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- PDB-3d9u: The BIR3 domain of cIAP1 in complex with the N terminal peptide f... -

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Basic information

Entry
Database: PDB / ID: 3d9u
TitleThe BIR3 domain of cIAP1 in complex with the N terminal peptide from SMAC/DIABLO (AVPIAQ).
Components
  • Baculoviral IAP repeat-containing protein 2
  • SMAC/DIABLO
KeywordsAPOPTOSIS / zinc finger / Cytoplasm / Metal-binding / Polymorphism / Zinc / Zinc-finger
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 / Release of apoptotic factors from the mitochondria / regulation of non-canonical NF-kappaB signal transduction / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / regulation of necroptotic process ...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 / Release of apoptotic factors from the mitochondria / 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 / SMAC, XIAP-regulated apoptotic response / Regulation of the apoptosome activity / SMAC (DIABLO) binds to IAPs / SMAC(DIABLO)-mediated dissociation of IAP:caspase complexes / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / intrinsic apoptotic signaling pathway in response to oxidative stress / regulation of toll-like receptor signaling pathway / regulation of cell differentiation / regulation of innate immune response / Apoptotic cleavage of cellular proteins / necroptotic process / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / extrinsic apoptotic signaling pathway via death domain receptors / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated signaling pathway / response to cAMP / intrinsic apoptotic signaling pathway / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / positive regulation of protein ubiquitination / TNFR1-induced NF-kappa-B signaling pathway / ubiquitin binding / 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 / : / mitochondrial intermembrane space / cytoplasmic side of plasma membrane / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / protein-folding chaperone binding / regulation of cell population proliferation / regulation of inflammatory response / transferase activity / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / transcription coactivator activity / cell surface receptor signaling pathway / regulation of cell cycle / response to hypoxia / Ub-specific processing proteases / positive regulation of apoptotic process / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / BIRC2/BIRC3, UBA domain / Caspase recruitment domain / : / BIRC2/3-like, UBA domain / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / : ...Smac/DIABLO-like superfamily / Smac/DIABLO protein / Second Mitochondria-derived Activator of Caspases / BIRC2/BIRC3, UBA domain / Caspase recruitment 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 2 / Diablo IAP-binding mitochondrial protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKulathila, R. / Price, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9.
Authors: Kulathila, R. / Vash, B. / Sage, D. / Cornell-Kennon, S. / Wright, K. / Koehn, J. / Stams, T. / Clark, K. / Price, A.
History
DepositionMay 27, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2
B: SMAC/DIABLO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8383
Polymers11,7722
Non-polymers651
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-5 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.983, 62.983, 115.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-97-

HOH

21A-208-

HOH

DetailsThe biological unit is a heterodimeric complex of CIAP1-BIR3 with N-terminal peptide from SMAC/DIABLO (AVPIAQ).

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Components

#1: Protein Baculoviral IAP repeat-containing protein 2 / Inhibitor of apoptosis protein 2 / HIAP2 / HIAP-2 / C-IAP1 / TNFR2-TRAF-signaling complex protein 2 ...Inhibitor of apoptosis protein 2 / HIAP2 / HIAP-2 / C-IAP1 / TNFR2-TRAF-signaling complex protein 2 / IAP homolog B / RING finger protein 48


Mass: 11174.601 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC2, API1, IAP2, MIHB, RNF48 / Plasmid: pNAT40 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q13490
#2: Protein/peptide SMAC/DIABLO


Mass: 597.703 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: peptide synthesized based on N-terminal fragment of SMAC/DIABLO (AVPIAQ).
References: UniProt: Q9NR28*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M BIS-TRIS PH 6.5, 0.2 M MGCL2, 22% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→54.6 Å / Num. all: 6497 / Num. obs: 6193 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 15.7 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.191 / Net I/σ(I): 20.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 4 / Num. unique all: 607 / % possible all: 96.8

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Processing

Software
NameClassification
CNXrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NW9

1nw9


Resolution: 2.3→31.43 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 309778.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 675 10.9 %RANDOM
Rwork0.201 ---
all0.228 6497 --
obs0.207 6193 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.1086 Å2 / ksol: 0.357278 e/Å3
Displacement parametersBiso mean: 31.3 Å2
Baniso -1Baniso -2Baniso -3
1-4.99 Å2-0.57 Å20 Å2
2--4.99 Å20 Å2
3----9.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 1 85 877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.272 98 10.1 %
Rwork0.235 873 -
obs-873 92.8 %

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