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- PDB-1m4m: Mouse Survivin -

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Basic information

Entry
Database: PDB / ID: 1m4m
TitleMouse Survivin
ComponentsBACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
KeywordsAPOPTOSIS / Zn Finger Baculovirus IAP repeat
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / SUMOylation of DNA replication proteins / kinetochore => GO:0000776 / establishment of chromosome localization / positive regulation of exit from mitosis / regulation of type B pancreatic cell proliferation / 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 ...small GTPase binding => GO:0031267 / SUMOylation of DNA replication proteins / kinetochore => GO:0000776 / establishment of chromosome localization / positive regulation of exit from mitosis / regulation of type B pancreatic cell proliferation / 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 / interphase microtubule organizing center / RHO GTPases Activate Formins / Separation of Sister Chromatids / regulation of insulin secretion involved in cellular response to glucose stimulus / Neddylation / protein-containing complex localization / chromosome passenger complex / nuclear chromosome / mitotic spindle assembly checkpoint signaling / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / cytoplasmic microtubule / positive regulation of cell cycle / regulation of mitotic cell cycle / centriole / positive regulation of mitotic cell cycle / tubulin binding / chromosome segregation / spindle microtubule / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / midbody / protein-folding chaperone binding / microtubule binding / negative regulation of neuron apoptotic process / apical plasma membrane / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / identical protein binding / nucleus / 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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.8 Å
AuthorsMuchmore, S.W. / Chen, J. / Jakob, C. / Zakula, D. / Matayoshi, E.D. / Wu, W. / Zhang, H. / Li, F. / Ng, S.C. / Altieri, D.C.
CitationJournal: MOL.CELL / Year: 2000
Title: CRYSTAL STRUCTURE AND MUTAGENIC ANALYSIS OF THE INHIBITOR-OF-APOPTOSIS PROTEIN SURVIVIN
Authors: Muchmore, S.W. / Chen, J. / Jakob, C. / Zakula, D. / Matayoshi, E.D. / Wu, W. / Zhang, H. / Li, F. / Ng, S.C. / Altieri, D.C.
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4503
Polymers16,3201
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
hetero molecules

A: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9016
Polymers32,6392
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1050 Å2
ΔGint-55 kcal/mol
Surface area13500 Å2
MethodPISA
3
A: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
hetero molecules

A: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9016
Polymers32,6392
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
MethodPQS
Unit cell
Length a, b, c (Å)41.43, 41.43, 291.34
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-501-

ZN

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Components

#1: Protein BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 5 / Apoptosis inhibitor survivin / Apoptosis inhibitor 4 / TIAP


Mass: 16319.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O70201
#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: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Isopropanol, cacodylate potassium chloride, magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110-20 %isopropanol1reservoir
20.05 Msodium cacodylate1reservoirpH6.0
30.1 M1reservoirKCl
40.05 M1reservoirMgCl2
510 mMHEPES1droppH7.5
6150 mM1dropNaCl
72 mMBME1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11.2822, 1.2831, 1.2716
SYNCHROTRONAPS 17-ID21.2
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 20, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28221
21.28311
31.27161
41.21
ReflectionResolution: 2.7→50 Å / Num. obs: 4576 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.043
Reflection shellHighest resolution: 2.7 Å / % possible all: 81
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 50 Å / Num. obs: 4579 / % possible obs: 94.1 % / Num. measured all: 23422 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 85.2 % / Rmerge(I) obs: 0.135

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNXrefinement
HKL-2000data reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.8→50 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 388 -Random
Rwork0.243 ---
obs-3891 94.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 2 0 930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.54
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 35 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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