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- PDB-4eb9: cIAP1-BIR3 in complex with a divalent Smac mimetic -

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Basic information

Entry
Database: PDB / ID: 4eb9
TitlecIAP1-BIR3 in complex with a divalent Smac mimetic
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS INHIBITOR / zinc finger
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination ...negative regulation of ripoptosome assembly involved in necroptotic process / regulation of cysteine-type endopeptidase activity / FBXO family protein binding / regulation of RIG-I signaling pathway / positive regulation of protein K48-linked ubiquitination / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / positive regulation of protein K63-linked ubiquitination / CD40 receptor complex / XY body / negative regulation of necroptotic process / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / non-canonical NF-kappaB signal transduction / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / response to cAMP / tumor necrosis factor-mediated signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / placenta development / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / positive regulation of protein ubiquitination / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / protein-folding chaperone binding / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / Zinc finger, C3HC4 type (RING finger) / Death-like domain superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-0O6 / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCossu, F. / Mastrangelo, E. / Bolognesi, M. / Milani, M.
CitationJournal: Plos One / Year: 2012
Title: Structural insight into inhibitor of apoptosis proteins recognition by a potent divalent smac-mimetic.
Authors: Cossu, F. / Milani, M. / Vachette, P. / Malvezzi, F. / Grassi, S. / Lecis, D. / Delia, D. / Drago, C. / Seneci, P. / Bolognesi, M. / Mastrangelo, E.
History
DepositionMar 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
B: Baculoviral IAP repeat-containing protein 2
C: Baculoviral IAP repeat-containing protein 2
D: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,18610
Polymers57,5614
Non-polymers2,6256
Water2,000111
1
A: Baculoviral IAP repeat-containing protein 2
C: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0935
Polymers28,7802
Non-polymers1,3123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 2
D: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0935
Polymers28,7802
Non-polymers1,3123
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.110, 81.310, 96.880
Angle α, β, γ (deg.)90.00, 95.67, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 2 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger ...C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / hIAP2 / RING finger protein 48 / TNFR2-TRAF-signaling complex protein 2


Mass: 14390.241 Da / Num. of mol.: 4 / Fragment: BIR3 domain (UNP residues 251-363)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, IAP2, MIHB, RNF48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13490, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-0O6 / (3S,6S,7S,9aS,3'S,6'S,7'S,9a'S)-N,N'-(benzene-1,4-diylbis{butane-4,1-diyl-1H-1,2,3-triazole-1,4-diyl[(S)-phenylmethanediyl]})bis[7-(hydroxymethyl)-6-{[(2S)-2-(methylamino)butanoyl]amino}-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide]


Mass: 1181.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C64H88N14O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.69 Å3/Da / Density % sol: 54.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 6% PEG3350, 0.1 M Bis-Tris, pH 5.2, 0.2 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.973 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2010
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.973 Å / Relative weight: 1
ReflectionResolution: 2.6→48.203 Å / Num. obs: 18610 / % possible obs: 98.5 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 5.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.585 / Mean I/σ(I) obs: 1.6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DNAdata collection
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MUP, CHAIN A

3mup


Resolution: 2.6→48.203 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.872 / SU B: 30.809 / SU ML: 0.302 / Cross valid method: THROUGHOUT / ESU R: 0.753 / ESU R Free: 0.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32202 962 5.2 %RANDOM
Rwork0.25687 ---
obs0.26026 17648 98.26 %-
all-18530 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.028 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å2-3.22 Å2
2---1.05 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 176 111 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223668
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9764977
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4635414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.63123.043184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77715569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2681530
X-RAY DIFFRACTIONr_chiral_restr0.0890.2487
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212890
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_it1.0041.52059
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69923314
X-RAY DIFFRACTIONr_scbond_it2.32431609
X-RAY DIFFRACTIONr_scangle_it3.7634.51658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 75 -
Rwork0.342 1326 -
obs--99.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.42610.5197-0.05063.81151.18011.27960.11760.0203-0.04520.0326-0.002-0.1251-0.0208-0.1177-0.11560.08880.00740.02990.14280.02820.086631.5254-3.746810.8446
20.9855-0.33071.2983.9457-0.24192.85480.0209-0.04280.0178-0.0074-0.024-0.0014-0.0813-0.02270.0030.06020.01430.05730.1298-0.0370.088543.00784.648737.3913
32.6449-1.19811.86835.1814-1.63512.94790.14180.0377-0.11330.0888-0.0302-0.21710.0670.1208-0.11160.0388-0.05340.00370.1197-0.04350.104326.1371-34.599614.0871
41.74130.53451.04785.28481.05193.19030.194-0.0856-0.2339-0.1180.0052-0.02630.1923-0.1558-0.19920.05390.0332-0.01030.12720.0280.124348.6091-26.078333.7614
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A254 - 355
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION2B254 - 354
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION3C255 - 356
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION4D254 - 356
8X-RAY DIFFRACTION4D401

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