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

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Basic information

Entry
Database: PDB / ID: 4zvo
TitleCaspase-7 Variant 4 (V4) with reprogrammed substrate specificity due to Y230V/W232Y/S234V/Q276D substitutions bound to VEID inhibitor.
Components
  • (Caspase-7) x 2
  • Peptide ACE-VAL-GLU-ILE-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 / 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-hydroxypropan-2-yl]-L-isoleucinamide / Caspase-7
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 / _software.classification
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 / 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
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

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


Theoretical massNumber of molelcules
Total (without water)71,6236
Polymers71,6236
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15780 Å2
ΔGint-90 kcal/mol
Surface area17920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.268, 88.268, 187.278
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
11chain A
21chain C
12chain B
22chain D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: GLN / End label comp-ID: GLN

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRTYRchain AAA58 - 19658 - 196
21THRTHRchain CCC357 - 49657 - 196
12TYRTYRchain BBB211 - 30313 - 105
22TYRTYRchain DDD511 - 60313 - 105

NCS ensembles :
ID
1
2

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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-VAL-GLU-ILE-ASJ


Type: Peptide-like / Class: Inhibitor / Mass: 486.559 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-hydroxypropan-2-yl]-L-isoleucinamide
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 300 mM diammonium citrate, 14% PEG 3350, 10 mM GuHCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 20412 / % possible obs: 99.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 68.72 Å2 / Rsym value: 0.111 / Χ2: 1.628 / Net I/av σ(I): 15.669 / Net I/σ(I): 8.2 / Num. measured all: 91241
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.85-2.954.30.5952.119971.38199.8
2.95-3.074.40.45719931.36799.9
3.07-3.214.50.34819851.48599.8
3.21-3.384.50.26420351.4799.9
3.38-3.594.40.15419981.83699.8
3.59-3.874.40.12720361.83399.9
3.87-4.264.40.120341.92999.6
4.26-4.874.50.07320531.97999.9
4.87-6.144.70.07320791.544100
6.14-504.50.04122021.45499.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.5phasing
PHENIX1.9-169refinement
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
iMOSFLM7.1.1data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EDR

3edr


Resolution: 2.85→38.221 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 975 4.85 %Retained from MR search model 3EDR
Rwork0.2092 19119 --
obs0.2112 20094 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.13 Å2 / Biso mean: 65.5049 Å2 / Biso min: 44.18 Å2
Refinement stepCycle: final / Resolution: 2.85→38.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 0 7 3796
Biso mean---59.46 -
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053865
X-RAY DIFFRACTIONf_angle_d1.1765200
X-RAY DIFFRACTIONf_chiral_restr0.051564
X-RAY DIFFRACTIONf_plane_restr0.005675
X-RAY DIFFRACTIONf_dihedral_angle_d15.3091436
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1248X-RAY DIFFRACTION10.216TORSIONAL
12C1248X-RAY DIFFRACTION10.216TORSIONAL
21B844X-RAY DIFFRACTION10.216TORSIONAL
22D844X-RAY DIFFRACTION10.216TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.85-2.99990.32331250.31542567269295
2.9999-3.18780.3421680.29342667283599
3.1878-3.43380.36411110.27032711282299
3.4338-3.7790.26731320.21452739287199
3.779-4.32520.25081310.19142736286799
4.3252-5.44680.18681600.16842776293699
5.4468-38.22460.23811480.192729233071100

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