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- PDB-3siq: Crystal Structure of autoinhibited dIAP1-BIR1 domain -

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Basic information

Entry
Database: PDB / ID: 3siq
TitleCrystal Structure of autoinhibited dIAP1-BIR1 domain
ComponentsApoptosis 1 inhibitor
KeywordsLIGASE / dIAP1-BIR1 domain
Function / homology
Function and homology information


SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / negative regulation of compound eye retinal cell programmed cell death / 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 ...SMAC, XIAP-regulated apoptotic response / DS ligand bound to FT receptor / negative regulation of compound eye retinal cell programmed cell death / 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 / caspase binding / 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 / 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 / regulation of cell cycle / apoptotic process / ubiquitin protein ligase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / zinc ion binding / nucleus / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Jul 25, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.3Nov 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_label_asym_id / _struct_ref_seq_dif.details / _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: Apoptosis 1 inhibitor
C: Apoptosis 1 inhibitor
D: Apoptosis 1 inhibitor
E: Apoptosis 1 inhibitor
F: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,37412
Polymers95,9826
Non-polymers3926
Water724
1
A: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Apoptosis 1 inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0622
Polymers15,9971
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.782, 99.782, 71.344
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A30 - 200
2114C30 - 200
3114E30 - 200
1124B30 - 200
2124D30 - 200
3124F30 - 200

NCS ensembles :
ID
1
2

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Components

#1: Protein
Apoptosis 1 inhibitor / E3 ubiquitin-protein ligase th / Inhibitor of apoptosis 1 / dIAP1 / Protein thread


Mass: 15996.921 Da / Num. of mol.: 6 / Fragment: BIR1 domain (UNP RESIDIES 1-136) / Mutation: C89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli
References: UniProt: Q24306, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 100mM Bis-Tris pH 5.4, 0.2M (NH4)2SO4, 3%( vol/vol) CH3OH, 22% (wt/vol) Polyethylene Glycol 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 16, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.317
11-H, H+K, -L20.182
11-h,-k,l30.305
11K, H, -L40.197
ReflectionResolution: 2.4→50 Å / Num. obs: 30880 / % possible obs: 99.4 % / Observed criterion σ(F): 11.5 / Observed criterion σ(I): 2.3

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SDZ

1sdz


Resolution: 2.4→32.98 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.816 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21709 1622 5.3 %RANDOM
Rwork0.14575 ---
obs0.14959 29236 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.83 Å20 Å20 Å2
2--7.83 Å20 Å2
3----15.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4790 0 6 4 4800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0224926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.991.9436709
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1075576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17923.696257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.35915807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7891548
X-RAY DIFFRACTIONr_chiral_restr0.0830.2716
X-RAY DIFFRACTIONr_gen_planes_refined0.020.0223844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3661.52948
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.09124805
X-RAY DIFFRACTIONr_scbond_it3.61131978
X-RAY DIFFRACTIONr_scangle_it4.7334.51903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A744medium positional0.520.5
11C744medium positional0.520.5
11E744medium positional0.520.5
22B733medium positional0.540.5
22D733medium positional0.640.5
22F733medium positional0.580.5
11A744medium thermal2.152
11C744medium thermal1.742
11E744medium thermal2.072
22B733medium thermal1.942
22D733medium thermal1.832
22F733medium thermal1.862
LS refinement shellResolution: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 224 -
Rwork0.175 1978 -
obs--95.37 %

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