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- PDB-1jd5: Crystal Structure of DIAP1-BIR2/GRIM -

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Basic information

Entry
Database: PDB / ID: 1jd5
TitleCrystal Structure of DIAP1-BIR2/GRIM
Components
  • APOPTOSIS 1 INHIBITOR
  • cell death protein GRIM
KeywordsHydrolase/Peptide / APOPTOSIS / GRIM / IAP / CASPASE ACTIVATION / DROSOPHILA / Hydrolase-Peptide complex
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 / sensory organ precursor cell division ...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 / 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 / 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 / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of protein ubiquitination / apoptotic signaling pathway / determination of adult lifespan / RING-type E3 ubiquitin transferase / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / 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 / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y.
CitationJournal: Mol.Cell / Year: 2001
Title: Structural analysis of a functional DIAP1 fragment bound to grim and hid peptides.
Authors: Wu, J.W. / Cocina, A.E. / Chai, J. / Hay, B.A. / Shi, Y.
History
DepositionJun 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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: APOPTOSIS 1 INHIBITOR
B: cell death protein GRIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2523
Polymers15,1872
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area6660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.7, 62.7, 130.7
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein APOPTOSIS 1 INHIBITOR / DIAP1


Mass: 14078.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DIAP1 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24306
#2: Protein/peptide cell death protein GRIM /


Mass: 1108.243 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This peptide was chemically synthesized. The sequence is naturally found in Drosophila melanogaster (fruit fly).
References: UniProt: Q24570
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TRIS, AMMONIUM DIHROGEN PHOSPHATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMTris1reservoirpH8.5
31.4 Mammonium dihydrogen phosphate1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 5, 2001 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→99 Å / Num. all: 12677 / Num. obs: 12525 / % possible obs: 98.8 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 19 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 75
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 12 % / Rmerge(I) obs: 0.16 / % possible all: 97.3

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.243 -random
Rwork0.202 --
all0.21 12677 -
obs0.203 11697 -
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 1 0 925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.253
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.261 50 -
Rwork0.237 --
obs-1061 97.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 1 / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.261 / Rfactor Rwork: 0.237

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