[English] 日本語
Yorodumi
- PDB-3sip: Crystal structure of drICE and dIAP1-BIR1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / sensory organ precursor cell division / negative regulation of peptidoglycan recognition protein signaling pathway / Activation of caspases through apoptosome-mediated cleavage / Regulation of PTEN stability and activity / Regulation of the apoptosome activity / compound eye retinal cell programmed cell death / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / chaeta development / positive regulation of border follicle cell migration / spermatid differentiation / programmed cell death involved in cell development / caspase binding / programmed cell death / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein neddylation / ubiquitin conjugating enzyme binding / NEDD8 ligase activity / negative regulation of JNK cascade / ubiquitin-like protein conjugating enzyme binding / execution phase of apoptosis / neuron remodeling / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity / response to X-ray / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of protein ubiquitination / RING-type E3 ubiquitin transferase / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / positive regulation of neuron apoptotic process / spermatogenesis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of cell cycle / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / proteolysis / zinc ion binding / nucleus / plasma membrane / cytoplasm / cytosol
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 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 / 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 drICE / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more