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- PDB-4zvr: Caspase-7 Variant 4 (V4) with reprogrammed substrate specificity ... -

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Basic information

Entry
Database: PDB / ID: 4zvr
TitleCaspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to DEVD inhibitor.
Components
  • (Caspase-7) x 2
  • Peptide ACE-ASP-GLU-VAL-ASJ
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 / positive regulation of neuron apoptotic process / peptidase activity / 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 / cytosol / cytoplasm
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
Ac-Asp-Glu-Val-Asp-Aldehyde / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 6, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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-ASP-GLU-VAL-ASJ
F: Peptide ACE-ASP-GLU-VAL-ASJ


Theoretical massNumber of molelcules
Total (without water)71,6276
Polymers71,6276
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-82 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.980, 87.980, 187.311
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: 13135.732 Da / Num. of mol.: 2 / Fragment: UNP residues 232-336 / Mutation: Y230V,W232Y,S234V,Q276D
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-ASP-GLU-VAL-ASJ


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
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: 2.3→76.19 Å / Num. obs: 38059 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Rsym value: 0.104 / Net I/σ(I): 12.3 / Num. measured all: 282011 / Scaling rejects: 14
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
2.3-2.387.60.7942.82769736620.8620.32999.7
8.91-76.196.60.02729.448917420.9990.01198.3

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Processing

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

3edr


Resolution: 2.3→70.577 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 24.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1838 4.82 %Random Selection
Rwork0.1829 ---
obs0.1848 38013 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→70.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 0 129 3907
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093858
X-RAY DIFFRACTIONf_angle_d1.3235190
X-RAY DIFFRACTIONf_dihedral_angle_d15.6131434
X-RAY DIFFRACTIONf_chiral_restr0.06560
X-RAY DIFFRACTIONf_plane_restr0.006676
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33150.34131150.29142741X-RAY DIFFRACTION100
2.3315-2.36480.31491520.2672679X-RAY DIFFRACTION100
2.3648-2.40010.3261700.27392716X-RAY DIFFRACTION100
2.4001-2.43760.26631320.26612771X-RAY DIFFRACTION100
2.4376-2.47760.32511290.25222700X-RAY DIFFRACTION100
2.4776-2.52030.321200.25542798X-RAY DIFFRACTION100
2.5203-2.56620.23511330.24722723X-RAY DIFFRACTION100
2.5662-2.61550.3071450.24072759X-RAY DIFFRACTION100
2.6155-2.66890.25341500.22932746X-RAY DIFFRACTION100
2.6689-2.72690.27361330.23352720X-RAY DIFFRACTION100
2.7269-2.79040.27661280.21792757X-RAY DIFFRACTION100
2.7904-2.86020.26451420.21432697X-RAY DIFFRACTION100
2.8602-2.93750.27071190.20892792X-RAY DIFFRACTION100
2.9375-3.02390.26441440.20242770X-RAY DIFFRACTION100
3.0239-3.12150.23421840.19652647X-RAY DIFFRACTION100
3.1215-3.23310.22011390.19432780X-RAY DIFFRACTION100
3.2331-3.36260.231170.18532728X-RAY DIFFRACTION100
3.3626-3.51560.1951310.17312763X-RAY DIFFRACTION100
3.5156-3.70090.19661330.15852730X-RAY DIFFRACTION100
3.7009-3.93280.1931310.15962748X-RAY DIFFRACTION100
3.9328-4.23640.19111430.14342772X-RAY DIFFRACTION100
4.2364-4.66270.18261460.12962724X-RAY DIFFRACTION100
4.6627-5.33720.16761600.13272712X-RAY DIFFRACTION100
5.3372-6.72340.1731150.17062775X-RAY DIFFRACTION100
6.7234-70.61050.23531530.16422702X-RAY DIFFRACTION99

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