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- PDB-1q4q: Crystal structure of a DIAP1-Dronc complex -

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Basic information

Entry
Database: PDB / ID: 1q4q
TitleCrystal structure of a DIAP1-Dronc complex
Components
  • Apoptosis 1 inhibitor
  • Nedd2-like caspase CG8091-PA
KeywordsAPOPTOSIS INHIBITOR / caspase / IAP / ubiquitination / apoptosis
Function / homology
Function and homology information


hemocyte development / nurse cell apoptotic process / SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / negative regulation of compound eye retinal cell programmed cell death / melanization defense response ...hemocyte development / nurse cell apoptotic process / SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / head involution / embryonic development via the syncytial blastoderm / salivary gland histolysis / positive regulation of compound eye retinal cell programmed cell death / 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 / metamorphosis / spermatid nucleus differentiation / positive regulation of Toll signaling pathway / border follicle cell migration / compound eye development / positive regulation of border follicle cell migration / chaeta development / sperm individualization / apoptosome / programmed cell death involved in cell development / programmed necrotic cell death / caspase binding / CARD domain binding / programmed cell death / cysteine-type endopeptidase activity involved in apoptotic signaling pathway / negative regulation of JNK cascade / protein neddylation / ubiquitin conjugating enzyme binding / ubiquitin-like protein conjugating enzyme binding / zymogen activation / dendrite morphogenesis / NEDD8 ligase activity / neuron remodeling / cysteine-type endopeptidase inhibitor activity / ubiquitin-specific protease binding / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / protein autoprocessing / protein K48-linked ubiquitination / ectopic germ cell programmed cell death / protein autoubiquitination / positive regulation of protein ubiquitination / central nervous system development / regulation of autophagy / 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 / endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / regulation of cell cycle / positive regulation of apoptotic process / negative regulation of cell population proliferation / cysteine-type endopeptidase activity / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / 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 / Peptidase C14, caspase non-catalytic subunit p10 / Peptidase family C14A, cysteine active site / Caspase family cysteine active site. ...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 / 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) / Death-like domain superfamily / 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 / Caspase Dronc
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChai, J. / Yan, N. / Shi, Y.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Molecular mechanism of Reaper-Grim-Hid-mediated suppression of DIAP1-dependent Dronc ubiquitination
Authors: Chai, J. / Yan, N. / Huh, J.R. / Wu, J.-W. / Li, W. / Hay, B.A. / Shi, Y.
History
DepositionAug 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 22, 2020Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.4Feb 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_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

Downloads & links

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Assembly

Deposited unit
A: Apoptosis 1 inhibitor
B: Apoptosis 1 inhibitor
C: Apoptosis 1 inhibitor
D: Apoptosis 1 inhibitor
E: Apoptosis 1 inhibitor
F: Apoptosis 1 inhibitor
G: Apoptosis 1 inhibitor
H: Apoptosis 1 inhibitor
I: Apoptosis 1 inhibitor
J: Apoptosis 1 inhibitor
K: Nedd2-like caspase CG8091-PA
L: Nedd2-like caspase CG8091-PA
M: Nedd2-like caspase CG8091-PA
N: Nedd2-like caspase CG8091-PA
O: Nedd2-like caspase CG8091-PA
P: Nedd2-like caspase CG8091-PA
Q: Nedd2-like caspase CG8091-PA
R: Nedd2-like caspase CG8091-PA
S: Nedd2-like caspase CG8091-PA
T: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,18830
Polymers155,53420
Non-polymers65410
Water10,034557
1
E: Apoptosis 1 inhibitor
S: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
J: Apoptosis 1 inhibitor
T: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Apoptosis 1 inhibitor
O: Nedd2-like caspase CG8091-PA
hetero molecules


  • defined by author&software
  • 15.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-6 kcal/mol
Surface area6130 Å2
MethodPISA
4
B: Apoptosis 1 inhibitor
R: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-5 kcal/mol
Surface area6590 Å2
MethodPISA
5
C: Apoptosis 1 inhibitor
P: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area6190 Å2
MethodPISA
6
D: Apoptosis 1 inhibitor
Q: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-6 kcal/mol
Surface area5970 Å2
MethodPISA
7
F: Apoptosis 1 inhibitor
N: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-7 kcal/mol
Surface area6110 Å2
MethodPISA
8
G: Apoptosis 1 inhibitor
K: Nedd2-like caspase CG8091-PA
hetero molecules


  • defined by author&software
  • 15.6 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-5 kcal/mol
Surface area6600 Å2
MethodPISA
9
H: Apoptosis 1 inhibitor
L: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area6040 Å2
MethodPISA
10
I: Apoptosis 1 inhibitor
M: Nedd2-like caspase CG8091-PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6193
Polymers15,5532
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-7 kcal/mol
Surface area5920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.900, 128.900, 183.695
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 14078.695 Da / Num. of mol.: 10 / Fragment: DIAP1 BIR2 domain, residues 201-324
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q24306
#2: Protein/peptide
Nedd2-like caspase CG8091-PA / Dronc


Mass: 1474.688 Da / Num. of mol.: 10 / Fragment: Dronc peptide, residues 114-125 / Source method: obtained synthetically / Details: The peptide was synthesized. / References: UniProt: Q9XYF4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Citrate, PEG 4000, ammonium sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMsodium citrate1reservoirpH5.8
315 %(w/v)PEG40001reservoir
4120 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→99 Å / Num. obs: 94061 / % possible obs: 94.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Rsym value: 0.057
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 70.5 % / Rsym value: 0.173
Reflection
*PLUS
Lowest resolution: 99 Å / Num. measured all: 582663 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 82 % / Rmerge(I) obs: 0.173

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 0
RfactorNum. reflection
Rfree0.246 -
Rwork0.199 -
all0.203 -
obs0.203 93347
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8599 0 10 557 9166
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.009
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.531

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