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- PDB-3r85: Crystal structure of human SOUL BH3 domain in complex with Bcl-xL -

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Basic information

Entry
Database: PDB / ID: 3r85
TitleCrystal structure of human SOUL BH3 domain in complex with Bcl-xL
Components
  • Bcl-2-like protein 1
  • Heme-binding protein 2
KeywordsAPOPTOSIS / Bcl-2-like protein / Inhibitor of cell death / SOUL 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 / negative regulation of release of cytochrome c from mitochondria / cellular response to alkaloid / negative regulation of intrinsic apoptotic signaling pathway / apoptotic mitochondrial changes / germ cell development / negative regulation of reproductive process / negative regulation of developmental process / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of protein localization to plasma membrane / ectopic germ cell programmed cell death / 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 / 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 / azurophil granule lumen / 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 / heme binding / Neutrophil degranulation / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm
Similarity search - Function
SOUL haem-binding protein / SOUL heme-binding protein / Regulatory factor, effector binding domain superfamily / 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. ...SOUL haem-binding protein / SOUL heme-binding protein / Regulatory factor, effector binding domain superfamily / 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
Bcl-2-like protein 1 / Heme-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsAmbrosi, E.K. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
CitationJournal: Biochem.J. / Year: 2011
Title: Structural changes in the BH3 domain of SOUL protein upon interaction with the anti-apoptotic protein Bcl-xL.
Authors: Ambrosi, E. / Capaldi, S. / Bovi, M. / Saccomani, G. / Perduca, M. / Monaco, H.L.
History
DepositionMar 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn / software
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Bcl-2-like protein 1
C: Bcl-2-like protein 1
D: Bcl-2-like protein 1
E: Heme-binding protein 2
F: Heme-binding protein 2
G: Heme-binding protein 2
H: Heme-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1129
Polymers83,0168
Non-polymers961
Water3,099172
1
A: Bcl-2-like protein 1
E: Heme-binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8503
Polymers20,7542
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area9380 Å2
MethodPISA
2
B: Bcl-2-like protein 1
F: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,7542
Polymers20,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-18 kcal/mol
Surface area9540 Å2
MethodPISA
3
C: Bcl-2-like protein 1
G: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,7542
Polymers20,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-14 kcal/mol
Surface area9400 Å2
MethodPISA
4
D: Bcl-2-like protein 1
H: Heme-binding protein 2


Theoretical massNumber of molelcules
Total (without water)20,7542
Polymers20,7542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area9710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.830, 66.830, 175.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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


Mass: 17788.781 Da / Num. of mol.: 4
Fragment: residues 1-209 with the deletion of residues 27-82
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q07817
#2: Protein/peptide
Heme-binding protein 2 / Placental protein 23 / PP23 / Protein SOUL


Mass: 2965.315 Da / Num. of mol.: 4 / Fragment: residues 147 to 172 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y5Z4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium sulphate, 15% PEG 6000, 0.3M 1-butyl-3-methylimidazolium 2-(2-methoxyethoxy)ethyl sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2010
RadiationMonochromator: liquid-nitrogen-cooled channel-cut silicon [111] monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
Reflection twinType: merohedral / Operator: h,-k,-l / Fraction: 0.503
ReflectionResolution: 1.95→53.1 Å / Num. all: 54709 / Num. obs: 54709 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 17.6
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 6 / % possible all: 96.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXJ

2yxj


Resolution: 1.95→36.737 Å / Cross valid method: THROUGHOUT / σ(F): 1.44 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 2802 5.12 %Random
Rwork0.211 ---
all0.2143 54709 --
obs0.2143 54700 97.97 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.97 Å2 / ksol: 0.421 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3523 Å2-0 Å20 Å2
2---3.3523 Å2-0 Å2
3---6.7046 Å2
Refinement stepCycle: LAST / Resolution: 1.95→36.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 5 172 5309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095248
X-RAY DIFFRACTIONf_angle_d1.1247095
X-RAY DIFFRACTIONf_dihedral_angle_d17.1871869
X-RAY DIFFRACTIONf_chiral_restr0.068753
X-RAY DIFFRACTIONf_plane_restr0.004916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.98290.32291310.30612519X-RAY DIFFRACTION90
1.9829-2.01890.32451460.28882602X-RAY DIFFRACTION92
2.0189-2.05770.31461310.28172547X-RAY DIFFRACTION93
2.0577-2.09970.31461430.27462607X-RAY DIFFRACTION93
2.0997-2.14530.34631340.28042576X-RAY DIFFRACTION93
2.1453-2.19520.28681440.25922581X-RAY DIFFRACTION93
2.1952-2.250.29491500.25882605X-RAY DIFFRACTION93
2.25-2.31080.25681220.26462605X-RAY DIFFRACTION94
2.3108-2.37870.31281320.25342593X-RAY DIFFRACTION94
2.3787-2.45540.28731510.24472587X-RAY DIFFRACTION93
2.4554-2.54310.33311670.24712556X-RAY DIFFRACTION92
2.5431-2.64480.28091430.24252603X-RAY DIFFRACTION93
2.6448-2.7650.27961330.22632623X-RAY DIFFRACTION94
2.765-2.91050.26591330.21432608X-RAY DIFFRACTION94
2.9105-3.09250.24561480.20722594X-RAY DIFFRACTION93
3.0925-3.33060.23071570.19942624X-RAY DIFFRACTION93
3.3306-3.66470.22771210.16442634X-RAY DIFFRACTION94
3.6647-4.19230.19281350.14932620X-RAY DIFFRACTION94
4.1923-5.2720.23551380.15072607X-RAY DIFFRACTION93
5.272-23.44280.28161290.21852591X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 30.6976 Å / Origin y: 36.4093 Å / Origin z: 96.1212 Å
111213212223313233
T0.0598 Å2-0.005 Å20.0183 Å2-0.0493 Å20.0206 Å2--0.0633 Å2
L0.0481 °2-0.0047 °2-0.0037 °2-0.0316 °2-0.0162 °2---0.0053 °2
S0.0071 Å °0.0014 Å °0.0153 Å °0.0291 Å °-0.0195 Å °0.0121 Å °-0.0022 Å °0.0028 Å °0.0046 Å °
Refinement TLS groupSelection details: all

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