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- PDB-5ic6: Crystal structure of caspase-7 DEVE peptide complex -

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Basic information

Entry
Database: PDB / ID: 5ic6
TitleCrystal structure of caspase-7 DEVE peptide complex
Components
  • Caspase-7 subunit p11
  • Caspase-7 subunit p20
  • DEVE peptide
KeywordsHYDROLASE/HYDROLASE INHIBITOR / apoptosis / 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: 2.7 Å
AuthorsSeaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A.
CitationJournal: Cell Death Differ. / Year: 2016
Title: Cacidases: caspases can cleave after aspartate, glutamate and phosphoserine residues.
Authors: Seaman, J.E. / Julien, O. / Lee, P.S. / Rettenmaier, T.J. / Thomsen, N.D. / Wells, J.A.
History
DepositionFeb 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-7 subunit p20
B: Caspase-7 subunit p11
C: Caspase-7 subunit p20
D: Caspase-7 subunit p11
E: DEVE peptide
F: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)71,8036
Polymers71,8036
Non-polymers00
Water00
1
A: Caspase-7 subunit p20
B: Caspase-7 subunit p11
E: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)35,9013
Polymers35,9013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-34 kcal/mol
Surface area10960 Å2
MethodPISA
2
C: Caspase-7 subunit p20
D: Caspase-7 subunit p11
F: DEVE peptide


Theoretical massNumber of molelcules
Total (without water)35,9013
Polymers35,9013
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-34 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.142, 88.501, 103.383
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Caspase-7 subunit p20 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 22189.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#2: Protein Caspase-7 subunit p11 / CASP-7 / Apoptotic protease Mch-3 / CMH-1 / ICE-like apoptotic protease 3 / ICE-LAP3


Mass: 13223.800 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP7, MCH3 / Production host: Escherichia coli (E. coli) / References: UniProt: P55210, caspase-7
#3: Protein/peptide DEVE peptide


Mass: 488.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium fluoride, 0.1 M sodium acetate pH 4.6, 20% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115856 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115856 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17178 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.4
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.7 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QL5

2ql5


Resolution: 2.7→47.15 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 876 5.11 %
Rwork0.1972 --
obs0.1995 17139 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 0 0 3750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053828
X-RAY DIFFRACTIONf_angle_d0.8145150
X-RAY DIFFRACTIONf_dihedral_angle_d14.2861420
X-RAY DIFFRACTIONf_chiral_restr0.034554
X-RAY DIFFRACTIONf_plane_restr0.004668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-2.86950.34191500.28772611X-RAY DIFFRACTION98
2.8695-3.0910.32051390.25832658X-RAY DIFFRACTION100
3.091-3.40190.29291370.23342697X-RAY DIFFRACTION100
3.4019-3.8940.2491440.1942715X-RAY DIFFRACTION100
3.894-4.90520.17281590.14812714X-RAY DIFFRACTION100
4.9052-47.1570.21731470.17472868X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1491-0.4060.0472.4312-0.78992.7738-0.02950.0082-0.106-0.10680.07620.2957-0.1606-0.0882-0.0480.22470.0237-0.05440.233-0.01130.3003-16.9796-3.585714.2596
22.4231-0.1646-0.63832.8381-1.4453.14470.11490.491-0.0684-0.5729-0.0262-0.02750.3602-0.0103-0.01660.46370.0124-0.05490.2923-0.04370.2372-9.6867-15.309311.4172
31.9323-1.1661-0.27163.0294-0.45022.67780.1313-0.01010.0480.1906-0.1157-0.24360.08460.3194-0.02010.21470.0047-0.02890.20460.01790.26993.1221-22.485931.8331
40.9872-1.1489-0.442.67671.30913.27520.1648-0.0149-0.10510.20980.00460.15010.2627-0.1374-0.15090.315-0.02690.01440.26150.06690.3231-10.3624-18.662133.3005
54.3025-1.2128-1.06140.8958-1.04484.1396-0.19080.1892-0.08330.0170.0046-0.06330.09360.27260.20690.64230.23530.00360.7989-0.06370.4935-1.7041-5.67782.2503
64.25480.656-0.99075.0799-1.7092.7543-0.4416-0.6112-0.79520.3843-0.1988-0.45610.45910.61030.50360.68150.1577-0.00030.36430.04940.4219-4.8389-11.187345.5374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F

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