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- PDB-4zvq: Caspase-7 Variant 2 (V2) with reprogrammed substrate specificity ... -

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Basic information

Entry
Database: PDB / ID: 4zvq
TitleCaspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to VEID inhibitor.
Components
  • (Caspase-7) x 2
  • Peptide ACE-VAL-GLU-ILE-ASA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Directed Evolution / Protease / Peptide Inhibitor / Designed Active Site Specificity / HYDROLASE-HYDROLASE 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
Caspase-like / Rossmann fold - #1460 / 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-like / Rossmann fold - #1460 / 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 / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHill, M.E. / MacPherson, D.J. / Hardy, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM080532 United States
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Reprogramming Caspase-7 Specificity by Regio-Specific Mutations and Selection Provides Alternate Solutions for Substrate Recognition.
Authors: Hill, M.E. / MacPherson, D.J. / Wu, P. / Julien, O. / Wells, J.A. / Hardy, J.A.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Structure summary
Revision 1.2Jul 6, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Caspase-7
D: Caspase-7
E: Peptide ACE-VAL-GLU-ILE-ASA
F: Peptide ACE-VAL-GLU-ILE-ASA


Theoretical massNumber of molelcules
Total (without water)71,5076
Polymers71,5076
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16270 Å2
ΔGint-85 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.890, 86.890, 187.711
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 22189.203 Da / Num. of mol.: 2 / Fragment: UNP residues 34-231
Source method: isolated from a genetically manipulated source
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 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13079.757 Da / Num. of mol.: 2 / Fragment: UNP residues 232-336 / Mutation: Y230V/W232M/Q276C
Source method: isolated from a genetically manipulated source
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: Protein/peptide Peptide ACE-VAL-GLU-ILE-ASA


Type: Polypeptide / Class: Inhibitor / Mass: 484.543 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-acetyl-L-valyl-L-alpha-glutamyl-N-[(2S)-1-carboxy-3-oxopropan-2-yl]-L-isoleucinamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.5→93.86 Å / Num. obs: 29209 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 38.19 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.042 / Rsym value: 0.097 / Net I/σ(I): 12.4 / Num. measured all: 196222 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.5-2.66.90.533.42238632330.860.231100
9.01-93.865.90.03723.941957140.9980.01798.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.1.1data reduction
PHASER2.5.5phasing
PDB_EXTRACT3.15data extraction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EDR

3edr


Resolution: 2.5→69.846 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1415 4.85 %Random selection
Rwork0.1753 ---
obs0.1769 29152 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→69.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 0 99 3874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033849
X-RAY DIFFRACTIONf_angle_d0.875174
X-RAY DIFFRACTIONf_dihedral_angle_d14.5671434
X-RAY DIFFRACTIONf_chiral_restr0.034562
X-RAY DIFFRACTIONf_plane_restr0.003671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.54560.31611310.26812758X-RAY DIFFRACTION100
2.5456-2.59460.29911540.27022717X-RAY DIFFRACTION100
2.5946-2.64760.27021510.24772799X-RAY DIFFRACTION100
2.6476-2.70510.26981250.23982714X-RAY DIFFRACTION100
2.7051-2.76810.27691210.22072787X-RAY DIFFRACTION100
2.7681-2.83730.24871450.22882726X-RAY DIFFRACTION100
2.8373-2.9140.29481310.21042769X-RAY DIFFRACTION100
2.914-2.99980.2841440.20922752X-RAY DIFFRACTION100
2.9998-3.09660.25581810.20572651X-RAY DIFFRACTION100
3.0966-3.20720.27111410.19382783X-RAY DIFFRACTION100
3.2072-3.33570.21481160.1882796X-RAY DIFFRACTION100
3.3357-3.48750.22971320.17642734X-RAY DIFFRACTION100
3.4875-3.67130.18661340.14762715X-RAY DIFFRACTION100
3.6713-3.90130.18421350.15082762X-RAY DIFFRACTION100
3.9013-4.20250.16851330.14132721X-RAY DIFFRACTION100
4.2025-4.62540.13171460.13322764X-RAY DIFFRACTION100
4.6254-5.29450.17431610.13972724X-RAY DIFFRACTION100
5.2945-6.66960.18821200.18452777X-RAY DIFFRACTION100
6.6696-69.8730.17381560.15342709X-RAY DIFFRACTION99

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