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- PDB-4j8n: Aurora A Kinase Apo -

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Basic information

Entry
Database: PDB / ID: 4j8n
TitleAurora A Kinase Apo
ComponentsAurora kinase A
KeywordsTRANSFERASE / Aurora A / kinase domain
Function / homology
Function and homology information


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 ...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 / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / neuron projection extension / spindle organization / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / spindle midzone / regulation of G2/M transition of mitotic cell cycle / negative regulation of protein binding / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / 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 / 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 / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / glutamatergic synapse / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.135 Å
AuthorsMeyerowitz, J.G. / Gustafson, W.C. / Shokat, K.M. / Weiss, W.A.
CitationJournal: Cancer Cell / Year: 2014
Title: Drugging MYCN through an Allosteric Transition in Aurora Kinase A.
Authors: Gustafson, W.C. / Meyerowitz, J.G. / Nekritz, E.A. / Chen, J. / Benes, C. / Charron, E. / Simonds, E.F. / Seeger, R. / Matthay, K.K. / Hertz, N.T. / Eilers, M. / Shokat, K.M. / Weiss, W.A.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
B: Aurora kinase A
C: Aurora kinase A
D: Aurora kinase A


Theoretical massNumber of molelcules
Total (without water)129,4364
Polymers129,4364
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aurora kinase A


Theoretical massNumber of molelcules
Total (without water)32,3591
Polymers32,3591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Aurora kinase A


Theoretical massNumber of molelcules
Total (without water)32,3591
Polymers32,3591
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Aurora kinase A


Theoretical massNumber of molelcules
Total (without water)32,3591
Polymers32,3591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Aurora kinase A


Theoretical massNumber of molelcules
Total (without water)32,3591
Polymers32,3591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.783, 83.783, 171.777
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor- ...Aurora 2 / Aurora/IPL1-related kinase 1 / ARK-1 / Aurora-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine-protein kinase 15 / Serine/threonine-protein kinase 6 / Serine/threonine-protein kinase aurora-A


Mass: 32359.123 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: AIK, AIRK1, ARK1, AURA, AURKA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7
Details: 20 mg/ml Aurora A protein, 10% Tacsimate, 20% (w/v) PEG3350, pH 7.0, Hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0088 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2012
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0088 Å / Relative weight: 1
ReflectionResolution: 3.13→50 Å / Num. obs: 23697 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.059 / Χ2: 1.003 / Net I/σ(I): 18.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.13-3.186.20.40411840.9411100
3.18-3.246.20.30111961.0041100
3.24-3.36.20.24312121.0251100
3.3-3.376.20.19511690.9761100
3.37-3.446.20.16611810.9741100
3.44-3.536.20.13211750.9831100
3.53-3.616.20.11212051.0161100
3.61-3.716.20.0911560.9861100
3.71-3.826.20.08120411100
3.82-3.946.20.07111710.9981100
3.94-4.086.20.06111740.966199.9
4.08-4.256.20.05912040.9911100
4.25-4.446.20.05811891.0671100
4.44-4.676.20.06511931.064199.9
4.67-4.976.20.07311591.0821100
4.97-5.356.20.08311900.9991100
5.35-5.896.10.07811761.0021100
5.89-6.746.10.06111751.0011100
6.74-8.4860.03812081.024199.9
8.48-506.10.0311760.958199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.135→44.949 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7991 / SU ML: 0.45 / σ(F): 1.98 / Phase error: 27.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 2031 8.6 %
Rwork0.1841 --
obs0.1884 23622 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 243.24 Å2 / Biso mean: 114.8341 Å2 / Biso min: 38.39 Å2
Refinement stepCycle: LAST / Resolution: 3.135→44.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8731 0 0 8 8739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048951
X-RAY DIFFRACTIONf_angle_d0.88612097
X-RAY DIFFRACTIONf_chiral_restr0.051295
X-RAY DIFFRACTIONf_plane_restr0.0031551
X-RAY DIFFRACTIONf_dihedral_angle_d14.3233399
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1347-3.20760.35171330.291514571590100
3.2076-3.28780.34361280.252214351563100
3.2878-3.37670.33431340.253514621596100
3.3767-3.4760.29061400.245714531593100
3.476-3.58810.28751340.242714181552100
3.5881-3.71630.37781340.225514431577100
3.7163-3.8650.24361340.207614371571100
3.865-4.04080.18761440.182114431587100
4.0408-4.25370.17381420.166414421584100
4.2537-4.520.18791340.143314371571100
4.52-4.86860.24441380.155514371575100
4.8686-5.35790.25491340.16614401574100
5.3579-6.13150.21781290.189914351564100
6.1315-7.71870.23431400.175114581598100
7.7187-44.95340.19531330.16281394152797
Refinement TLS params.Method: refined / Origin x: 32.8179 Å / Origin y: 126.1441 Å / Origin z: 0.0191 Å
111213212223313233
T0.8358 Å2-0.0283 Å2-0.0338 Å2-0.8036 Å2-0.0606 Å2--0.8275 Å2
L0.7024 °2-0.4523 °2-0.0024 °2-0.1556 °20.048 °2--0.2642 °2
S-0.003 Å °-0.0383 Å °0.0154 Å °-0.027 Å °-0.0235 Å °0.0429 Å °0.0255 Å °0.0208 Å °0.0394 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA125 - 390
2X-RAY DIFFRACTION1allB125 - 390
3X-RAY DIFFRACTION1allC125 - 390
4X-RAY DIFFRACTION1allD126 - 390
5X-RAY DIFFRACTION1allA - D1 - 502

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