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- PDB-7yaa: Crystal structure analysis of cp3 bound BCLxl -

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Basic information

Entry
Database: PDB / ID: 7yaa
TitleCrystal structure analysis of cp3 bound BCLxl
Components
  • Bcl-2-like protein 1
  • cp3 peptide
KeywordsAPOPTOSIS / Complex
Function / homology
Function and homology information


apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis ...apoptotic process in bone marrow cell / SARS-CoV-1-mediated effects on programmed cell death / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of dendritic cell apoptotic process / negative regulation of execution phase of apoptosis / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / fertilization / regulation of mitochondrial membrane permeability / negative regulation of protein localization to plasma membrane / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / cellular response to alkaloid / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / negative regulation of reproductive process / negative regulation of developmental process / negative regulation of release of cytochrome c from mitochondria / BH3 domain binding / germ cell development / apoptotic mitochondrial changes / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of 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 / negative regulation of autophagy / release of cytochrome c from mitochondria / regulation of mitochondrial membrane potential / regulation of cytokinesis / epithelial cell proliferation / response to cytokine / cellular response to amino acid stimulus / cellular response to gamma radiation / synaptic vesicle membrane / endocytosis / RAS processing / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / nuclear membrane / Interleukin-4 and Interleukin-13 signaling / neuron apoptotic process / defense response to virus / in utero embryonic development / mitochondrial outer membrane / negative regulation of neuron apoptotic process / mitochondrial inner membrane / mitochondrial matrix / protein heterodimerization activity / centrosome / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein homodimerization activity / 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 (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-JJ9 / Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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: Bcl-2-like protein 1
B: cp3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8784
Polymers17,4692
Non-polymers4092
Water2,864159
1
A: Bcl-2-like protein 1
B: cp3 peptide
hetero molecules

A: Bcl-2-like protein 1
B: cp3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7568
Polymers34,9374
Non-polymers8194
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area7010 Å2
ΔGint-38 kcal/mol
Surface area14640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.520, 99.874, 51.197
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.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07817
#2: Protein/peptide cp3 peptide


Mass: 1278.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-JJ9 / N-(2-acetamidoethyl)-4-(4-methanoyl-1,3-thiazol-2-yl)benzamide


Mass: 317.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15N3O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: PEG 400, Tris, Magnesium chloride

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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: DECTRIS PILATUS 6M / Detector: PIXEL / 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: 1.4→50 Å / Num. obs: 35428 / % possible obs: 99.4 % / Redundancy: 12.5 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.04 / Rrim(I) all: 0.142 / Χ2: 0.977 / Net I/σ(I): 5.7 / Num. measured all: 444458
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.4-1.4210.40.59617470.8810.9680.1820.6250.90397.4
1.42-1.4511.50.52817140.920.9790.1560.5520.91298.9
1.45-1.4812.10.47517370.940.9840.1390.4960.94299.6
1.48-1.5112.50.41517670.9580.9890.120.4330.94899.8
1.51-1.5412.50.38417510.9620.990.1120.4010.97199.7
1.54-1.5811.90.35917370.9590.990.1070.3750.9999.7
1.58-1.6212.60.31517650.9730.9930.0910.3281.0399.5
1.62-1.6613.40.28317790.9770.9940.080.2941.05499.8
1.66-1.7113.20.25917470.980.9950.0740.271.03999.7
1.71-1.7613.10.23117550.9840.9960.0660.2411.03199.6
1.76-1.8312.80.21517660.9820.9950.0620.2241.07199.5
1.83-1.911.80.1917710.9830.9960.0570.1991.05599.3
1.9-1.9913.50.17317550.9880.9970.0490.1791.0499.8
1.99-2.0913.30.15517810.9890.9970.0440.1611.01999.7
2.09-2.2213.10.14417710.9860.9960.0420.151.01699.4
2.22-2.3912.20.13717810.9880.9970.0410.1430.98399.4
2.39-2.6313.30.12817890.9940.9980.0360.1330.96199.9
2.63-3.0213.20.12118090.990.9970.0350.1260.92199.7
3.02-3.812.30.11118040.9930.9980.0330.1160.85398.9
3.8-5012.10.10319020.9940.9990.0310.1080.76799

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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: 1.4→24.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.795 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18147 1743 5 %RANDOM
Rwork0.16222 ---
obs0.1632 32773 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å20 Å2
2---0.06 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.4→24.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 28 159 1405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181144
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.6551740
X-RAY DIFFRACTIONr_angle_other_deg2.6911.5942620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3985151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.97222.32973
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7415195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.631158
X-RAY DIFFRACTIONr_chiral_restr0.0940.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021472
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02331
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_it1.7711.356603
X-RAY DIFFRACTIONr_mcbond_other1.6931.353602
X-RAY DIFFRACTIONr_mcangle_it2.5072.024752
X-RAY DIFFRACTIONr_mcangle_other2.512.025753
X-RAY DIFFRACTIONr_scbond_it3.0171.641681
X-RAY DIFFRACTIONr_scbond_other3.0151.642682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5972.355988
X-RAY DIFFRACTIONr_long_range_B_refined5.5425.9945259
X-RAY DIFFRACTIONr_long_range_B_other5.5425.9925259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.434 Å
RfactorNum. reflection% reflection
Rfree0.271 120 -
Rwork0.241 1852 -
obs--75.88 %

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