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- PDB-2p2c: Inhibition of caspase-2 by a designed ankyrin repeat protein (DARPin) -

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Basic information

Entry
Database: PDB / ID: 2p2c
TitleInhibition of caspase-2 by a designed ankyrin repeat protein (DARPin)
Components(Caspase-2) x 3
KeywordsHYDROLASE / apoptosis / caspase / caspase-2 / inhibition / protein design / protein libraries / designed ankyrin repeat proteins / ribosome display
Function / homology
Function and homology information


caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death ...caspase-2 / endopeptidase complex / neural retina development / NADE modulates death signalling / luteolysis / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cysteine-type endopeptidase activity involved in execution phase of apoptosis / execution phase of apoptosis / TP53 Regulates Transcription of Caspase Activators and Caspases / ectopic germ cell programmed cell death / extrinsic apoptotic signaling pathway in absence of ligand / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / NOD1/2 Signaling Pathway / protein processing / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / positive regulation of apoptotic process / protein domain specific binding / cysteine-type endopeptidase activity / apoptotic process / DNA damage response / nucleolus / negative regulation of apoptotic process / enzyme binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Ankyrin repeat-containing domain / Peptidase family C14A, His active site / Caspase family histidine active site. ...Caspase-2 / Caspase recruitment domain / Caspase-like / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Rossmann fold - #1460 / Ankyrin repeat-containing domain / 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 / Death-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsRoschitzki Voser, H. / Briand, C. / Capitani, G. / Gruetter, M.G.
CitationJournal: Structure / Year: 2007
Title: Inhibition of Caspase-2 by a Designed Ankyrin Repeat Protein: Specificity, Structure, and Inhibition Mechanism.
Authors: Schweizer, A. / Roschitzki-Voser, H. / Amstutz, P. / Briand, C. / Gulotti-Georgieva, M. / Prenosil, E. / Binz, H.K. / Capitani, G. / Baici, A. / Pluckthun, A. / Grutter, M.G.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Aug 30, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase-2
B: Caspase-2
P: Caspase-2
C: Caspase-2
D: Caspase-2
Q: Caspase-2
E: Caspase-2
F: Caspase-2
R: Caspase-2
G: Caspase-2
H: Caspase-2
S: Caspase-2
I: Caspase-2
J: Caspase-2
T: Caspase-2
K: Caspase-2
L: Caspase-2
U: Caspase-2


Theoretical massNumber of molelcules
Total (without water)297,02018
Polymers297,02018
Non-polymers00
Water52229
1
A: Caspase-2
B: Caspase-2
P: Caspase-2
C: Caspase-2
D: Caspase-2
Q: Caspase-2


Theoretical massNumber of molelcules
Total (without water)99,0076
Polymers99,0076
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Caspase-2
F: Caspase-2
R: Caspase-2
G: Caspase-2
H: Caspase-2
S: Caspase-2


Theoretical massNumber of molelcules
Total (without water)99,0076
Polymers99,0076
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: Caspase-2
J: Caspase-2
T: Caspase-2
K: Caspase-2
L: Caspase-2
U: Caspase-2


Theoretical massNumber of molelcules
Total (without water)99,0076
Polymers99,0076
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.020, 229.210, 114.930
Angle α, β, γ (deg.)90.00, 90.11, 90.00
Int Tables number4
Space group name H-MP1211
Details3 molecule of homodimeric human caspase-2 in complex with 2 DARPins in the asymmetric unit.

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Components

#1: Protein
Caspase-2


Mass: 19006.562 Da / Num. of mol.: 6 / Fragment: Residues 167-333 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Strain: BL21(DE3)
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein
Caspase-2


Mass: 12052.160 Da / Num. of mol.: 6 / Fragment: Residues 348-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2
References: UniProt: P42575, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#3: Protein
Caspase-2


Mass: 18444.572 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASP2
References: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 17% PEG 5000-MME, 0.1 M Tris-HOAc, 0.1 M KSCN, 30% ethylene glycol, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.899 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899 Å / Relative weight: 1
ReflectionResolution: 3.24→30 Å / Num. all: 94083 / Num. obs: 92159 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 1.79 % / Biso Wilson estimate: 84.879 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 5.9 / Net I/σ(I): 9.81
Reflection shellResolution: 3.24→3.5 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.11 / Num. unique all: 94083 / Rsym value: 37.9 / % possible all: 98

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PYO and 1MJO

1pyo

1mjo


Resolution: 3.24→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.305 1023 -RANDOM
Rwork0.262 ---
all-47330 --
obs-46491 98.2 %-
Displacement parametersBiso mean: 95.93 Å2
Baniso -1Baniso -2Baniso -3
1--3.546 Å20 Å2-1.875 Å2
2---3.993 Å20 Å2
3---7.539 Å2
Refinement stepCycle: LAST / Resolution: 3.24→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19256 0 0 29 19285
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.905
X-RAY DIFFRACTIONc_angle_d3.378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
3.24-3.30.258510.279X-RAY DIFFRACTION2249
3.3-3.360.258500.279X-RAY DIFFRACTION2241
3.36-3.420.258520.279X-RAY DIFFRACTION2314
3.42-3.490.258510.279X-RAY DIFFRACTION2222
3.49-3.560.258510.279X-RAY DIFFRACTION2271
3.56-3.650.258510.279X-RAY DIFFRACTION2289

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