[English] 日本語
Yorodumi
- PDB-8pr7: Aurora-A in complex with CEP192 and an inhibitory monobody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pr7
TitleAurora-A in complex with CEP192 and an inhibitory monobody
Components
  • Aurora kinase A
  • Centrosomal protein of 192 kDa
  • Monobody
KeywordsTRANSFERASE / kinase / inhibitor / allosteric / disordered / phosphorylation
Function / homology
Function and homology information


centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex ...centrosome-templated microtubule nucleation / procentriole / procentriole replication complex / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / germinal vesicle / meiotic spindle / centrosome cycle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / pericentriolar material / mitotic spindle pole / centriole replication / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / phosphatase binding / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / liver regeneration / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / mitotic spindle organization / response to bacterium / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / kinetochore / response to wounding / spindle / spindle pole / G2/M transition of mitotic cell cycle / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / peptidyl-serine phosphorylation / microtubule cytoskeleton / midbody / protein autophosphorylation / basolateral plasma membrane / Regulation of TP53 Activity through Phosphorylation / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein phosphorylation / protein heterodimerization activity / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / centrosome
Similarity search - Function
Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 ...Centrosomal protein Spd-2/CEP192 / : / : / : / : / : / Cep192 domain 1 / Cep192 domain 2 / Cep192 domain 7 / Cep192 domain 8 / Cep192 domain 3 / : / : / : / Cep192 domain 4 / Cep192 domain 5 / Cep192 domain 6 / Aurora kinase A / Aurora kinase / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / Centrosomal protein of 192 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsMiles, J.A. / Bayliss, R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
CitationJournal: Embo J. / Year: 2024
Title: CEP192 localises mitotic Aurora-A activity by priming its interaction with TPX2.
Authors: Holder, J. / Miles, J.A. / Batchelor, M. / Popple, H. / Walko, M. / Yeung, W. / Kannan, N. / Wilson, A.J. / Bayliss, R. / Gergely, F.
History
DepositionJul 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aurora kinase A
B: Monobody
C: Centrosomal protein of 192 kDa
D: Aurora kinase A
E: Monobody
F: Centrosomal protein of 192 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,49110
Polymers101,5216
Non-polymers9714
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.580, 112.580, 216.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 2 types, 4 molecules ADCF

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / Breast tumor-amplified kinase / Ipl1- and aurora-related kinase 1 / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase Ayk1 / Serine/threonine-protein kinase aurora-A


Mass: 32581.432 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Production host: Escherichia coli (E. coli)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#3: Protein Centrosomal protein of 192 kDa / Cep192 / Cep192/SPD-2


Mass: 8049.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP192, KIAA1569, PP8407 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TEP8

-
Antibody , 1 types, 2 molecules BE

#2: Antibody Monobody


Mass: 10129.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 91 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.06M Divalents, Buffer system 1 pH 6.5, 40% Ethylene glycol, 20% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.76→64.112 Å / Num. obs: 36627 / % possible obs: 100 % / Redundancy: 25.9 % / CC1/2: 1 / Net I/σ(I): 19.7
Reflection shellResolution: 2.76→2.81 Å / Num. unique obs: 49063 / CC1/2: 0.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.76→64.112 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.256 / WRfactor Rwork: 0.201 / SU B: 14.791 / SU ML: 0.28 / Average fsc free: 0.939 / Average fsc work: 0.959 / Cross valid method: FREE R-VALUE / ESU R: 0.418 / ESU R Free: 0.298
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2564 1904 5.209 %
Rwork0.2023 34648 -
all0.205 --
obs-36552 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 92.224 Å2
Baniso -1Baniso -2Baniso -3
1-1.438 Å2-0 Å2-0 Å2
2--1.438 Å20 Å2
3----2.875 Å2
Refinement stepCycle: LAST / Resolution: 2.76→64.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5772 0 61 87 5920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0125982
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165283
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6518184
X-RAY DIFFRACTIONr_angle_other_deg0.4971.56412073
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3225764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.636527
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.21552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12210812
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.21510241
X-RAY DIFFRACTIONr_chiral_restr0.0650.2930
X-RAY DIFFRACTIONr_chiral_restr_other0.0440.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021375
X-RAY DIFFRACTIONr_nbd_refined0.2360.21105
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.24873
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22919
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.23167
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.25
X-RAY DIFFRACTIONr_nbd_other0.1770.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2460.24
X-RAY DIFFRACTIONr_mcbond_it10.52510.343080
X-RAY DIFFRACTIONr_mcbond_other10.51610.343080
X-RAY DIFFRACTIONr_mcangle_it14.31218.5753836
X-RAY DIFFRACTIONr_mcangle_other14.3118.5763837
X-RAY DIFFRACTIONr_scbond_it11.95510.6142902
X-RAY DIFFRACTIONr_scbond_other11.95310.6172903
X-RAY DIFFRACTIONr_scangle_it16.61619.2444348
X-RAY DIFFRACTIONr_scangle_other16.61419.2464349
X-RAY DIFFRACTIONr_lrange_it19.922122.59723532
X-RAY DIFFRACTIONr_lrange_other19.925122.60123519
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.76-2.8320.4141260.37525130.37626390.860.8811000.374
2.832-2.9090.3951160.36724360.36825520.8830.9061000.366
2.909-2.9930.3991100.31924210.32225310.90.9291000.311
2.993-3.0850.3451400.26423130.26824530.9270.9561000.25
3.085-3.1860.2991400.22322340.22823740.940.9661000.202
3.186-3.2980.2751230.21521680.21822910.9510.9681000.191
3.298-3.4220.2591150.21321020.21522170.9510.971000.19
3.422-3.5610.321120.2120280.21521400.930.9731000.187
3.561-3.7190.2711140.19319560.19820700.9530.9771000.176
3.719-3.90.261870.17518810.17919680.9530.9811000.161
3.9-4.110.2251100.15517700.15918800.9680.9851000.146
4.11-4.3580.216870.14917160.15318030.970.9871000.144
4.358-4.6570.204930.14615890.14916820.9740.9871000.146
4.657-5.0280.211900.15115010.15415910.9730.9861000.155
5.028-5.5050.259760.16913830.17414590.9570.9831000.174
5.505-6.1490.27670.2212710.22213380.9560.9721000.224
6.149-7.0890.286650.24411310.24611960.9430.9631000.255
7.089-8.6560.279540.1989810.20210350.9460.9761000.226
8.656-12.1310.203510.177660.1728170.9780.9841000.209
12.131-64.1120.282280.3594880.3545190.9440.90699.4220.468

+
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