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- PDB-3mup: cIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac037 -

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Basic information

Entry
Database: PDB / ID: 3mup
TitlecIAP1-BIR3 domain in complex with the Smac-mimetic compound Smac037
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS INHIBITOR / Zinc-Finger motif
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 / positive regulation of protein K63-linked ubiquitination / 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 / regulation of necroptotic process / positive regulation of protein K63-linked ubiquitination / 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 / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / non-canonical NF-kappaB signal transduction / regulation of cell differentiation / 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 / 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 / placenta development / 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 / protein-folding chaperone binding / transferase activity / regulation of inflammatory response / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / response to hypoxia / 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 / cytoplasm / cytosol
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-SMK / 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. / Malvezzi, F. / Canevari, G. / Milani, M.
CitationJournal: Protein Sci. / Year: 2010
Title: Recognition of Smac-mimetic compounds by the BIR 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
DepositionMay 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2014Group: Database references / Refinement description
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_auth_seq_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_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_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)59,84512
Polymers57,5614
Non-polymers2,2848
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.630, 79.790, 98.410
Angle α, β, γ (deg.)90.00, 92.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Baculoviral IAP repeat-containing protein 2 / Inhibitor of Apoptosis Proteins 1 (cIAP1) / Inhibitor of apoptosis protein 2 / IAP-2 / hIAP-2 / ...Inhibitor of Apoptosis Proteins 1 (cIAP1) / 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: API1, BIRC2, IAP2, MIHB, RNF48 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q13490
#2: Chemical
ChemComp-SMK / (3S,6S,7R,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-7-(2-aminoethyl)-N-(diphenylmethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide


Mass: 505.652 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H39N5O3
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.1M HEPES pH 7.5, 0.2M Litium Sulphate; Drop volume: 0.3ul; Protein proportion: 67%; Protein concentration: 10 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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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: Nov 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.6→53.27 Å / Num. all: 17109 / Num. obs: 15911 / % possible obs: 93.3 % / Redundancy: 2.3 % / Biso Wilson estimate: 55.24 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 5.5
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / % possible all: 96.3

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
BUSTER2.9.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D9U, chain A

3d9u


Resolution: 2.6→53.27 Å / Cor.coef. Fo:Fc: 0.9254 / Cor.coef. Fo:Fc free: 0.8752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2876 798 5.02 %RANDOM
Rwork0.2259 ---
obs0.229 15907 92.7 %-
all-15911 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.83 Å2
Baniso -1Baniso -2Baniso -3
1--4.4624 Å20 Å29.983 Å2
2---2.2137 Å20 Å2
3---6.676 Å2
Refine analyzeLuzzati coordinate error obs: 0.358 Å
Refinement stepCycle: LAST / Resolution: 2.6→53.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 152 78 3555
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1171SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes521HARMONIC5
X-RAY DIFFRACTIONt_it3438HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion400SEMIHARMONIC5
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_contact3750SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3598HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4875HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion21.51
LS refinement shellResolution: 2.6→2.78 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2961 157 5.3 %
Rwork0.205 2804 -
all0.2095 2961 -
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)
11.9664-0.66110.69535.54940.93814.85750.0094-0.01470.0412-0.06620.07380.0727-0.04460.0747-0.08320.03190.0023-0.0441-0.19070.0619-0.14729.0098-2.947310.9623
21.59830.59380.76723.5142-0.10745.94730.00310.080.01250.11810.0834-0.0985-0.19910.1437-0.0865-0.03120.0047-0.0198-0.1421-0.0409-0.136140.3284-11.394338.0576
32.8886-0.58522.12254.93160.55223.23850.0981-0.137-0.16290.1742-0.033-0.02830.0894-0.0859-0.0651-0.063-0.0545-0.0929-0.1129-0.0386-0.102123.876-34.350614.6506
42.8960.27731.59684.3306-1.22433.45960.10980.0525-0.0603-0.1403-0.00640.09460.23260.0609-0.1034-0.03390.0592-0.0554-0.15140.0403-0.097145.2922-43.121534.8782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|1 A|254 - A|354 A|600 - A|600 }A1
2X-RAY DIFFRACTION1{ A|1 - A|1 A|254 - A|354 A|600 - A|600 }A254 - 354
3X-RAY DIFFRACTION1{ A|1 - A|1 A|254 - A|354 A|600 - A|600 }A600
4X-RAY DIFFRACTION2{ B|2 - B|2 B|255 - B|354 B|600 - B|600 }B2
5X-RAY DIFFRACTION2{ B|2 - B|2 B|255 - B|354 B|600 - B|600 }B255 - 354
6X-RAY DIFFRACTION2{ B|2 - B|2 B|255 - B|354 B|600 - B|600 }B600
7X-RAY DIFFRACTION3{ C|3 - C|3 C|254 - C|356 C|600 - C|600 }C3
8X-RAY DIFFRACTION3{ C|3 - C|3 C|254 - C|356 C|600 - C|600 }C254 - 356
9X-RAY DIFFRACTION3{ C|3 - C|3 C|254 - C|356 C|600 - C|600 }C600
10X-RAY DIFFRACTION4{ D|4 - D|4 D|254 - D|355 D|600 - D|600 }D4
11X-RAY DIFFRACTION4{ D|4 - D|4 D|254 - D|355 D|600 - D|600 }D254 - 355
12X-RAY DIFFRACTION4{ D|4 - D|4 D|254 - D|355 D|600 - D|600 }D600

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