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- PDB-7trl: Crystal structure of human BIRC2 BIR3 domain in complex with hist... -

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Basic information

Entry
Database: PDB / ID: 7trl
TitleCrystal structure of human BIRC2 BIR3 domain in complex with histone H3
Components
  • Baculoviral IAP repeat-containing protein 2
  • Histone H3
KeywordsAPOPTOSIS / Nuclear protein / inhibitor / histone H3 / DNA binding
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 / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / CARD domain ...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
Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsKlein, B.J. / Tencer, A.H. / 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 / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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: Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5739
Polymers12,1352
Non-polymers4387
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, NMR titration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint2 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.655, 34.972, 35.605
Angle α, β, γ (deg.)90.000, 103.870, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-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: Protein/peptide Histone H3


Mass: 1308.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.68 Å3/Da / Density % sol: 26.63 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M SPG buffer (2:7:7 molar ratio of succinic acid:sodium dihydrogen phosphate: glycine), 25% PEG 1,500

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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: Dec 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 8045 / % possible obs: 97 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.27 Å2 / Rpim(I) all: 0.026 / Net I/σ(I): 21.8
Reflection shellResolution: 1.73→1.76 Å / Num. unique obs: 334 / Rpim(I) all: 0.293

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D9T

3d9t


Resolution: 1.74→24.58 Å / SU ML: 0.1911 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8459
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 769 10.07 %
Rwork0.1623 6866 -
obs0.1667 7635 91.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.72 Å2
Refinement stepCycle: LAST / Resolution: 1.74→24.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 25 34 826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017819
X-RAY DIFFRACTIONf_angle_d1.39281095
X-RAY DIFFRACTIONf_chiral_restr0.0741104
X-RAY DIFFRACTIONf_plane_restr0.0091142
X-RAY DIFFRACTIONf_dihedral_angle_d18.2778110
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.880.23771070.1935971X-RAY DIFFRACTION64.63
1.88-2.070.22681560.1761370X-RAY DIFFRACTION93.73
2.07-2.370.24131660.15611500X-RAY DIFFRACTION99.46
2.37-2.980.1981660.16951493X-RAY DIFFRACTION100
2.98-24.580.18961740.15461532X-RAY DIFFRACTION99.65

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