[English] 日本語
Yorodumi
- PDB-9sv0: Crystal structure of Aurora-A bound to DBS4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9sv0
TitleCrystal structure of Aurora-A bound to DBS4
Components
  • Aurora kinase A
  • DBS4
KeywordsTRANSFERASE / Kinase / Binder / Complex
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / cilium disassembly / spindle pole centrosome / mitotic centrosome separation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / regulation of G2/M transition of mitotic cell cycle / germinal vesicle / meiotic spindle organization / meiotic spindle / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / positive regulation of mitotic cell cycle / positive regulation of mitotic nuclear division / protein serine/threonine/tyrosine kinase activity / centriole / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / AURKA Activation by TPX2 / regulation of signal transduction by p53 class mediator / molecular function activator activity / mitotic spindle organization / regulation of cytokinesis / G2/M transition of mitotic cell cycle / response to wounding / regulation of protein stability / peptidyl-serine phosphorylation / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spindle / kinetochore / spindle pole / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / protein autophosphorylation / mitotic cell cycle / ciliary basal body / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / microtubule / protein kinase activity / protein phosphorylation / non-specific serine/threonine protein kinase / postsynaptic density / protein heterodimerization activity / negative regulation of gene expression / protein serine kinase activity / cell division / ubiquitin protein ligase binding / protein serine/threonine kinase activity / centrosome / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
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. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHATE ION / Aurora kinase A
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsMiles, J.A. / Bayliss, R.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V003577/1 United Kingdom
CitationJournal: Biorxiv / Year: 2026
Title: Selective miniprotein inhibitors of Aurora-A kinase designed using interaction-motif scaffolding
Authors: Miles, J.A. / Schiffrin, B. / Holder, J. / Wallis, E.J. / Manfield, I.W. / Burnap, S.A. / Struwe, W.B. / Gergely, F. / Bayliss, R.
History
DepositionSep 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DBS4
B: Aurora kinase A
C: DBS4
D: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,53111
Polymers81,1154
Non-polymers1,4177
Water4,270237
1
A: DBS4
B: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4276
Polymers40,5572
Non-polymers8704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-19 kcal/mol
Surface area15130 Å2
MethodPISA
2
C: DBS4
D: Aurora kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1045
Polymers40,5572
Non-polymers5463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-25 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.33, 88.33, 240.29
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21C
32B
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGASPASPAA9 - 649 - 64
211ARGARGASPASPCC9 - 649 - 64
322GLNGLNSERSERBB127 - 3879 - 269
422GLNGLNSERSERDD127 - 3879 - 269

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein DBS4


Mass: 7657.715 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)
#2: 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: 32899.668 Da / Num. of mol.: 2 / Mutation: C290A C393A D274N
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

-
Non-polymers , 5 types, 244 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.09M NPS, 0.1M Buffer system 2 pH 7.5, 30% Precipitant mix 1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 22, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.23→60.45 Å / Num. obs: 47348 / % possible obs: 99.9 % / Redundancy: 26.4 % / CC1/2: 1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.23→2.27 Å / Num. unique obs: 2234 / CC1/2: 0.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.23→60.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.237 / WRfactor Rwork: 0.19 / SU B: 8.017 / SU ML: 0.183 / Average fsc free: 0.9336 / Average fsc work: 0.9537 / Cross valid method: FREE R-VALUE / ESU R: 0.219 / ESU R Free: 0.196
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2493 2318 4.906 %
Rwork0.2014 44933 -
all0.204 --
obs-47251 99.698 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.602 Å2
Baniso -1Baniso -2Baniso -3
1--0.349 Å20 Å2-0 Å2
2---0.349 Å2-0 Å2
3---0.697 Å2
Refinement stepCycle: LAST / Resolution: 2.23→60.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 87 237 5363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125270
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164868
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.8457190
X-RAY DIFFRACTIONr_angle_other_deg0.4691.74411209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.461539
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75710819
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.38710229
X-RAY DIFFRACTIONr_chiral_restr0.0660.2815
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026190
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021216
X-RAY DIFFRACTIONr_nbd_refined0.2160.21130
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24426
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22601
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2226
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.212
X-RAY DIFFRACTIONr_nbd_other0.1530.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.211
X-RAY DIFFRACTIONr_mcbond_it5.2466.1952590
X-RAY DIFFRACTIONr_mcbond_other5.2396.1942590
X-RAY DIFFRACTIONr_mcangle_it7.27911.1293234
X-RAY DIFFRACTIONr_mcangle_other7.27811.1293235
X-RAY DIFFRACTIONr_scbond_it6.1816.4942680
X-RAY DIFFRACTIONr_scbond_other6.1696.4912676
X-RAY DIFFRACTIONr_scangle_it8.91311.7583956
X-RAY DIFFRACTIONr_scangle_other8.88711.7493951
X-RAY DIFFRACTIONr_lrange_it11.2558.3065946
X-RAY DIFFRACTIONr_lrange_other11.25558.2565925
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.051544
X-RAY DIFFRACTIONr_ncsr_local_group_20.080.058279
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.087750.05009
12AX-RAY DIFFRACTIONLocal ncs0.087750.05009
23AX-RAY DIFFRACTIONLocal ncs0.080410.05009
24AX-RAY DIFFRACTIONLocal ncs0.080410.05009
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
2.23-2.2880.3811450.39431710.39434380.8010.83196.45140.395
2.288-2.3510.3791690.31731770.3233460.8760.9161000.317
2.351-2.4190.3221700.30430820.30532520.9220.931000.303
2.419-2.4930.3241520.28430180.28631700.9280.9431000.279
2.493-2.5740.3071420.26129280.26330700.9350.9551000.247
2.574-2.6650.3321640.25328360.25830000.9360.961000.231
2.665-2.7650.3351340.23227460.23728800.9280.9641000.207
2.765-2.8780.2911340.21126270.21527610.9420.9721000.185
2.878-3.0050.2671390.21325420.21626810.9460.9711000.186
3.005-3.1520.2511280.20624380.20825660.9540.9721000.177
3.152-3.3220.2551240.20623030.20924270.9570.9741000.185
3.322-3.5220.2391150.20822120.2123290.9620.97599.91410.19
3.522-3.7650.2521070.19720770.221860.9620.97799.90850.182
3.765-4.0650.246950.17519400.17920490.9620.98499.31670.166
4.065-4.4510.1981000.14618130.14919130.9790.9871000.144
4.451-4.9730.163740.14416460.14417200.9860.9881000.146
4.973-5.7360.237770.18714650.18915420.9680.9811000.188
5.736-7.0090.271690.21512630.21813320.9530.9751000.221
7.009-9.8470.184500.16910170.16910670.9810.9831000.191
9.847-60.450.278300.2136320.2166620.9310.9721000.276

+
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