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- PDB-6bdv: Crystal structure of Caspase 3 S150A -

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Basic information

Entry
Database: PDB / ID: 6bdv
TitleCrystal structure of Caspase 3 S150A
Components
  • (Caspase-3 subunit ...Caspase 3) x 2
  • Acetyl-Asp-Glu-Val-Asp-CMK
KeywordsAPOPTOSIS / allosteric regulation / biophysics / caspase / computational biology / fluorescence / molecular dynamics / protein evolution
Function / homology
Function and homology information


caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis ...caspase-3 / Stimulation of the cell death response by PAK-2p34 / phospholipase A2 activator activity / anterior neural tube closure / intrinsic apoptotic signaling pathway in response to osmotic stress / leukocyte apoptotic process / positive regulation of pyroptotic inflammatory response / glial cell apoptotic process / NADE modulates death signalling / luteolysis / response to cobalt ion / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / death-inducing signaling complex / cyclin-dependent protein serine/threonine kinase inhibitor activity / cellular response to staurosporine / Apoptosis induced DNA fragmentation / cysteine-type endopeptidase activity involved in execution phase of apoptosis / Caspase activation via Dependence Receptors in the absence of ligand / Apoptotic cleavage of cell adhesion proteins / death receptor binding / SMAC, XIAP-regulated apoptotic response / axonal fasciculation / Activation of caspases through apoptosome-mediated cleavage / Signaling by Hippo / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process / fibroblast apoptotic process / execution phase of apoptosis / negative regulation of cytokine production / epithelial cell apoptotic process / platelet formation / Other interleukin signaling / positive regulation of amyloid-beta formation / Apoptotic cleavage of cellular proteins / negative regulation of B cell proliferation / pyroptotic inflammatory response / T cell homeostasis / negative regulation of activated T cell proliferation / neurotrophin TRK receptor signaling pathway / B cell homeostasis / protein maturation / negative regulation of cell cycle / response to X-ray / regulation of macroautophagy / Caspase-mediated cleavage of cytoskeletal proteins / cell fate commitment / response to amino acid / Pyroptosis / response to tumor necrosis factor / enzyme activator activity / response to glucose / response to UV / response to glucocorticoid / keratinocyte differentiation / striated muscle cell differentiation / Degradation of the extracellular matrix / intrinsic apoptotic signaling pathway / erythrocyte differentiation / hippocampus development / apoptotic signaling pathway / sensory perception of sound / response to nicotine / protein catabolic process / regulation of protein stability / neuron differentiation / response to hydrogen peroxide / protein processing / response to wounding / positive regulation of neuron apoptotic process / response to estradiol / heart development / peptidase activity / neuron apoptotic process / protease binding / response to lipopolysaccharide / aspartic-type endopeptidase activity / learning or memory / response to hypoxia / response to xenobiotic stimulus / cysteine-type endopeptidase activity / neuronal cell body / apoptotic process / DNA damage response / protein-containing complex binding / proteolysis / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues ...Caspase-like / Rossmann fold - #1460 / Peptidase family C14A, His active site / Caspase family histidine active site. / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. / Caspase family p10 domain profile. / Peptidase C14A, caspase catalytic domain / Caspase, interleukin-1 beta converting enzyme (ICE) homologues / Peptidase C14, p20 domain / Caspase family p20 domain profile. / : / Caspase domain / Caspase-like domain superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-CMK / AZIDE ION / Caspase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.938 Å
AuthorsThomas, M.E. / Grinshpon, R. / Swartz, P.D. / Clark, A.C.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Modifications to a common phosphorylation network provide individualized control in caspases.
Authors: Thomas, M.E. / Grinshpon, R. / Swartz, P. / Clark, A.C.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3086
Polymers32,1893
Non-polymers1193
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-43 kcal/mol
Surface area10980 Å2
MethodPISA
2
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules

A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules

A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules

A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,23424
Polymers128,75612
Non-polymers47812
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area35720 Å2
ΔGint-217 kcal/mol
Surface area31050 Å2
MethodPISA
3
A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules

A: Caspase-3 subunit p17
B: Caspase-3 subunit p12
C: Acetyl-Asp-Glu-Val-Asp-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,61712
Polymers64,3786
Non-polymers2396
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+21
Buried area16190 Å2
ΔGint-104 kcal/mol
Surface area17190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.753, 84.405, 96.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Caspase-3 subunit ... , 2 types, 2 molecules AB

#1: Protein Caspase-3 subunit p17 / Caspase 3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1


Mass: 19743.344 Da / Num. of mol.: 1 / Fragment: UNP residues 1-175 / Mutation: S150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3
#2: Protein Caspase-3 subunit p12 / Caspase 3 / CASP-3 / Apopain / Cysteine protease CPP32 / CPP-32 / Protein Yama / SREBP cleavage activity 1 / SCA-1


Mass: 11910.604 Da / Num. of mol.: 1 / Mutation: S150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP3, CPP32 / Production host: Escherichia coli (E. coli) / References: UniProt: P42574, caspase-3

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Acetyl-Asp-Glu-Val-Asp-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 534.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Ac-Asp-Glu-Val-Asp-CMK

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Non-polymers , 3 types, 178 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM ...Details: Crystals were obtained at 18 C by the hanging drop vapor diffusion method using 4 mL drops that contained equal volumes of protein and reservoir solutions over a 0.5 mL solution of 100 mM sodium citrate, pH 4.9-5.2, 8-18 % PEG 6000 (w/v), 10 mM DTT, and 3 mM NaN3. Crystals appeared within 3-5 days and were briefly immersed in a cryogenic solution containing 10% MPD (2-methylpentane-2,4-diol) and 90% reservoir solution.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.938→50 Å / Num. obs: 20793 / % possible obs: 99.8 % / Redundancy: 6.9 % / Net I/σ(I): 25.47

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.938→35.585 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1963 1999 9.62 %
Rwork0.1587 --
obs0.1623 20780 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.938→35.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 7 175 2091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062037
X-RAY DIFFRACTIONf_angle_d0.8492759
X-RAY DIFFRACTIONf_dihedral_angle_d7.0941658
X-RAY DIFFRACTIONf_chiral_restr0.055302
X-RAY DIFFRACTIONf_plane_restr0.004355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9377-1.98620.27391310.24071227X-RAY DIFFRACTION94
1.9862-2.03990.25281410.20981330X-RAY DIFFRACTION99
2.0399-2.09990.25861420.20021332X-RAY DIFFRACTION100
2.0999-2.16760.2371420.18741328X-RAY DIFFRACTION100
2.1676-2.24510.2211410.16571323X-RAY DIFFRACTION100
2.2451-2.3350.22381430.16211341X-RAY DIFFRACTION100
2.335-2.44120.19911410.15411329X-RAY DIFFRACTION100
2.4412-2.56990.2091430.1551348X-RAY DIFFRACTION100
2.5699-2.73080.21541440.16341342X-RAY DIFFRACTION100
2.7308-2.94160.20871420.17081338X-RAY DIFFRACTION100
2.9416-3.23750.21561440.16091359X-RAY DIFFRACTION100
3.2375-3.70550.17271440.13671355X-RAY DIFFRACTION100
3.7055-4.66690.14371480.12341379X-RAY DIFFRACTION100
4.6669-35.59140.17921530.16871450X-RAY DIFFRACTION100

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