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- PDB-1jd6: Crystal Structure of DIAP1-BIR2/Hid Complex -

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Basic information

Entry
Database: PDB / ID: 1jd6
TitleCrystal Structure of DIAP1-BIR2/Hid Complex
Components
  • APOPTOSIS 1 INHIBITOR
  • head involution defective protein
KeywordsHydrolase/Peptide / APOPTOSIS / IAP / HID / CASPASE ACTIVATION / DROSOPHILA / Hydrolase-Peptide complex
Function / homology
Function and homology information


: / instar larval or pupal development / positive regulation of cellular response to X-ray / BIR domain binding / larval midgut cell programmed cell death / SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / response to red light / head involution / negative regulation of compound eye retinal cell programmed cell death ...: / instar larval or pupal development / positive regulation of cellular response to X-ray / BIR domain binding / larval midgut cell programmed cell death / SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / response to red light / head involution / negative regulation of compound eye retinal cell programmed cell death / antennal morphogenesis / positive regulation of apoptotic process involved in development / 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 / open tracheal system development / regulation of cysteine-type endopeptidase activity involved in apoptotic process / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / : / positive regulation of border follicle cell migration / chaeta development / cell death / sex differentiation / caspase binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / programmed cell death / negative regulation of JNK cascade / regulation of organ growth / positive regulation of cysteine-type endopeptidase activity / protein neddylation / ubiquitin conjugating enzyme binding / ubiquitin-like protein conjugating enzyme binding / dendrite morphogenesis / NEDD8 ligase activity / cysteine-type endopeptidase inhibitor activity / ubiquitin-specific protease binding / entrainment of circadian clock by photoperiod / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of macroautophagy / protein K48-linked ubiquitination / protein autoubiquitination / cellular response to starvation / positive regulation of protein ubiquitination / apoptotic signaling pathway / RING-type E3 ubiquitin transferase / cellular response to gamma radiation / Wnt signaling pathway / protein polyubiquitination / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / 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
: / Cell death protein hid / Death-associated inhibitor of apoptosis 1
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / pdbx_struct_conn_angle / struct_conn / 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_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

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Assembly

Deposited unit
A: APOPTOSIS 1 INHIBITOR
B: head involution defective protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1933
Polymers15,1282
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-6 kcal/mol
Surface area6430 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: PGEX2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q24306
#2: Protein/peptide head involution defective protein


Mass: 1049.176 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: GenBank: Q24106, UniProt: Q24106*PLUS
#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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TRIS, AMMONIUM DIHYDROGEN 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 8, 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: 2.7→99 Å / Num. all: 4613 / Num. obs: 4535 / % possible obs: 98.3 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2 / Redundancy: 19 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 25
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 12 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 87781
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.381

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 -random
Rwork0.217 --
all0.22 4613 -
obs0.219 4613 -
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms907 0 1 0 908
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.434
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.415 29 -
Rwork0.276 --
obs-538 98.4 %

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