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- PDB-7trm: Crystal structure of human BIRC2 BIR3 domain in complex with inhi... -

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Basic information

Entry
Database: PDB / ID: 7trm
TitleCrystal structure of human BIRC2 BIR3 domain in complex with inhibitor LCL-161
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS / Nuclear protein / inhibitor / histone H3 / DNA binding
Function / homology
Function and homology information


negative regulation of ripoptosome assembly involved in necroptotic process / 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 ...negative regulation of ripoptosome assembly involved in necroptotic process / 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 / negative regulation of necroptotic process / XY body / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / non-canonical NF-kappaB signal transduction / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / RIPK1-mediated regulated necrosis / regulation of reactive oxygen species metabolic process / regulation of toll-like receptor signaling pathway / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / regulation of cell differentiation / response to cAMP / canonical NF-kappaB signal transduction / TICAM1, RIP1-mediated IKK complex recruitment / placenta development / IKK complex recruitment mediated by RIP1 / ubiquitin binding / positive regulation of protein ubiquitination / tumor necrosis factor-mediated signaling pathway / 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 / 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 / response to ethanol / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / response to hypoxia / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / regulation of cell cycle / Ub-specific processing proteases / apoptotic process / negative regulation of apoptotic process / protein-containing complex binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / : / 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
Similarity search - Domain/homology
LCL-161 / Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTencer, A.H. / Klein, B.J. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2023
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
DepositionJan 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5796
Polymers10,8261
Non-polymers7525
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, HSQC NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.710, 104.710, 27.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / ...Cellular inhibitor of apoptosis 1 / C-IAP1 / IAP homolog B / Inhibitor of apoptosis protein 2 / hIAP-2 / hIAP2 / RING finger protein 48 / RING-type E3 ubiquitin transferase BIRC2 / TNFR2-TRAF-signaling complex protein 2


Mass: 10826.264 Da / Num. of mol.: 1 / Fragment: BIR3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, MIHB, RNF48 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13490, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IUN / LCL-161 / N-[(1S)-1-cyclohexyl-2-{(2S)-2-[4-(4-fluorobenzoyl)-1,3-thiazol-2-yl]pyrrolidin-1-yl}-2-oxoethyl]-N~2~-methyl-L-alaninamide


Mass: 500.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C26H33FN4O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.4→2.44 Å / Num. unique obs: 337 / Rpim(I) all: 0.13

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D9T

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 1286 9.88 %RANDOM
Rwork0.1741 11724 --
obs0.1791 6846 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.56 Å2
Refinement stepCycle: LAST / Resolution: 2.4→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 48 45 807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069785
X-RAY DIFFRACTIONf_angle_d0.84321057
X-RAY DIFFRACTIONf_chiral_restr0.049499
X-RAY DIFFRACTIONf_plane_restr0.0052137
X-RAY DIFFRACTIONf_dihedral_angle_d16.5156298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.490.28831410.21991297X-RAY DIFFRACTION99.58
2.5-2.610.29021390.20521315X-RAY DIFFRACTION100
2.61-2.750.28971400.19571322X-RAY DIFFRACTION100
2.75-2.920.23241430.20551284X-RAY DIFFRACTION99.93
2.92-3.140.32321440.21741281X-RAY DIFFRACTION99.93
3.14-3.460.2441440.16761331X-RAY DIFFRACTION100
3.46-3.960.20241460.17261295X-RAY DIFFRACTION99.86
3.96-4.980.1691440.13861277X-RAY DIFFRACTION99.02
4.98-27.130.19551450.15861322X-RAY DIFFRACTION99.8

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