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- PDB-8dgz: Caspase-7 bound to substrate mimic and allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 8dgz
TitleCaspase-7 bound to substrate mimic and allosteric inhibitor
Components
  • Ac-Asp-Glu-Val-Asp-Aldehyde
  • Caspase-7
KeywordsAPOPTOSIS/APOPTOSIS INHIBITOR / allostery / inhibitor / ternary / APOPTOSIS-APOPTOSIS INHIBITOR complex
Function / homology
Function and homology information


caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / 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 / fibroblast apoptotic process / execution phase of apoptosis ...caspase-7 / lymphocyte apoptotic process / positive regulation of plasma membrane repair / cellular response to staurosporine / 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 / fibroblast apoptotic process / execution phase of apoptosis / Apoptotic cleavage of cellular proteins / Caspase-mediated cleavage of cytoskeletal proteins / response to UV / striated muscle cell differentiation / cysteine-type peptidase activity / protein maturation / protein catabolic process / protein processing / fibrillar center / peptidase activity / positive regulation of neuron apoptotic process / heart development / cellular response to lipopolysaccharide / neuron apoptotic process / aspartic-type endopeptidase activity / defense response to bacterium / cysteine-type endopeptidase activity / apoptotic process / proteolysis / extracellular space / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Peptidase C14 family / 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 ...Peptidase C14 family / 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
Similarity search - Domain/homology
Ac-Asp-Glu-Val-Asp-Aldehyde / Chem-8YJ / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPropp, J. / Kalenkiewicz, A. / Kathryn, F.H. / Spies, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138471-01 United States
CitationJournal: Chemistry / Year: 2023
Title: Allosteric Tuning of Caspase-7: Establishing the Nexus of Structure and Catalytic Power.
Authors: Hobbs, K.F. / Propp, J. / Vance, N.R. / Kalenkiewicz, A. / Witkin, K.R. / Ashley Spies, M.
History
DepositionJun 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 22, 2023Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7
B: Caspase-7
C: Ac-Asp-Glu-Val-Asp-Aldehyde
D: Ac-Asp-Glu-Val-Asp-Aldehyde
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4165
Polymers70,1094
Non-polymers3071
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-23 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.045, 89.045, 183.623
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
11(chain A and (resid 57 through 94 or (resid 95...
21(chain B and (resid 57 through 58 or (resid 59...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRALAALA(chain A and (resid 57 through 94 or (resid 95...AA57 - 9459 - 96
12GLUGLUALAALA(chain A and (resid 57 through 94 or (resid 95...AA95 - 9697 - 98
13THRTHRSERSER(chain A and (resid 57 through 94 or (resid 95...AA57 - 30259 - 304
14THRTHRSERSER(chain A and (resid 57 through 94 or (resid 95...AA57 - 30259 - 304
15THRTHRSERSER(chain A and (resid 57 through 94 or (resid 95...AA57 - 30259 - 304
16THRTHRSERSER(chain A and (resid 57 through 94 or (resid 95...AA57 - 30259 - 304
21THRTHRTYRTYR(chain B and (resid 57 through 58 or (resid 59...BB57 - 5859 - 60
22GLNGLNGLNGLN(chain B and (resid 57 through 58 or (resid 59...BB5961
23ARGARGGLNGLN(chain B and (resid 57 through 58 or (resid 59...BB52 - 30354 - 305
24ARGARGGLNGLN(chain B and (resid 57 through 58 or (resid 59...BB52 - 30354 - 305
25ARGARGGLNGLN(chain B and (resid 57 through 58 or (resid 59...BB52 - 30354 - 305
26ARGARGGLNGLN(chain B and (resid 57 through 58 or (resid 59...BB52 - 30354 - 305

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Components

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


Mass: 34566.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein/peptide Ac-Asp-Glu-Val-Asp-Aldehyde


Type: Peptide-like / Class: Inhibitor / Mass: 488.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: Ac-Asp-Glu-Val-Asp-Aldehyde
#3: Chemical ChemComp-8YJ / 2-{[2-(4-chlorophenyl)-2-oxoethyl]sulfanyl}benzoic acid


Mass: 306.764 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11ClO3S / Feature type: SUBJECT OF INVESTIGATION
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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M sodium citrate and 2.1 M sodium formate / PH range: 5-5.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→47.94 Å / Num. obs: 21470 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.036 / Rrim(I) all: 0.111 / Net I/σ(I): 15 / Num. measured all: 211549
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.9510.42.4193191730560.5540.7842.5450.9100
8.85-47.948.10.04162397720.9990.0150.04443.899.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1f1j

1f1j


Resolution: 2.8→47.94 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2535 1103 5.16 %
Rwork0.2333 20261 -
obs0.2344 21364 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.33 Å2 / Biso mean: 107.8184 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.8→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 90 0 3210
Biso mean--136.42 --
Num. residues----428
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1647X-RAY DIFFRACTION9.364TORSIONAL
12B1647X-RAY DIFFRACTION9.364TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.930.49031490.42892448259799
2.93-3.080.37871280.32725172645100
3.08-3.270.32731160.312124972613100
3.27-3.530.33831370.247724982635100
3.53-3.880.23151400.223725002640100
3.88-4.440.231190.214225772696100
4.44-5.590.2161300.217625612691100
5.6-47.940.24331840.218826632847100

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