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- PDB-6cpg: Structure of dephosphorylated Aurora A (122-403) in complex with ... -

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Basic information

Entry
Database: PDB / ID: 6cpg
TitleStructure of dephosphorylated Aurora A (122-403) in complex with inhibiting monobody and AT9283 in an inactive conformation
Components
  • Aurora kinase A
  • Monobody
Keywordstransferase/inhibitor / protein kinase / DFG-loop / monobody / AT9283 / TRANSFERASE / transferase-inhibitor complex
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 / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-35R / Aurora kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsOtten, R. / Kutter, S. / Zorba, A. / Padua, R.A.P. / Koide, A. / Koide, S. / Kern, D.
Funding support United States, 4items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
Office of Basic Energy Sciences, Catalysis Science Program United States
Department of Energy (DOE, United States)DE-FG02-05ER15699 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100966-01 United States
CitationJournal: Elife / Year: 2018
Title: Dynamics of human protein kinase Aurora A linked to drug selectivity.
Authors: Pitsawong, W. / Buosi, V. / Otten, R. / Agafonov, R.V. / Zorba, A. / Kern, N. / Kutter, S. / Kern, G. / Padua, R.A. / Meniche, X. / Kern, D.
History
DepositionMar 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Sep 5, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.6Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurora kinase A
B: Monobody
D: Aurora kinase A
E: Monobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4526
Polymers85,6894
Non-polymers7632
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: confirmed by analytical ultracentrifugation (sedimentation runs).
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-33 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.860, 69.700, 175.560
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

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Components

#1: Protein Aurora kinase A / Aurora 2 / Aurora/IPL1-related kinase 1 / hARK1 / Breast tumor-amplified kinase / Serine/threonine- ...Aurora 2 / Aurora/IPL1-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: 32990.754 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
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein Monobody


Mass: 9853.987 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pHBT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Chemical ChemComp-35R / 1-cyclopropyl-3-{3-[5-(morpholin-4-ylmethyl)-1H-benzimidazol-2-yl]-1H-pyrazol-4-yl}urea


Mass: 381.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O2 / Feature type: SUBJECT OF INVESTIGATION

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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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: A 1:1 ratio of protein mixture to mother liquor was obtained by combining 0.5 uL of sample [240 uM deP Aurora A + 1.0 mM AT9283 + 250 uM Mb] with 0.5 uL of mother liquor [0.1 M Bis-Tris, pH ...Details: A 1:1 ratio of protein mixture to mother liquor was obtained by combining 0.5 uL of sample [240 uM deP Aurora A + 1.0 mM AT9283 + 250 uM Mb] with 0.5 uL of mother liquor [0.1 M Bis-Tris, pH 5.5, 0.2 M magnesium chloride, 19% (w/v) PEG-3350].

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2017
RadiationMonochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.8→43.14 Å / Num. obs: 19845 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 90.44 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.074 / Rrim(I) all: 0.183 / Net I/σ(I): 8.9
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1418 / CC1/2: 0.625 / Rpim(I) all: 0.559 / Rrim(I) all: 1.338 / % possible all: 98.8

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Processing

Software
NameVersionClassification
xia2v0.4.0.0-158-gd975537data reduction
XDSBUILT 20161205data reduction
XDSBUILT 20161205data scaling
PHASERphasing
PHENIX1.13_2998refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MQ4, 3K2M

1mq4

3k2m


Resolution: 2.8→36.17 Å / SU ML: 0.5484 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.7707
RfactorNum. reflection% reflection
Rfree0.3349 1955 10 %
Rwork0.2792 --
obs0.2847 19556 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 85.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→36.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5122 0 56 0 5178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00175323
X-RAY DIFFRACTIONf_angle_d0.55457280
X-RAY DIFFRACTIONf_chiral_restr0.0411814
X-RAY DIFFRACTIONf_plane_restr0.0027929
X-RAY DIFFRACTIONf_dihedral_angle_d7.48583083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.42231310.40571179X-RAY DIFFRACTION94.38
2.87-2.950.4761320.42451189X-RAY DIFFRACTION94.22
2.95-3.030.391350.38471222X-RAY DIFFRACTION95.9
3.03-3.130.39021360.35721212X-RAY DIFFRACTION97.54
3.13-3.240.39231370.34841237X-RAY DIFFRACTION97.86
3.24-3.370.39471400.34111256X-RAY DIFFRACTION98.24
3.37-3.530.39771380.33671250X-RAY DIFFRACTION98.79
3.53-3.710.34321400.30681265X-RAY DIFFRACTION99.57
3.71-3.950.36081410.281269X-RAY DIFFRACTION99.16
3.95-4.250.33961420.271277X-RAY DIFFRACTION99.02
4.25-4.680.33261420.26521276X-RAY DIFFRACTION99.37
4.68-5.350.28741430.25071283X-RAY DIFFRACTION97.81
5.35-6.740.33011430.28281298X-RAY DIFFRACTION98.9
6.74-36.170.29351550.22951388X-RAY DIFFRACTION99.04

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