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- PDB-4ec4: XIAP-BIR3 in complex with a potent divalent Smac mimetic -

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Basic information

Entry
Database: PDB / ID: 4ec4
TitleXIAP-BIR3 in complex with a potent divalent Smac mimetic
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsAPOPTOSIS INHIBITOR / zinc finger
Function / homology
Function and homology information


endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway ...endopeptidase regulator activity / regulation of apoptosis involved in tissue homeostasis / inhibition of cysteine-type endopeptidase activity / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / nucleotide-binding oligomerization domain containing 1 signaling pathway / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / protein serine/threonine kinase binding / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / Activation of caspases through apoptosome-mediated cleavage / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / positive regulation of type I interferon production / negative regulation of tumor necrosis factor-mediated signaling pathway / Regulation of PTEN localization / TNFR1-induced NF-kappa-B signaling pathway / positive regulation of protein ubiquitination / Deactivation of the beta-catenin transactivating complex / Regulation of TNFR1 signaling / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / positive regulation of canonical Wnt signaling pathway / ubiquitin protein ligase activity / regulation of cell population proliferation / regulation of inflammatory response / neuron apoptotic process / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
XIAP/BIRC8, 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 / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...XIAP/BIRC8, 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 / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsMastrangelo, E. / Cossu, F. / 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 26, 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / 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: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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_seq_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 4
B: Baculoviral IAP repeat-containing protein 4
C: Baculoviral IAP repeat-containing protein 4
D: Baculoviral IAP repeat-containing protein 4
E: Baculoviral IAP repeat-containing protein 4
J: Baculoviral IAP repeat-containing protein 4
F: Baculoviral IAP repeat-containing protein 4
G: Baculoviral IAP repeat-containing protein 4
K: Baculoviral IAP repeat-containing protein 4
L: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,59630
Polymers141,22610
Non-polymers8,37020
Water1,72996
1
A: Baculoviral IAP repeat-containing protein 4
F: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8846
Polymers28,2452
Non-polymers1,6394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Baculoviral IAP repeat-containing protein 4
G: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9726
Polymers28,2452
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Baculoviral IAP repeat-containing protein 4
J: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8846
Polymers28,2452
Non-polymers1,6394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Baculoviral IAP repeat-containing protein 4
K: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8846
Polymers28,2452
Non-polymers1,6394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Baculoviral IAP repeat-containing protein 4
L: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9726
Polymers28,2452
Non-polymers1,7274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.420, 130.490, 215.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 10 molecules ABCDEJFGKL

#1: Protein
Baculoviral IAP repeat-containing protein 4 / E3 ubiquitin-protein ligase XIAP / IAP-like protein / ILP / hILP / Inhibitor of apoptosis protein 3 ...E3 ubiquitin-protein ligase XIAP / IAP-like protein / ILP / hILP / Inhibitor of apoptosis protein 3 / IAP-3 / hIAP-3 / hIAP3 / X-linked inhibitor of apoptosis protein / X-linked IAP


Mass: 14122.637 Da / Num. of mol.: 10 / Fragment: BIR3 domain (UNP residues 241-356)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XIAP, API3, BIRC4, IAP3 / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 5 types, 116 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / 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.: 5 / Source method: obtained synthetically / Formula: C64H88N14O8
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.26 Å3/Da / Density % sol: 62.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% PEG400, 0.2 M sodium citrate, 0.1 M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 3.3→51.412 Å / Num. all: 28624 / Num. obs: 28624 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.258 / Net I/σ(I): 5
Reflection shellHighest resolution: 3.3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CLX

3clx


Resolution: 3.3→51.412 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.795 / SU B: 56.742 / SU ML: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.545 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27632 1440 5 %RANDOM
Rwork0.20979 ---
all0.21313 28624 --
obs0.21313 27126 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å20 Å2
2---1.63 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 3.3→51.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8691 0 562 96 9349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219611
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.98212975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67651059
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24624.304474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.737151426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3641540
X-RAY DIFFRACTIONr_chiral_restr0.0910.21246
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217458
X-RAY DIFFRACTIONr_mcbond_it0.3321.55328
X-RAY DIFFRACTIONr_mcangle_it0.65128523
X-RAY DIFFRACTIONr_scbond_it1.07734283
X-RAY DIFFRACTIONr_scangle_it1.8174.54451
LS refinement shellResolution: 3.3→3.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 90 -
Rwork0.259 1975 -
obs--99.85 %
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)
13.8704-0.4358-1.63551.49990.97983.6275-0.0148-0.0483-0.1230.0384-0.0495-0.0431-0.01440.01860.06430.0208-0.0253-0.03760.10080.01750.08848.78424.99719.0912
25.34363.1359-1.02182.89361.24233.7686-0.00360.08740.1228-0.1680.2068-0.183-0.17010.3409-0.20330.29580.05670.10050.26730.02860.249539.69399.2797-38.0399
32.7125-0.60751.03162.2973-1.73866.40060.2601-0.1984-0.25160.3795-0.2209-0.30391.0465-0.0536-0.03920.4523-0.0648-0.1480.17960.0140.2376-11.8589-23.429139.8714
42.3703-0.80390.65992.7584-0.73886.05370.1124-0.043-0.0620.15420.0639-0.10030.00130.1228-0.17630.0686-0.03730.03560.10140.00990.108424.851118.7257-7.3808
53.9433-1.57370.34822.83950.47384.7545-0.1336-0.29370.02810.1629-0.0098-0.01090.0703-0.13810.14340.0739-0.0646-0.04720.13710.02940.162827.7882-17.0373-7.6731
64.9356-0.17131.96861.6292-0.21214.65060.152-0.2356-0.08640.1128-0.11290.22680.0495-0.2791-0.03910.08630.01110.00980.10540.00550.0858-23.8124-9.141624.1433
73.6723-0.14252.10353.48330.24597.35710.0792-0.18350.12980.5043-0.1201-0.0647-0.76340.12590.04090.2864-0.0010.04350.063-0.00520.16594.953520.622837.5882
84.09650.90982.09642.84760.8288.3545-0.04720.3071-0.3139-0.2654-0.01070.09850.0842-0.33280.05790.1521-0.01450.03840.18060.0090.205321.0865-6.6467-40.7444
98.31021.1871-0.09681.6634-1.05982.85380.0496-0.09190.1666-0.079-0.05950.5228-0.3956-0.42640.00990.26020.1004-0.04250.2734-0.04460.27159.122633.231-19.571
108.47720.96240.52474.15910.022.7822-0.1777-0.2347-0.63580.1006-0.1751-0.610.40060.59780.35280.31720.08510.09740.24890.11310.256445.0482-31.842-16.3392
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 354
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2B248 - 353
4X-RAY DIFFRACTION2B401 - 402
5X-RAY DIFFRACTION3C249 - 353
6X-RAY DIFFRACTION3C401
7X-RAY DIFFRACTION3J401
8X-RAY DIFFRACTION4D249 - 353
9X-RAY DIFFRACTION4D401 - 402
10X-RAY DIFFRACTION5E246 - 353
11X-RAY DIFFRACTION5E401 - 402
12X-RAY DIFFRACTION6J246 - 353
13X-RAY DIFFRACTION6J402
14X-RAY DIFFRACTION7F248 - 352
15X-RAY DIFFRACTION7F401
16X-RAY DIFFRACTION8G247 - 353
17X-RAY DIFFRACTION8G401
18X-RAY DIFFRACTION9K246 - 352
19X-RAY DIFFRACTION9K401
20X-RAY DIFFRACTION10L247 - 353
21X-RAY DIFFRACTION10L401

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