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- PDB-2l9m: Structure of cIAP1 CARD -

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Basic information

Entry
Database: PDB / ID: 2l9m
TitleStructure of cIAP1 CARD
ComponentsBaculoviral IAP repeat-containing protein 2
KeywordsAPOPTOSIS INHIBITOR / CARD / IAP / caspase
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 / 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 / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / 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 / regulation of cell differentiation / non-canonical NF-kappaB signal transduction / 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 / placenta development / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / NOD1/2 Signaling Pathway / 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 / regulation of inflammatory response / transferase activity / 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 / cytosol / cytoplasm
Similarity search - Function
BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / BIR repeat. / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. ...BIRC2/BIRC3, UBA domain / : / BIRC2/3-like, UBA domain / Death Domain, Fas / Death Domain, Fas / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsDay, C.L. / Rautureau, G.J.P. / Hinds, M.G.
CitationJournal: Mol.Cell / Year: 2011
Title: CARD-mediated autoinhibition of cIAP1's E3 ligase activity suppresses cell proliferation and migration.
Authors: Lopez, J. / John, S.W. / Tenev, T. / Rautureau, G.J. / Hinds, M.G. / Francalanci, F. / Wilson, R. / Broemer, M. / Santoro, M.M. / Day, C.L. / Meier, P.
History
DepositionFeb 21, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 2


Theoretical massNumber of molelcules
Total (without water)15,1471
Polymers15,1471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

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


Mass: 15147.399 Da / Num. of mol.: 1 / Fragment: cIAP1-CARD (UNP RESIDUES 435-562)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: API1, BIRC2, IAP2, MIHB, RNF48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13490

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Caspase recruitment domain of cIAP1
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-15N HSQC
1333D HNCA
1433D HN(CA)CB
153CC(CO)NH
1633D HNCO
1733D (H)CCH-TOCSY
1823D HNHA
1923D HNHB
11023D 1H-15N NOESY
11133D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM cIAP1-CARD-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 5 mM TCEP-4, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] cIAP1-CARD-5, 20 mM sodium phosphate-6, 50 mM sodium chloride-7, 5 mM TCEP-8, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-100% 13C; U-100% 15N] cIAP1-CARD-9, 20 mM sodium phosphate-10, 50 mM sodium chloride-11, 5 mM TCEP-12, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMcIAP1-CARD-11
20 mMsodium phosphate-21
50 mMsodium chloride-31
5 mMTCEP-41
1 mMcIAP1-CARD-5[U-100% 15N]2
20 mMsodium phosphate-62
50 mMsodium chloride-72
5 mMTCEP-82
0.4 mMcIAP1-CARD-9[U-100% 13C; U-100% 15N]3
20 mMsodium phosphate-103
50 mMsodium chloride-113
5 mMTCEP-123
Sample conditionsIonic strength: 0.140 / pH: 5.5 / Pressure: ambient / Temperature: 303.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE5003
Bruker DRXBrukerDRX6004

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2783 / NOE intraresidue total count: 799 / NOE long range total count: 591 / NOE medium range total count: 744 / NOE sequential total count: 649
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 256 / Conformers submitted total number: 20 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.015 Å / Distance rms dev error: 0.002 Å

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