[English] 日本語
Yorodumi
- PDB-6yie: Structure of a Borealin-INCENP-Survivin complex -

+
Open data


ID or keywords:

Loading...

-
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 / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly ...central element / meiotic spindle midzone / survivin complex / meiotic spindle midzone assembly / establishment of chromosome localization / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of exit from mitosis / 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 / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / mitotic cytokinesis / mitotic sister chromatid segregation / SUMOylation of DNA replication proteins / chromosome, centromeric region / cysteine-type endopeptidase inhibitor activity / mitotic spindle assembly / chromosome organization / spindle midzone / 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 / sensory perception of sound / RHO GTPases Activate Formins / small GTPase binding / kinetochore / spindle / G2/M transition of mitotic cell cycle / Separation of Sister Chromatids / mitotic cell cycle / protein-folding chaperone binding / Neddylation / microtubule cytoskeleton / midbody / microtubule binding / Interleukin-4 and Interleukin-13 signaling / microtubule / nuclear body / protein heterodimerization activity / cell division / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / 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 / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more