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- PDB-3sip: Crystal structure of drICE and dIAP1-BIR1 complex -

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Basic information

Entry
Database: PDB / ID: 3sip
TitleCrystal structure of drICE and dIAP1-BIR1 complex
Components
  • (Caspase) x 2
  • Apoptosis 1 inhibitor
KeywordsHYDROLASE/LIGASE/HYDROLASE / caspase / BIR domain / HYDROLASE-LIGASE-HYDROLASE complex
Function / homology
Function and homology information


AKT phosphorylates targets in the cytosol / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / BIR domain binding / Apoptotic cleavage of cellular proteins / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of Toll signaling pathway / Apoptosis induced DNA fragmentation / nurse cell apoptotic process ...AKT phosphorylates targets in the cytosol / Apoptotic cleavage of cell adhesion proteins / Caspase activation via Dependence Receptors in the absence of ligand / BIR domain binding / Apoptotic cleavage of cellular proteins / Signaling by Hippo / Caspase-mediated cleavage of cytoskeletal proteins / negative regulation of Toll signaling pathway / Apoptosis induced DNA fragmentation / nurse cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / Regulation of TNFR1 signaling / negative regulation of compound eye retinal cell programmed cell death / Formation of apoptosome / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / negative regulation of peptidoglycan recognition protein signaling pathway / sensory organ precursor cell division / Activation of caspases through apoptosome-mediated cleavage / Regulation of PTEN stability and activity / Regulation of the apoptosome activity / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / positive regulation of border follicle cell migration / spermatid differentiation / chaeta development / programmed cell death involved in cell development / caspase binding / programmed cell death / negative regulation of JNK cascade / : / protein neddylation / ubiquitin conjugating enzyme binding / : / ubiquitin-like protein conjugating enzyme binding / NEDD8 ligase activity / cysteine-type endopeptidase inhibitor activity / neuron remodeling / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to X-ray / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / spermatogenesis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of cell cycle / cysteine-type endopeptidase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / apoptotic process / perinuclear region of cytoplasm / proteolysis / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / Caspase-like / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Rossmann fold - #1460 ...Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : / Caspase-like / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Rossmann fold - #1460 / 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 / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Caspase / Death-associated inhibitor of apoptosis 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.496 Å
AuthorsLi, X. / Wang, J. / Shi, Y.
CitationJournal: Nat Commun / Year: 2011
Title: Structural mechanisms of DIAP1 auto-inhibition and DIAP1-mediated inhibition of drICE.
Authors: Li, X. / Wang, J. / Shi, Y.
History
DepositionJun 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2May 21, 2014Group: Other
Revision 1.3Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.4Nov 1, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Caspase
C: Caspase
E: Apoptosis 1 inhibitor
F: Apoptosis 1 inhibitor
B: Caspase
D: Caspase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4048
Polymers87,2736
Non-polymers1312
Water00
1
A: Caspase
C: Caspase
E: Apoptosis 1 inhibitor
F: Apoptosis 1 inhibitor
B: Caspase
D: Caspase
hetero molecules

A: Caspase
C: Caspase
E: Apoptosis 1 inhibitor
F: Apoptosis 1 inhibitor
B: Caspase
D: Caspase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,80716
Polymers174,54612
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y,-z+1/21
Buried area43390 Å2
ΔGint-258 kcal/mol
Surface area53690 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19380 Å2
ΔGint-120 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.350, 148.115, 156.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 1:149 )
211chain C and (resseq 1:152 )
112chain B and (resseq 162:264 )
212chain D and (resseq 164:263 )
113chain E and (resseq 1:1 or resseq 40:139 )
213chain F and (resseq 1:1 or resseq 38:145 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Caspase / drICE large subunit / drICE / Caspase subunit p21 / Caspase subunit p12


Mass: 17908.191 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 78-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
References: UniProt: O01382, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Apoptosis 1 inhibitor / dIAP1-BIR1 / E3 ubiquitin-protein ligase th / Inhibitor of apoptosis 1 / dIAP1 / Protein thread


Mass: 13423.024 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 31-145 / Mutation: C89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
References: UniProt: Q24306, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein Caspase / drICE small subunit / drICE / Caspase subunit p21 / Caspase subunit p12


Mass: 12305.184 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 231-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
References: UniProt: O01382, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Sequence detailsALGS IS A COVALENT PEPTIDE FOR BINDING OF BIR1 MOLECULAR

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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: 3.04 Å3/Da / Density % sol: 59.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes pH7.0, 0.3M(NH4)2SO4, 20% (wt/vol) Polyethylene Glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.25627 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.25627 Å / Relative weight: 1
ReflectionResolution: 3.496→50 Å / Num. obs: 13767 / % possible obs: 100 % / Observed criterion σ(F): 10.6 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.3_473) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I3O

1i3o


Resolution: 3.496→47.091 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 26.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 720 5.25 %
Rwork0.2096 --
obs0.2122 13710 99.14 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.607 Å2 / ksol: 0.319 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.9555 Å20 Å2-0 Å2
2---4.4332 Å20 Å2
3----15.5223 Å2
Refinement stepCycle: LAST / Resolution: 3.496→47.091 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5712 0 2 0 5714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0426053
X-RAY DIFFRACTIONf_angle_d1.4058135
X-RAY DIFFRACTIONf_dihedral_angle_d23.0823560
X-RAY DIFFRACTIONf_chiral_restr0.066867
X-RAY DIFFRACTIONf_plane_restr0.0031027
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1188X-RAY DIFFRACTIONPOSITIONAL
12C1188X-RAY DIFFRACTIONPOSITIONAL0.021
21B800X-RAY DIFFRACTIONPOSITIONAL
22D800X-RAY DIFFRACTIONPOSITIONAL0.025
31E821X-RAY DIFFRACTIONPOSITIONAL
32F821X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4955-3.76530.32611170.2742253097
3.7653-4.1440.32671400.2334256099
4.144-4.74320.20862130.16842505100
4.7432-5.9740.28091530.192619100
5.974-47.09490.2328970.21492776100

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