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- PDB-2raw: Crystal structure of the Borealin-Survivin complex -

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Basic information

Entry
Database: PDB / ID: 2raw
TitleCrystal structure of the Borealin-Survivin complex
Components
  • Baculoviral IAP repeat-containing protein 5
  • BorealinCDCA8
KeywordsCELL CYCLE / DasraB / chromosomal passender complex / IAP / BIR / Apoptosis / Cell division / Centromere / Chromosomal protein / Metal-binding / Mitosis / Nucleus / Phosphorylation / Protease inhibitor / Thiol protease inhibitor
Function / homology
Function and homology information


survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center ...survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / protein-containing complex localization / chromosome passenger complex / cobalt ion binding / mitotic metaphase chromosome alignment / cysteine-type endopeptidase inhibitor activity / intercellular bridge / 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 / mitotic sister chromatid segregation / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / chromosome organization / spindle midzone / cytoplasmic microtubule / 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 / positive regulation of mitotic cell cycle / tubulin binding / RHO GTPases Activate Formins / spindle microtubule / sensory perception of sound / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / spindle / kinetochore / small GTPase binding / Separation of Sister Chromatids / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / mitotic cell cycle / Neddylation / midbody / protein-folding chaperone binding / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / protein heterodimerization activity / cell division / protein phosphorylation / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1900 / Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A / BIR repeat / Inhibitor of Apoptosis domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1900 / Borealin, N-terminal / Cell division protein borealin / Borealin, C-terminal / Nbl1 / Borealin N terminal / Cell division cycle-associated protein 8 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Borealin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHymowitz, S.G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The mitotic regulator Survivin binds as a monomer to its functional interactor Borealin.
Authors: Bourhis, E. / Hymowitz, S.G. / Cochran, A.G.
History
DepositionSep 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0283
Polymers24,9632
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-24 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.700, 51.681, 46.289
Angle α, β, γ (deg.)90.00, 98.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16697.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 pLysS Rosetta 2 / References: UniProt: O15392
#2: Protein Borealin / CDCA8 / Dasra-B / hDasra-B / Cell division cycle-associated protein 8 / Pluripotent embryonic stem cell- ...Dasra-B / hDasra-B / Cell division cycle-associated protein 8 / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 8265.524 Da / Num. of mol.: 1 / Fragment: N-terminal region (residues 20-78)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Plasmid: pET-21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 pLysS Rosetta 2 / References: UniProt: Q53HL2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 ul protein and 0.5 ul well solution (0.1 M Na HEPES, pH 7.5; 0.2 M CaCl2; 28% (w/v) PEG 400), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2007
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 10387 / Num. obs: 10387 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 51 Å2 / Rsym value: 0.048 / Net I/σ(I): 14.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 1045 / Rsym value: 0.21 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3H chain A

1f3h


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.904 / SU B: 23.825 / SU ML: 0.251 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS refinement / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.45 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; Data was very anisotropic which limited resolution
RfactorNum. reflection% reflectionSelection details
Rfree0.29829 1044 10.2 %RANDOM
Rwork0.24826 ---
all0.25354 10207 --
obs0.25354 9163 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.453 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-7.11 Å2
2---0.21 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1597 0 1 0 1598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221591
X-RAY DIFFRACTIONr_bond_other_d0.0010.021144
X-RAY DIFFRACTIONr_angle_refined_deg1.1491.962143
X-RAY DIFFRACTIONr_angle_other_deg0.8513.0022755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2315191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11324.4379
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3915282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.41510
X-RAY DIFFRACTIONr_chiral_restr0.0630.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021755
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02328
X-RAY DIFFRACTIONr_nbd_refined0.2010.2343
X-RAY DIFFRACTIONr_nbd_other0.1840.21066
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2764
X-RAY DIFFRACTIONr_nbtor_other0.0890.2839
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.080.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.222
X-RAY DIFFRACTIONr_mcbond_it3.1842.51256
X-RAY DIFFRACTIONr_mcbond_other0.5552.5379
X-RAY DIFFRACTIONr_mcangle_it3.97151546
X-RAY DIFFRACTIONr_scbond_it2.992.5731
X-RAY DIFFRACTIONr_scangle_it4.4375597
LS refinement shellResolution: 2.401→2.484 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.316 88 -
Rwork0.277 762 -
obs-850 99.53 %
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)
14.45990.698.2881.15111.651720.04220.2624-0.0313-0.15690.21190.0124-0.15381.0952-0.2995-0.2748-0.307-0.00370.1313-0.20740.0005-0.295711.6573-1.3744.6104
212.91192.72267.32047.93222.19038.4564-1.9081-0.08732.9531-0.66850.11231.0594-2.0004-0.40191.79580.14230.1336-0.4868-0.1885-0.12740.41878.639418.372911.7541
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA94 - 14197 - 144
2X-RAY DIFFRACTION1BB21 - 763 - 58
3X-RAY DIFFRACTION2AA5 - 938 - 96
4X-RAY DIFFRACTION2AC341

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