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- PDB-2qfa: Crystal structure of a Survivin-Borealin-INCENP core complex -

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Basic information

Entry
Database: PDB / ID: 2qfa
TitleCrystal structure of a Survivin-Borealin-INCENP core complex
Components
  • Baculoviral IAP repeat-containing protein 5
  • BorealinCDCA8
  • Inner centromere protein
KeywordsCell cycle/Cell cycle/Cell cycle / three-helical-bundle / long helix / protein complex / Alternative splicing / Apoptosis / Cell cycle / Cell division / Centromere / Chromosomal protein / Cytoplasm / Metal-binding / Mitosis / Nucleus / Phosphorylation / Polymorphism / Protease inhibitor / Thiol protease inhibitor / Zinc / Coiled coil / Microtubule / Cell cycle-Cell cycle-Cell cycle COMPLEX
Function / homology
Function and homology information


meiotic spindle midzone / meiotic spindle midzone assembly / central element / survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint ...meiotic spindle midzone / meiotic spindle midzone assembly / central element / survivin complex / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of exit from mitosis / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / 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 / lateral element / 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 / pericentric heterochromatin / 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 / molecular function activator activity / chromosome segregation / 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 / nuclear body / 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 - #3600 / 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 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3600 / 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 / Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Baculoviral IAP repeat-containing protein 5 / Borealin / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsJeyaprakash, A.A. / Klein, U.R. / Lindner, D. / Ebert, J. / Nigg, E.A. / Conti, E.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Structure of a Survivin-Borealin-INCENP Core Complex Reveals How Chromosomal Passengers Travel Together.
Authors: Jeyaprakash, A.A. / Klein, U.R. / Lindner, D. / Ebert, J. / Nigg, E.A. / Conti, E.
History
DepositionJun 27, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_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_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
C: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8715
Polymers29,6103
Non-polymers2612
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.467, 78.793, 100.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 16414.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / 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: 7649.897 Da / Num. of mol.: 1 / Fragment: UNP residues 15-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q53HL2

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Inner centromere protein


Mass: 5545.409 Da / Num. of mol.: 1 / Fragment: UNP residues 1-47
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q9NQS7

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Non-polymers , 3 types, 329 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6
Details: 50mM MES pH6, 10% PEG3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.4→42 Å / Num. obs: 64114 / % possible obs: 96 % / Redundancy: 5.1 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7613 / Rsym value: 0.327 / % possible all: 80.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→42 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.826 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3802 5.9 %RANDOM
Rwork0.184 ---
obs0.186 64044 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.956 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.4→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2090 0 13 327 2430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222156
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9792916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4225264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03624.483116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74115423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4071518
X-RAY DIFFRACTIONr_chiral_restr0.1390.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021650
X-RAY DIFFRACTIONr_nbd_refined0.2030.21037
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21500
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1090.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.227
X-RAY DIFFRACTIONr_mcbond_it1.0131.51306
X-RAY DIFFRACTIONr_mcangle_it1.54422048
X-RAY DIFFRACTIONr_scbond_it2.1223955
X-RAY DIFFRACTIONr_scangle_it3.3214.5856
X-RAY DIFFRACTIONr_rigid_bond_restr1.25932261
X-RAY DIFFRACTIONr_sphericity_free2.5173328
X-RAY DIFFRACTIONr_sphericity_bonded1.73832102
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 201 -
Rwork0.228 3366 -
obs-3567 73.33 %

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