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- PDB-5k20: Caspase-7 S239E Phosphomimetic -

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Basic information

Entry
Database: PDB / ID: 5k20
TitleCaspase-7 S239E Phosphomimetic
Components
  • Caspase-7 large subunitCaspase 7
  • Caspase-7 small subunitCaspase 7
KeywordsHYDROLASE / protease / phosphomimetic / PAK2 / phosphorylation
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / cysteine-type endopeptidase activity involved in apoptotic process ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / 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 / Apoptotic cleavage of cellular proteins / protein maturation / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / cysteine-type peptidase activity / striated muscle cell differentiation / protein catabolic process / protein processing / positive regulation of neuron apoptotic process / heart development / peptidase activity / neuron apoptotic process / cellular response to lipopolysaccharide / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / 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
FORMIC ACID / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsEron, S.J. / Hardy, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM080532 United States
CitationJournal: To Be Published
Title: PAK2 Phosphorylation Inhibits Caspase-7 by Two Divergent Mechanisms: Slowing Activation and Blocking Substrate Binding
Authors: Eron, S.J. / Hardy, J.A.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7 large subunit
B: Caspase-7 small subunit
C: Caspase-7 large subunit
D: Caspase-7 small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0487
Polymers70,9104
Non-polymers1383
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-82 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.757, 88.757, 185.141
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRGLNGLNAA57 - 19657 - 196
21THRTHRGLNGLNCC357 - 49657 - 196
12LYSLYSSERSERBB212 - 30214 - 104
22LYSLYSSERSERDD512 - 60214 - 104

NCS ensembles :
ID
1
2
Detailstetramer according to gel filtration, mass spectrometry, gel electroporesis, literature reports. This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303).

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Components

#1: Protein Caspase-7 large subunit / Caspase 7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 22189.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The large subunit of caspase-7 crystallized here consisted of residues 24-198.
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 small subunit / Caspase 7 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13265.836 Da / Num. of mol.: 2 / Mutation: S272E
Source method: isolated from a genetically manipulated source
Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This ...Details: This structure is of active, cleaved caspase-7. A procaspase-7 dimer becomes active, cleaved caspase-7 upon proteolytic processing, which cleaves after residues D23, D198 and D206. This generates four chains from each monomer. The prodomain (residues 1-23) and the intersubunit linker (residues 199-206) are both released. Thus active, cleaved caspase-7 has two copies of the large subunit (residues 24-198) and two copies of the small subunit (residues 206-303). The small subunit of caspase-7 crystallized here consisted of residues 206-303 (including a 6xHis tag).
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55210, caspase-7
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.07 Å3/Da / Density % sol: 59.87 % / Description: Rhomboids of 240 x 340 microns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 2.1 M Sodium Formate 100 mM Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→76.98 Å / Num. obs: 43569 / % possible obs: 99.53 % / Redundancy: 10.9 % / Biso Wilson estimate: 66.3 Å2 / Rsym value: 0.076 / Net I/σ(I): 37.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALAdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IBF

3ibf


Resolution: 2.2→76.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 12.25 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 4298 9.9 %RANDOM
Rwork0.1912 ---
obs0.1948 39208 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 150.17 Å2 / Biso mean: 66.342 Å2 / Biso min: 40.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å20 Å2
3----4.99 Å2
Refinement stepCycle: final / Resolution: 2.2→76.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3734 0 9 92 3835
Biso mean--68.7 57.58 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193804
X-RAY DIFFRACTIONr_bond_other_d0.0050.023579
X-RAY DIFFRACTIONr_angle_refined_deg1.7691.9545117
X-RAY DIFFRACTIONr_angle_other_deg1.1538255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2385461
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85324.324185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.15415679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191520
X-RAY DIFFRACTIONr_chiral_restr0.1010.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024306
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02898
X-RAY DIFFRACTIONr_mcbond_it3.3464.2921856
X-RAY DIFFRACTIONr_mcbond_other3.3564.2941857
X-RAY DIFFRACTIONr_mcangle_it4.4336.4172313
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76060.14
12C76060.14
21B50330.09
22D50330.09
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 326 -
Rwork0.312 2862 -
all-3188 -
obs--99.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.20550.0181-0.13022.43910.68283.1275-0.04610.25740.2948-0.3340.065-0.0407-0.31710.1396-0.01890.2116-0.0852-0.03430.1348-0.01250.0681122.8256-26.6215179.6025
25.4323-0.9380.44734.43330.1513.8758-0.00810.2571-0.0619-0.09090.0889-0.42880.17780.5016-0.08080.1635-0.0345-0.01440.1566-0.04010.0593129.0836-27.3294192.1863
31.3798-0.6322-0.29983.3749-0.03561.9230.05360.1296-0.0379-0.12580.0413-0.03460.02630.0678-0.09490.0699-0.0286-0.01230.0765-0.0180.0136124.8821-6.1454205.4867
45.2692-0.99950.33374.2230.19814.3199-0.01340.14740.2634-0.0563-0.01410.4503-0.2123-0.47120.02750.1338-0.0365-0.01170.1105-0.0080.0958115.1274-14.0748200.0693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A57 - 196
2X-RAY DIFFRACTION2B212 - 303
3X-RAY DIFFRACTION3C357 - 496
4X-RAY DIFFRACTION4D511 - 603

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