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- PDB-3oz1: cIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac066 -

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Basic information

Entry
Database: PDB / ID: 3oz1
TitlecIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac066
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS INHIBITOR / Zinc-finger / Caspases
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 / positive regulation of protein K63-linked ubiquitination / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway ...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 / positive regulation of protein K63-linked ubiquitination / regulation of necroptotic process / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / 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 / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of cell differentiation / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / response to cAMP / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / ubiquitin binding / TNFR1-induced NF-kappa-B signaling pathway / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / NOD1/2 Signaling Pathway / RING-type E3 ubiquitin transferase / placenta development / Regulation of necroptotic cell death / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-folding chaperone binding / regulation of cell population proliferation / regulation of inflammatory response / transferase activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / regulation of cell cycle / response to hypoxia / Ub-specific processing proteases / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / Caspase recruitment domain / : / BIRC2/3-like, UBA domain / 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 ...BIRC2/BIRC3, UBA domain / Caspase recruitment domain / : / BIRC2/3-like, UBA domain / 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 / 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-BMB / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCossu, F. / Malvezzi, F. / Mastrangelo, E. / Canevari, G. / Bolognesi, M. / Milani, M.
CitationJournal: Protein Sci. / Year: 2010
Title: Recognition of Smac-mimetic compounds by the BIR3 domain of cIAP1
Authors: Cossu, F. / Malvezzi, F. / Canevari, G. / Mastrangelo, E. / Lecis, D. / Delia, D. / Seneci, P. / Scolastico, C. / Bolognesi, M. / Milani, M.
History
DepositionSep 24, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_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)60,26212
Polymers57,5614
Non-polymers2,7018
Water1629
1
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0653
Polymers14,3901
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0653
Polymers14,3901
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0653
Polymers14,3901
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0653
Polymers14,3901
Non-polymers6752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.589, 114.630, 92.962
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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


Mass: 14390.241 Da / Num. of mol.: 4 / Fragment: Repeat 3 (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 / Plasmid: pET21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13490
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BMB / (3S,6S,7R,9aS)-7-[2-(benzylamino)ethyl]-N-(diphenylmethyl)-6-{[(2S)-2-(methylamino)butanoyl]amino}-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide


Mass: 609.801 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H47N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.65 Å3/Da / Density % sol: 53.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 400, 0.1M Sodium Citrate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2010
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 3→92.9 Å / Num. all: 11909 / Num. obs: 11333 / % possible obs: 95.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: 78.37 Å2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.9.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→60.93 Å / Cor.coef. Fo:Fc: 0.9153 / Cor.coef. Fo:Fc free: 0.8493 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 575 4.83 %RANDOM
Rwork0.1917 ---
obs0.1949 11333 --
all-11909 --
Displacement parametersBiso mean: 85.03 Å2
Baniso -1Baniso -2Baniso -3
1-4.1053 Å20 Å20 Å2
2---17.3415 Å20 Å2
3---13.2362 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: LAST / Resolution: 3→60.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3386 0 184 9 3579
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1183SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes532HARMONIC5
X-RAY DIFFRACTIONt_it3493HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion405SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4005SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3689HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4989HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion2.56
X-RAY DIFFRACTIONt_other_torsion21.25
LS refinement shellResolution: 3→3.29 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2801 133 4.68 %
Rwork0.1996 2707 -
all0.2035 2840 -
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)
17.7949-2.18111.74536.06180.26535.99930.0477-0.35660.1131-0.15010.1841-0.0285-0.3152-0.6082-0.2317-0.18180.07170.02960.24380.0369-0.2548-16.7643-38.6883-5.795
26.8125-2.5446-2.4474.94130.93956.4585-0.02210.07350.36470.38880.1276-0.06860.0374-0.25-0.1055-0.203-0.0386-0.00280.1068-0.0225-0.23-8.7902-43.52124.7651
37.951-0.71772.09134.5222-0.23674.20440.02-0.3827-0.3697-0.0595-0.01740.31910.1719-0.3911-0.0026-0.10310.0401-0.01360.10380.0872-0.2907-19.8987-41.589754.1137
45.89432.38570.70592.7755-1.13836.308-0.0359-0.8015-0.72370.2979-0.3728-0.17440.18230.08150.4086-0.58320.0440.03110.13070.3040.5311-42.9998-64.957260.8679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1A253 - A355, A501 - A501, A600 - A600
4X-RAY DIFFRACTION2B253 - B356, B501 - B501, B600 - B600
7X-RAY DIFFRACTION3C252 - C354, C501 - C501, C600 - C600
10X-RAY DIFFRACTION4D252 - D354, D501 - D501, D600 - D600

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