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- PDB-3eyl: Crystal structure of XIAP BIR3 domain in complex with a Smac-mime... -

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Basic information

Entry
Database: PDB / ID: 3eyl
TitleCrystal structure of XIAP BIR3 domain in complex with a Smac-mimetic compound
ComponentsBaculoviral IAP repeat-containing protein 4
KeywordsLIGASE / Apoptosis / Smac-mimetics / Zinc-finger / Metal-binding / Phosphoprotein / Protease inhibitor / Thiol protease inhibitor / Ubl conjugation pathway
Function / homology
Function and homology information


endopeptidase regulator activity / inhibition of cysteine-type endopeptidase activity / regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response ...endopeptidase regulator activity / inhibition of cysteine-type endopeptidase activity / regulation of apoptosis involved in tissue homeostasis / positive regulation of protein linear polyubiquitination / regulation of BMP signaling pathway / copper ion homeostasis / regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / nucleotide-binding oligomerization domain containing 2 signaling pathway / SMAC, XIAP-regulated apoptotic response / Activation of caspases through apoptosome-mediated cleavage / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / cysteine-type endopeptidase inhibitor activity / regulation of innate immune response / positive regulation of type I interferon production / protein K63-linked ubiquitination / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / negative regulation of tumor necrosis factor-mediated signaling pathway / protein serine/threonine kinase binding / Regulation of PTEN localization / : / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / Deactivation of the beta-catenin transactivating complex / positive regulation of JNK cascade / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / Regulation of necroptotic cell death / Wnt signaling pathway / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of canonical Wnt signaling pathway / regulation of cell population proliferation / regulation of inflammatory response / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / neuron apoptotic process / regulation of cell cycle / defense response to bacterium / DNA damage response / negative regulation of apoptotic process / nucleoplasm / identical protein binding / nucleus / metal ion binding / 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. ...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-SMK / E3 ubiquitin-protein ligase XIAP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCossu, F. / Milani, M. / Mastrangelo, E. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Designing Smac-mimetics as antagonists of XIAP, cIAP1, and cIAP2.
Authors: Cossu, F. / Mastrangelo, E. / Milani, M. / Sorrentino, G. / Lecis, D. / Delia, D. / Manzoni, L. / Seneci, P. / Scolastico, C. / Bolognesi, M.
History
DepositionOct 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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: Baculoviral IAP repeat-containing protein 4
B: Baculoviral IAP repeat-containing protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3876
Polymers28,2452
Non-polymers1,1424
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-11 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.423, 170.423, 170.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-2-

HOH

21B-1-

HOH

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Components

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


Mass: 14122.637 Da / Num. of mol.: 2 / Fragment: UNP residues 241-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC4, API3, IAP3, XIAP / Production host: Escherichia coli (E. coli)
References: UniProt: P98170, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 2 / Source method: obtained synthetically / Formula: C29H39N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: Mg formate, pH 5.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.013 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2008
RadiationMonochromator: Channel-cut double-crystal silicon [111] crystal (5.2-20 keV)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.013 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. obs: 8740 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 20.9
Reflection shellResolution: 3→3.16 Å / Redundancy: 12 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1253 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3clx

3clx


Resolution: 3→38.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 32.623 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.645 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23877 414 4.7 %RANDOM
Rwork0.1888 ---
obs0.19111 8303 99.45 %-
all-8740 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.602 Å2
Refinement stepCycle: LAST / Resolution: 3→38.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 76 3 1717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221784
X-RAY DIFFRACTIONr_angle_refined_deg1.0661.9682424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6475204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.58624.54588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61615274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.366156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021402
X-RAY DIFFRACTIONr_nbd_refined0.2040.2768
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21218
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.26
X-RAY DIFFRACTIONr_mcbond_it1.29921037
X-RAY DIFFRACTIONr_mcangle_it2.32631624
X-RAY DIFFRACTIONr_scbond_it3.1014875
X-RAY DIFFRACTIONr_scangle_it5.0656798
LS refinement shellResolution: 3→3.079 Å / Rfactor Rfree error: 0.238 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 30 -
Rwork0.265 600 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 36.051 Å / Origin y: -15.941 Å / Origin z: -10.694 Å
111213212223313233
T0.2926 Å20.0596 Å2-0.0986 Å2-0.2987 Å20.0215 Å2--0.1856 Å2
L2.332 °2-0.8505 °2-0.9422 °2-1.0667 °20.2673 °2--8.1374 °2
S0.3115 Å °0.0644 Å °-0.3655 Å °-0.1191 Å °-0.0845 Å °0.2829 Å °0.1713 Å °-0.061 Å °-0.227 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A254 - 354
2X-RAY DIFFRACTION1B254 - 354

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