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- PDB-7trm: Crystal structure of human BIRC2 BIR3 domain in complex with inhi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7trm | ||||||
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Title | Crystal structure of human BIRC2 BIR3 domain in complex with inhibitor LCL-161 | ||||||
![]() | Baculoviral IAP repeat-containing protein 2 | ||||||
![]() | APOPTOSIS / Nuclear protein / inhibitor / histone H3 / DNA binding | ||||||
Function / homology | ![]() 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 / 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 / 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 / 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 / Ub-specific processing proteases / regulation of cell cycle / apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tencer, A.H. / Klein, B.J. / Kutateladze, T.G. | ||||||
Funding support | 1items
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![]() | ![]() Title: Molecular basis for nuclear accumulation and targeting of the inhibitor of apoptosis BIRC2. Authors: Tencer, A.H. / Yu, Y. / Causse, S.Z. / Campbell, G.R. / Klein, B.J. / Xuan, H. / Cartier, J. / Miles, M.A. / Gaurav, N. / Zadoroznyj, A. / Holt, T.A. / Wen, H. / Hawkins, C.J. / Spector, S.A. ...Authors: Tencer, A.H. / Yu, Y. / Causse, S.Z. / Campbell, G.R. / Klein, B.J. / Xuan, H. / Cartier, J. / Miles, M.A. / Gaurav, N. / Zadoroznyj, A. / Holt, T.A. / Wen, H. / Hawkins, C.J. / Spector, S.A. / Dubrez, L. / Shi, X. / Kutateladze, T.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 37.8 KB | Display | ![]() |
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PDB format | ![]() | 21.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420 KB | Display | ![]() |
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Full document | ![]() | 420 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 4.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7trlC ![]() 3d9tS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10826.264 Da / Num. of mol.: 1 / Fragment: BIR3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13490, RING-type E3 ubiquitin transferase | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | ChemComp-IUN / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.21 Å3/Da / Density % sol: 70.81 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Bis-Tris Propane, 0.2 M Sodium Citrate, and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 6853 / % possible obs: 99.79 % / Redundancy: 13.5 % / Biso Wilson estimate: 35.93 Å2 / Rpim(I) all: 0.038 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.4→2.44 Å / Num. unique obs: 337 / Rpim(I) all: 0.13 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3D9T Resolution: 2.4→27.13 Å / SU ML: 0.2834 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9653 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→27.13 Å
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Refine LS restraints |
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LS refinement shell |
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