[English] 日本語
Yorodumi
- PDB-1se0: Crystal structure of DIAP1 BIR1 bound to a Grim peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1se0
TitleCrystal structure of DIAP1 BIR1 bound to a Grim peptide
Components
  • Apoptosis 1 inhibitor
  • Cell death protein Grim
KeywordsAPOPTOSIS / IAP / BIR / Grim / caspase
Function / homology
Function and homology information


SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / larval central nervous system remodeling / negative regulation of compound eye retinal cell programmed cell death / melanization defense response / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / Activation of caspases through apoptosome-mediated cleavage ...SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / larval central nervous system remodeling / negative regulation of compound eye retinal cell programmed cell death / melanization defense response / antennal morphogenesis / Deactivation of the beta-catenin transactivating complex / Regulation of necroptotic cell death / Regulation of PTEN localization / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / sensory organ precursor cell division / Regulation of PTEN stability and activity / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / positive regulation of border follicle cell migration / chaeta development / programmed cell death involved in cell development / caspase binding / negative regulation of JNK cascade / programmed cell death / protein neddylation / ubiquitin conjugating enzyme binding / ubiquitin-like protein conjugating enzyme binding / NEDD8 ligase activity / cysteine-type endopeptidase inhibitor activity / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein autoubiquitination / protein K48-linked ubiquitination / positive regulation of protein ubiquitination / determination of adult lifespan / apoptotic signaling pathway / 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 / spermatogenesis / neuron apoptotic process / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / mitochondrion / 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 / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. ...Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Zinc finger, C3HC4 type (RING finger) / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death-associated inhibitor of apoptosis 1 / Cell death protein Grim
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsYan, N. / Wu, J.W. / Shi, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Molecular mechanisms of DrICE inhibition by DIAP1 and removal of inhibition by Reaper, Hid and Grim.
Authors: Yan, N. / Wu, J.W. / Chai, J. / Li, W. / Shi, Y.
History
DepositionFeb 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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: Apoptosis 1 inhibitor
B: Cell death protein Grim
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7263
Polymers14,6602
Non-polymers651
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-5 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.783, 84.783, 49.789
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Apoptosis 1 inhibitor / Inhibitor of apoptosis 1 / dIAP1 / Thread protein


Mass: 13552.203 Da / Num. of mol.: 1 / Fragment: DIAP1 BIR1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: IAP1, TH / Production host: Escherichia coli (E. coli) / References: UniProt: Q24306
#2: Protein/peptide Cell death protein Grim


Mass: 1108.243 Da / Num. of mol.: 1 / Fragment: Grim N-terminal peptide / Source method: obtained synthetically
Details: The sequence of this peptide occurs naturally in Drosophila (fruit fly).
References: UniProt: Q24570*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium sulfate, lithium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.961
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 1, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 1.75→99 Å / Num. all: 13359 / Num. obs: 13052 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.064
Reflection shellResolution: 1.75→1.82 Å / Rmerge(I) obs: 0.253 / Rsym value: 0.246 / % possible all: 98.6

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 587 random
Rwork0.212 --
all0.22 12367 -
obs0.22 12094 -
Refinement stepCycle: LAST / Resolution: 1.75→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms861 0 1 167 1029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.437
X-RAY DIFFRACTIONc_bond_d0.007

+
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://pdbjlvh1.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