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- PDB-4zvs: Caspase-7 Variant 1 (V1) with reprogrammed substrate specificity ... -

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Basic information

Entry
Database: PDB / ID: 4zvs
TitleCaspase-7 Variant 1 (V1) with reprogrammed substrate specificity due to Y230A/W232M/S234N substitutions, bound to DEVD inhibitor.
Components
  • (Caspase-7) x 2
  • DEVD inhibitor
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
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: 2.5 Å
AuthorsMacPherson, D.J. / Hill, M.E. / Hardy, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM080532 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

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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: DEVD inhibitor
F: DEVD inhibitor


Theoretical massNumber of molelcules
Total (without water)71,5636
Polymers71,5636
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15820 Å2
ΔGint-84 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.105, 88.105, 187.190
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 BL21(DE3) (bacteria) / 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: 13103.715 Da / Num. of mol.: 2 / Fragment: UNP residues 232-336 / Mutation: Y230A, W232M, S234N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P55210, caspase-7
#3: Protein/peptide DEVD inhibitor


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.: 111 / 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: 3.02 Å3/Da / Density % sol: 59.29 % / Description: Rhombus
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 300 mM Diammonium Hydrogren Citrate, 14% PEG 3350, 10 mM Guanidinium Chloride, 10 mM Dithiotheritol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 24, 2014
RadiationMonochromator: Si (111) channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 29874 / % possible obs: 100 % / Redundancy: 4 % / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.065 / Rrim(I) all: 0.131 / Χ2: 1.343 / Net I/av σ(I): 14.267 / Net I/σ(I): 6 / Num. measured all: 226896
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5440.84728020.7140.4880.9791.333100
2.54-2.5940.77528490.7880.4460.8961.254100
2.59-2.6440.71127500.7470.4080.8211.257100
2.64-2.6940.61528190.8330.3520.711.497100
2.69-2.7540.53528500.8470.3080.6181.304100
2.75-2.8240.49727690.8660.2860.5741.299100
2.82-2.8940.38328230.9170.2190.4421.301100
2.89-2.9640.32427750.9350.1860.3741.313100
2.96-3.0540.2628710.960.1480.2991.375100
3.05-3.1540.21828010.9710.1250.2521.312100
3.15-3.2640.17628110.9780.10.2031.343100
3.26-3.3940.13228140.9860.0760.1531.329100
3.39-3.554.10.09727900.9930.0550.1111.313100
3.55-3.734.10.07927860.9940.0450.0911.345100
3.73-3.974.10.07528240.9940.0420.0871.337100
3.97-4.274.10.06428010.9950.0370.0741.392100
4.27-4.74.10.05528140.9960.0310.0631.342100
4.7-5.384.10.05728030.9970.0320.0651.354100
5.38-6.784.10.06528400.9940.0370.0741.322100
6.78-5040.04927990.9960.0280.0561.54399.6

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Processing

Software
NameVersionClassification
PHENIX1.9-1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EDR

3edr


Resolution: 2.5→48.302 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1450 4.86 %Retained from molecular replacement search model 3EDR
Rwork0.2057 ---
obs0.2073 29842 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.44 Å2 / Biso mean: 48.7795 Å2 / Biso min: 23.03 Å2
Refinement stepCycle: final / Resolution: 2.5→48.302 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 0 111 3892
Biso mean---48.96 -
Num. residues----475
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1262X-RAY DIFFRACTION4.82TORSIONAL
12C1262X-RAY DIFFRACTION4.82TORSIONAL
21B890X-RAY DIFFRACTION4.82TORSIONAL
22D890X-RAY DIFFRACTION4.82TORSIONAL

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