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- PDB-1xox: SOLUTION STRUCTURE OF HUMAN SURVIVIN -

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Entry
Database: PDB / ID: 1xox
TitleSOLUTION STRUCTURE OF HUMAN SURVIVIN
ComponentsApoptosis inhibitor survivin
KeywordsAPOPTOSIS / Bir Domain
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / chromosome passenger complex ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / positive regulation of exit from mitosis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / interphase microtubule organizing center / chromosome passenger complex / protein-containing complex localization / cobalt ion binding / cysteine-type endopeptidase inhibitor activity / nuclear chromosome / mitotic spindle assembly checkpoint signaling / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / cytoplasmic microtubule / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / positive regulation of mitotic cell cycle / : / spindle microtubule / RHO GTPases Activate Formins / sensory perception of sound / kinetochore / small GTPase binding / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / mitotic cell cycle / protein-folding chaperone binding / Neddylation / midbody / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / negative regulation of apoptotic process / apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsSun, C. / Nettesheim, D. / Liu, Z. / Olejniczak, E.T.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure of human survivin and its binding interface with smac/diablo
Authors: Sun, C. / Nettesheim, D. / Liu, Z. / Olejniczak, E.T.
History
DepositionOct 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apoptosis inhibitor survivin
B: Apoptosis inhibitor survivin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0854
Polymers26,9552
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
RepresentativeModel #1minimized average structure

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Components

#1: Protein Apoptosis inhibitor survivin / Baculoviral IAP repeat-containing protein 5 / Apoptosis inhibitor 4


Mass: 13477.332 Da / Num. of mol.: 2 / Fragment: residues 1-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pet15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) / References: UniProt: O15392
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1343d 12C filtered 13C-sep NOESY
NMR detailsText: This structure was determined using standard 3D NMR techniques

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Sample preparation

Sample conditionsIonic strength: 50 mM phosphate / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Bruker DRXBrukerDRX8003

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Processing

NMR softwareName: CNX / Version: 2000.1 / Developer: Brunger / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structures were calculated using 1394 intra-monomer NOE constraints, thirty hydrogen bond restraints derived from an analysis of amide exchange rates and fifty-six torsional restraints from ...Details: Structures were calculated using 1394 intra-monomer NOE constraints, thirty hydrogen bond restraints derived from an analysis of amide exchange rates and fifty-six torsional restraints from an analysis of the backbone chemical shifts. Dimer structures were calculated using additional inter-monomer NOE constraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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