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

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Basic information

Entry
Database: PDB / ID: 4zvp
TitleCaspase-7 Variant 2 (V2) with reprogrammed substrate specificity due to Y230V/W232M/Q276C substitutions bound to DEVD inhibitor.
Components
  • (Caspase-7) x 2
  • Peptide ACE-ASP-GLU-VAL-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 / 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
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 1.1Jul 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 / 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 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 30, 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-ASP-GLU-VAL-ASA
F: Peptide ACE-ASP-GLU-VAL-ASA


Theoretical massNumber of molelcules
Total (without water)71,5116
Polymers71,5116
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16010 Å2
ΔGint-83 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 86.790, 187.571
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: 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-ASP-GLU-VAL-ASA


Mass: 486.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
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: 2.5→93.79 Å / Num. obs: 29117 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 45.27 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.058 / Rsym value: 0.142 / Net I/σ(I): 8.4 / Num. measured all: 217941 / Scaling rejects: 37
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
2.5-2.67.50.5163.32425432190.9260.212100
9.01-93.796.50.05313.746217090.9970.02298.3

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Processing

Software
NameVersionClassification
SCALA7.1.1data scaling
PHASER2.5.5phasing
PHENIX1.9-169refinement
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EDR

3edr


Resolution: 2.5→69.769 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 1409 4.85 %Random selection
Rwork0.1666 27645 --
obs0.1693 29054 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.29 Å2 / Biso mean: 45.4659 Å2 / Biso min: 26.47 Å2
Refinement stepCycle: final / Resolution: 2.5→69.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3775 0 0 76 3851
Biso mean---41.63 -
Num. residues----475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073849
X-RAY DIFFRACTIONf_angle_d1.135174
X-RAY DIFFRACTIONf_chiral_restr0.049560
X-RAY DIFFRACTIONf_plane_restr0.004673
X-RAY DIFFRACTIONf_dihedral_angle_d14.0251434
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1288X-RAY DIFFRACTION4.781TORSIONAL
12C1288X-RAY DIFFRACTION4.781TORSIONAL
21B890X-RAY DIFFRACTION4.781TORSIONAL
22D890X-RAY DIFFRACTION4.781TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58940.31631410.227126892830100
2.5894-2.69310.2841390.213627342873100
2.6931-2.81570.29011280.200427342862100
2.8157-2.96410.24041440.198827212865100
2.9641-3.14980.26571670.203727002867100
3.1498-3.3930.29091120.191727822894100
3.393-3.73440.2431370.155627512888100
3.7344-4.27480.19281300.14327952925100
4.2748-5.38550.16931630.134728012964100
5.3855-69.79640.20221480.15852938308699

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