Rrim(I) all: 0.109 / Χ2: 0.978 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2
2.1-2.1410.50.4485130.9750.9940.1410.4710.958
2.14-2.1810.60.4084880.9740.9930.130.4290.943
2.18-2.2211.40.365260.9790.9950.110.3760.98
2.22-2.2612.80.3355000.9890.9970.0970.3491.037
2.26-2.3113.10.3515000.9810.9950.1010.3661.015
2.31-2.3713.30.3065020.9860.9960.0870.3181.019
2.37-2.4213.20.2675230.9890.9970.0770.2781.008
2.42-2.4913.20.2515220.9890.9970.0720.2611.019
2.49-2.5613.30.2365050.9910.9980.0680.2461.053
2.56-2.6512.90.1945080.9920.9980.0560.2021.003
2.65-2.7412.10.1675230.9960.9990.050.1741.1
2.74-2.8511.90.1565180.9930.9980.0470.1631.045
2.85-2.9813.40.1385150.9930.9980.0390.1431.016
2.98-3.1413.50.1225190.9950.9990.0350.1271.023
3.14-3.3313.20.1055220.9970.9990.030.1090.96
3.33-3.5913.10.0925160.9960.9990.0270.0960.982
3.59-3.9512.10.0875280.9980.9990.0260.0911.009
3.95-4.52120.0785300.9980.9990.0240.0820.834
4.52-5.7130.0745410.9950.9990.0210.0770.743
5.7-5011.40.085810.9930.9980.0250.0840.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→32.82 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.861 / SU B: 5.383 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27562 488 5.1 %RANDOM
Rwork0.22002 ---
obs0.22281 9132 92.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.136 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0 Å2
2---0.1 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.09→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 111 87 1308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131254
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181111
X-RAY DIFFRACTIONr_angle_refined_deg1.8691.771699
X-RAY DIFFRACTIONr_angle_other_deg1.4011.6892527
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19620.70471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.7315177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8651511
X-RAY DIFFRACTIONr_chiral_restr0.080.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021417
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02340
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_it1.9462.428549
X-RAY DIFFRACTIONr_mcbond_other1.9472.428547
X-RAY DIFFRACTIONr_mcangle_it2.9623.619684
X-RAY DIFFRACTIONr_mcangle_other2.9613.619684
X-RAY DIFFRACTIONr_scbond_it3.3542.828704
X-RAY DIFFRACTIONr_scbond_other3.3512.827705
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0594.1191016
X-RAY DIFFRACTIONr_long_range_B_refined7.55846.3615313
X-RAY DIFFRACTIONr_long_range_B_other7.55946.3585311
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.094→2.148 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 22 -
Rwork0.217 471 -
obs--66.09 %

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