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- PDB-7nk0: Structure of the BIR1 domain of cIAP2 -

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Basic information

Entry
Database: PDB / ID: 7nk0
TitleStructure of the BIR1 domain of cIAP2
ComponentsBaculoviral IAP repeat-containing protein 3
KeywordsAPOPTOSIS / Baculoviral IAP Repeat / Inhibitor of Apoptosis Protein / E3 ligase
Function / homology
Function and homology information


regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / 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 / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway ...regulation of cysteine-type endopeptidase activity / regulation of RIG-I signaling pathway / 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 / negative regulation of necroptotic process / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / regulation of toll-like receptor signaling pathway / regulation of innate immune response / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / canonical NF-kappaB signal transduction / tumor necrosis factor-mediated 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 / TNFR2 non-canonical NF-kB pathway / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / transferase activity / regulation of inflammatory response / spermatogenesis / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / regulation of cell cycle / Ub-specific processing proteases / protein-containing complex binding / negative regulation of apoptotic process / apoptotic process / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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 ...: / BIRC2/3-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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsCossu, F. / Milani, M. / Mastrangelo, E. / Mirdita, D.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchMFAG-17083 Italy
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Structure-based identification of a new IAP-targeting compound that induces cancer cell death inducing NF-kappa B pathway.
Authors: Cossu, F. / Camelliti, S. / Lecis, D. / Sorrentino, L. / Majorini, M.T. / Milani, M. / Mastrangelo, E.
History
DepositionFeb 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Baculoviral IAP repeat-containing protein 3
E: Baculoviral IAP repeat-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2384
Polymers22,1072
Non-polymers1312
Water905
1
D: Baculoviral IAP repeat-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,0541
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Baculoviral IAP repeat-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1192
Polymers11,0541
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.430, 93.430, 42.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain D and (resid 26 through 98 or resid 401))
21(chain E and (resid 26 through 98 or resid 401))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain D and (resid 26 through 98 or resid 401))D0
211(chain E and (resid 26 through 98 or resid 401))E0

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Components

#1: Protein Baculoviral IAP repeat-containing protein 3 / Apoptosis inhibitor 2 / API2 / Cellular inhibitor of apoptosis 2 / C-IAP2 / IAP homolog C / ...Apoptosis inhibitor 2 / API2 / Cellular inhibitor of apoptosis 2 / C-IAP2 / IAP homolog C / Inhibitor of apoptosis protein 1 / hIAP-1 / hIAP1 / RING finger protein 49 / RING-type E3 ubiquitin transferase BIRC3 / TNFR2-TRAF-signaling complex protein 1


Mass: 11053.647 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC3, API2, MIHC, RNF49 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13489, RING-type E3 ubiquitin transferase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12 % w/v Polyethylene glycol 8,000, 10 % w/v Glycerol, 500 mM Potassium chloride

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.3→46.72 Å / Num. obs: 3285 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 147.95 Å2 / CC1/2: 0.77 / Net I/σ(I): 1.3
Reflection shellResolution: 3.3→3.39 Å / Num. unique obs: 3291 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M0A

3m0a


Resolution: 3.3→46.72 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3558 165 5.02 %RANDOM
Rwork0.2948 3120 --
obs0.2978 3285 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.78 Å2 / Biso mean: 129.4817 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.3→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1123 0 2 5 1130
Biso mean--122.85 93.07 -
Num. residues----148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11D434X-RAY DIFFRACTION9.89TORSIONAL
12E434X-RAY DIFFRACTION9.89TORSIONAL
LS refinement shellResolution: 3.3→46.72 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.3558 165 -
Rwork0.2948 3120 -
all-3285 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9019-0.3199-0.22980.15051.21269.26270.1022-0.29830.46330.3722-0.1715-0.2356-0.49410.929-0.00051.25880.08-0.15290.99720.23131.231459.0717-8.8587.3935
23.42370.8219-0.42391.5809-0.67838.2319-0.0431-0.07230.4576-0.4728-0.4760.1063-0.2723-1.069-0.00081.1836-0.1341-0.11730.9299-0.22651.353234.5047-8.8876-7.2225
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain D and resseq 25:401)D25 - 401
2X-RAY DIFFRACTION2(chain E and resseq 25:401)E25 - 401

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