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- PDB-6yie: Structure of a Borealin-INCENP-Survivin complex -

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Basic information

Entry
Database: PDB / ID: 6yie
TitleStructure of a Borealin-INCENP-Survivin complex
Components
  • Baculoviral IAP repeat-containing protein 5
  • Borealin
  • Inner centromere protein
KeywordsCELL CYCLE
Function / homology
Function and homology information


central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / : / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / positive regulation of exit from mitosis / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / interphase microtubule organizing center / lateral element / chromosome passenger complex / protein-containing complex localization / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / cobalt ion binding / mitotic metaphase chromosome alignment / nuclear chromosome / mitotic spindle assembly checkpoint signaling / spindle midzone / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic sister chromatid segregation / mitotic cytokinesis / SUMOylation of DNA replication proteins / chromosome, centromeric region / mitotic spindle assembly / cysteine-type endopeptidase inhibitor activity / chromosome organization / pericentric heterochromatin / intercellular bridge / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / centriole / tubulin binding / positive regulation of mitotic cell cycle / Resolution of Sister Chromatid Cohesion / molecular function activator activity / mitotic spindle organization / spindle microtubule / chromosome segregation / RHO GTPases Activate Formins / sensory perception of sound / kinetochore / small GTPase binding / G2/M transition of mitotic cell cycle / spindle / Separation of Sister Chromatids / mitotic cell cycle / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / midbody / Interleukin-4 and Interleukin-13 signaling / microtubule binding / microtubule / nuclear body / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / negative regulation of apoptotic process / nucleolus / enzyme binding / protein homodimerization activity / protein-containing complex / zinc ion binding / nucleoplasm / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
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 / 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 ...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 / Helix non-globular / Special / 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 / MOLECULAR REPLACEMENT / Resolution: 3.49 Å
AuthorsSerena, M. / Elliott, P.R. / Barr, F.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC20079/A15940 United Kingdom
CitationJournal: J.Cell Biol. / Year: 2020
Title: Molecular basis of MKLP2-dependent Aurora B transport from chromatin to the anaphase central spindle.
Authors: Serena, M. / Bastos, R.N. / Elliott, P.R. / Barr, F.A.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
C: Inner centromere protein
D: Baculoviral IAP repeat-containing protein 5
E: Borealin
F: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5398
Polymers70,4096
Non-polymers1312
Water00
1
A: Baculoviral IAP repeat-containing protein 5
B: Borealin
C: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2704
Polymers35,2043
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-65 kcal/mol
Surface area12300 Å2
MethodPISA
2
D: Baculoviral IAP repeat-containing protein 5
E: Borealin
F: Inner centromere protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2704
Polymers35,2043
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5550 Å2
ΔGint-66 kcal/mol
Surface area12780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.536, 78.824, 125.173
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRGLNGLN(chain 'A' and (resid 5 through 23 or (resid 24...AA5 - 1377 - 139
221THRTHRGLNGLN(chain 'D' and (resid 5 through 15 or (resid 16...DD5 - 1377 - 139
132ARGARGLEULEU(chain 'B' and ((resid 17 through 22 and (name N...BB17 - 768 - 67
242ARGARGLEULEU(chain 'E' and ((resid 17 through 22 and (name N...EE17 - 768 - 67
153GLYGLYPHEPHE(chain 'C' and (resid 7 through 42 or (resid 43...CC7 - 459 - 47
263GLYGLYPHEPHE(chain 'F' and (resid 7 through 34 or (resid 35...FF7 - 459 - 47

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 16568.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BIRC5, API4, IAP4 / Plasmid: pETDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: O15392
#2: Protein Borealin / Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell- ...Cell division cycle-associated protein 8 / Dasra-B / hDasra-B / Pluripotent embryonic stem cell-related gene 3 protein


Mass: 11617.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDCA8, PESCRG3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q53HL2
#3: Protein Inner centromere protein


Mass: 7018.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INCENP / Plasmid: PFAT2-His6-GST / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus (RIL) / References: UniProt: Q9NQS7
#4: Chemical ChemComp-ZN / ZINC ION


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

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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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 5 % (w/v) PEG 3,350, 50 mM MES pH 6.0

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.49→78.82 Å / Num. obs: 6947 / % possible obs: 88.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 65.27 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.162 / Net I/σ(I): 3.5
Reflection shellResolution: 3.49→3.83 Å / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1644 / CC1/2: 0.902

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFA

2qfa


Resolution: 3.49→66.7 Å / SU ML: 0.4279 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.3698
RfactorNum. reflection% reflection
Rfree0.3243 337 4.9 %
Rwork0.2686 --
obs0.2714 6882 87.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.38 Å2
Refinement stepCycle: LAST / Resolution: 3.49→66.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3583 0 2 0 3585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423666
X-RAY DIFFRACTIONf_angle_d0.81024990
X-RAY DIFFRACTIONf_chiral_restr0.0429561
X-RAY DIFFRACTIONf_plane_restr0.0061656
X-RAY DIFFRACTIONf_dihedral_angle_d12.55742190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.49-4.40.32291620.26763242X-RAY DIFFRACTION88.46
4.4-66.70.32521750.26933303X-RAY DIFFRACTION86.11
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)
10.9047604594620.01907341304450.8478580138910.1999777753740.1466403628141.87747193601-0.1340231265640.2404855289880.100825372603-0.07886665714820.1303832911240.3052663676130.5182039676620.57058988580.04628683750910.602281575280.006808735182020.1046140453170.0948705363937-0.01311226723260.327144478568-12.099799603821.4226293156-7.39132609556
20.536133570531-0.01141755447180.1641122574891.73217675518-0.4485803095020.872308761174-0.1843011209050.1373225286330.0239523264086-0.2701558164480.177632640736-0.09879812128870.3318174176390.06457464963610.1602639457281.14686666443-0.123729875284-0.1566303570230.162383691241-0.006810294452210.322843358939-19.433076175313.2581286366-22.9870933163
31.396273966880.529192678321-0.7559467636662.03932484946-1.283677413351.62987185451-0.287282810439-0.06844431289980.1702358306150.0747458544912-0.264942820331-0.698655495632-0.04606352488280.2439639039290.5697327013761.083858380770.09860748671820.05059567963360.2921756951110.1614385456770.39627285857-9.8410035529715.9357223823-31.8805902407
40.704322486143-0.1818187619240.3320631652491.84491939136-0.5769790000690.4979274271040.06639477045030.18214156308-0.127923736723-0.443450993371-0.148858346555-0.1651834786770.473827643619-0.0511214881870.04404783120731.311579763280.1927240732380.05083426965040.1760796795550.01625046106530.540145315432-14.615113467618.1684896852-82.3073492346
50.936729771135-0.300331146487-0.04538627912330.599591725314-0.02420894488670.461211811552-0.204998903153-0.2112391812790.0343729551467-0.0179095022860.1853785224730.132244103077-0.34240006355-0.1715879057980.072300097240.4002262030690.04439010401390.03759564947220.1336683952070.2879241821180.391794036384-23.179734756327.6232105005-68.1831937084
60.8462588391130.134019621565-0.2358606259661.32647990785-0.3365238991190.486170641971-0.0324821418523-0.4424056300310.1565414815430.385636570033-0.252515344434-0.338658361761-0.07256492431510.03816808552420.06492032965361.25902903095-0.132825253847-0.1494326996420.25501457971-0.1199276624220.433226998859-13.487549054325.2454075373-58.9069608798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 5 through 139)
2X-RAY DIFFRACTION2(chain 'B' and resid 15 through 76)
3X-RAY DIFFRACTION3(chain 'C' and resid 7 through 46)
4X-RAY DIFFRACTION4(chain 'D' and resid 5 through 137)
5X-RAY DIFFRACTION5(chain 'E' and resid 17 through 76)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 45)

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