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- PDB-2rax: Crystal structure of Borealin (20-78) bound to Survivin (1-120) -

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Basic information

Entry
Database: PDB / ID: 2rax
TitleCrystal structure of Borealin (20-78) bound to Survivin (1-120)
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 / mitotic spindle organization / 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 / positive regulation of protein phosphorylation / 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: 3.3 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 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
E: Baculoviral IAP repeat-containing protein 5
F: Borealin
X: Baculoviral IAP repeat-containing protein 5
Y: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3449
Polymers67,1486
Non-polymers1963
Water0
1
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4483
Polymers22,3832
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-16 kcal/mol
Surface area11510 Å2
MethodPISA
2
E: Baculoviral IAP repeat-containing protein 5
F: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4483
Polymers22,3832
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-16 kcal/mol
Surface area11650 Å2
MethodPISA
3
X: Baculoviral IAP repeat-containing protein 5
Y: Borealin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4483
Polymers22,3832
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-17 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.521, 145.521, 217.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 14116.995 Da / Num. of mol.: 3 / Fragment: residues 1-120
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.: 3 / Fragment: N-terminal fragment, 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.: 3 / 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: 4.29 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5 ul protein plus 0.5 uL well solution consisting of 0.1 M HEPES, pH 7.5; 10% (w/v) PEG 8000; 8 % (v/v) ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 23, 2007
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 17601 / Num. obs: 17601 / % possible obs: 98.7 % / Observed criterion σ(F): 0.008 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 80 Å2 / Rsym value: 0.105 / Net I/σ(I): 8.4
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Rsym value: 0.462 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Survivin 1-142 (truncated to 1-120) + borealin

Resolution: 3.3→29.63 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.89 / SU B: 55.308 / SU ML: 0.414 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R Free: 0.507 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28421 1010 6 %Thin shells
Rwork0.23625 ---
all0.239 16882 --
obs0.23896 15872 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.719 Å2
Refinement stepCycle: LAST / Resolution: 3.3→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4276 0 3 0 4279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224381
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.9615910
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2135513
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75324.721233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.29815792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6131527
X-RAY DIFFRACTIONr_chiral_restr0.090.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023368
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22005
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22987
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.612.52667
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.42254192
X-RAY DIFFRACTIONr_scbond_it2.3262.51925
X-RAY DIFFRACTIONr_scangle_it4.03451718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.304→3.371 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.338 179 -
Rwork0.298 651 -
obs-830 82.59 %
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)
11.34252.32240.62324.08181.79388.2557-0.26620.13160.0615-0.24230.41560.2185-0.062-0.2335-0.1494-0.14850.1077-0.1681-0.096-0.10080.022517.9126-52.7974-15.5462
211.0609-5.0141-4.18752.69371.88092.3438-0.1268-0.3206-0.653-0.04920.08680.38140.06170.08940.04-0.08530.2061-0.0813-0.1714-0.07110.000632.7223-51.83891.9042
38.22731.0307-4.08234.4876-0.93775.5488-0.50830.0515-1.397-0.0294-0.08030.88350.8069-0.63510.5886-0.05040.01750.0406-0.1016-0.14710.26843.0346-80.3962-11.6682
45.3656-4.1789-4.46674.1063.56373.72680.39830.2974-0.2428-0.592-0.48570.2272-0.332-0.27710.0873-0.0850.2766-0.14060.0063-0.086-0.098150.6802-58.8942-12.1981
55.1151-3.2542-4.6436.46013.11644.4241-0.22610.626-0.4404-1.39210.0334-0.4610.35170.23020.19270.4695-0.46060.14050.1286-0.0978-0.203515.0125-61.944925.2547
61.86765.3531-1.155616.2087-2.86660.9447-0.35460.15790.3119-0.86640.42440.89690.1726-0.0519-0.06980.0291-0.439-0.1288-0.01370.0355-0.0390.8588-61.098342.9303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 948 - 97
2X-RAY DIFFRACTION1AG341
3X-RAY DIFFRACTION2AA95 - 11998 - 122
4X-RAY DIFFRACTION2BB19 - 761 - 58
5X-RAY DIFFRACTION3EC5 - 948 - 97
6X-RAY DIFFRACTION3EH341
7X-RAY DIFFRACTION4EC95 - 11998 - 122
8X-RAY DIFFRACTION4FD19 - 761 - 58
9X-RAY DIFFRACTION5XE5 - 948 - 97
10X-RAY DIFFRACTION5XI341
11X-RAY DIFFRACTION6XE95 - 11998 - 122
12X-RAY DIFFRACTION6YF19 - 761 - 58

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