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- PDB-7ca4: The Crystal Structure of human Bcl-2-like protein 1 from Biortus -

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Basic information

Entry
Database: PDB / ID: 7ca4
TitleThe Crystal Structure of human Bcl-2-like protein 1 from Biortus
ComponentsBcl-2-like protein 1
KeywordsAPOPTOSIS / Apoptosis regulator proteins / Bcl-2 family
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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process ...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 execution phase of apoptosis / negative regulation of dendritic cell apoptotic process / 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
Bcl-2-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, F. / Lv, Z. / Lin, D. / Huang, Y.
CitationJournal: To Be Published
Title: The Crystal Structure of human Bcl-2-like protein 1 from Biortus.
Authors: Wang, F. / Lv, Z. / Lin, D. / Huang, Y.
History
DepositionJun 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Structure summary / Category: citation / database_2 / struct
Item: _citation.title / _database_2.pdbx_DOI ..._citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bcl-2-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9504
Polymers25,6621
Non-polymers2883
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.213, 63.213, 111.009
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 25662.111 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: Escherichia coli (E. coli) / References: UniProt: Q07817
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 43.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 50mM MES, pH6.2, 1.8M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 6656 / % possible obs: 99.7 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 16.69
Reflection shellResolution: 2.7→2.75 Å / Rmerge(I) obs: 0.601 / Num. unique obs: 330

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cva

3cva


Resolution: 2.7→31.954 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.373 / SU ML: 0.194 / Cross valid method: FREE R-VALUE / ESU R: 0.493 / ESU R Free: 0.275
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2284 327 4.936 %
Rwork0.1984 6298 -
all0.2 --
obs-6625 99.759 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.341 Å2-0 Å2-0 Å2
2--0.341 Å2-0 Å2
3----0.683 Å2
Refinement stepCycle: LAST / Resolution: 2.7→31.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 15 30 1206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131202
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181050
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.6281627
X-RAY DIFFRACTIONr_angle_other_deg1.1531.5712424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.485141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38622.36172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.82815192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.327158
X-RAY DIFFRACTIONr_chiral_restr0.050.2142
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02287
X-RAY DIFFRACTIONr_nbd_refined0.1920.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.2911
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2582
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.2530
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.213
X-RAY DIFFRACTIONr_nbd_other0.1890.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.26
X-RAY DIFFRACTIONr_mcbond_it1.8034.167570
X-RAY DIFFRACTIONr_mcbond_other1.8044.161569
X-RAY DIFFRACTIONr_mcangle_it3.1116.224709
X-RAY DIFFRACTIONr_mcangle_other3.1096.231710
X-RAY DIFFRACTIONr_scbond_it1.944.575632
X-RAY DIFFRACTIONr_scbond_other1.9094.437618
X-RAY DIFFRACTIONr_scangle_it3.3836.756918
X-RAY DIFFRACTIONr_scangle_other3.3626.561900
X-RAY DIFFRACTIONr_lrange_it7.02547.7571407
X-RAY DIFFRACTIONr_lrange_other7.02447.791405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.316280.223454X-RAY DIFFRACTION99.5868
2.77-2.8460.27190.242440X-RAY DIFFRACTION100
2.846-2.9280.21220.24423X-RAY DIFFRACTION100
2.928-3.0180.317150.232429X-RAY DIFFRACTION100
3.018-3.1170.235210.238399X-RAY DIFFRACTION100
3.117-3.2260.274190.218396X-RAY DIFFRACTION100
3.226-3.3470.248220.214381X-RAY DIFFRACTION100
3.347-3.4830.283240.222355X-RAY DIFFRACTION100
3.483-3.6380.166150.22356X-RAY DIFFRACTION100
3.638-3.8140.194250.186337X-RAY DIFFRACTION100
3.814-4.0190.204120.179325X-RAY DIFFRACTION100
4.019-4.2620.316140.177323X-RAY DIFFRACTION100
4.262-4.5540.18170.16290X-RAY DIFFRACTION100
4.554-4.9160.253140.166268X-RAY DIFFRACTION99.6466
4.916-5.3810.15120.179252X-RAY DIFFRACTION100
5.381-6.0090.284170.214236X-RAY DIFFRACTION100
6.009-6.9250.317120.228210X-RAY DIFFRACTION100
6.925-8.4480.21270.149183X-RAY DIFFRACTION99.4764
8.448-11.8080.13170.146153X-RAY DIFFRACTION99.3789
11.808-31.9540.1650.24788X-RAY DIFFRACTION89.4231

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