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- PDB-5g1x: Crystal structure of Aurora-A kinase in complex with N-Myc -

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Basic information

Entry
Database: PDB / ID: 5g1x
TitleCrystal structure of Aurora-A kinase in complex with N-Myc
Components
  • AURORA KINASE A
  • N-MYC PROTO-ONCOGENE PROTEIN
KeywordsTRANSFERASE / AURORA / AURORA-A / KINASE / N-MYC / MYC / NEUROBLASTOMA
Function / homology
Function and homology information


regulation of inner ear auditory receptor cell differentiation / embryonic skeletal system morphogenesis / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity ...regulation of inner ear auditory receptor cell differentiation / embryonic skeletal system morphogenesis / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / positive regulation of oocyte maturation / histone H3S10 kinase activity / chromosome passenger complex / pronucleus / astrocyte differentiation / positive regulation of programmed cell death / meiotic spindle / mitotic centrosome separation / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / positive regulation of mesenchymal cell proliferation / neuron projection extension / positive regulation of mitochondrial fission / spindle organization / embryonic digit morphogenesis / cartilage condensation / Signaling by ALK / branching morphogenesis of an epithelial tube / mitotic spindle pole / SUMOylation of DNA replication proteins / negative regulation of astrocyte differentiation / negative regulation of reactive oxygen species metabolic process / spindle midzone / regulation of G2/M transition of mitotic cell cycle / centriole / protein serine/threonine/tyrosine kinase activity / positive regulation of mitotic cell cycle / AURKA Activation by TPX2 / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of mitotic nuclear division / ciliary basal body / negative regulation of protein binding / regulation of cytokinesis / epithelial cell proliferation / regulation of signal transduction by p53 class mediator / molecular function activator activity / liver regeneration / positive regulation of epithelial cell proliferation / lung development / 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 / mitotic spindle / spindle / kinetochore / kinase binding / response to wounding / positive regulation of miRNA transcription / microtubule cytoskeleton / G2/M transition of mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / sequence-specific double-stranded DNA binding / mitotic cell cycle / midbody / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription activator activity, RNA polymerase II-specific / basolateral plasma membrane / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / microtubule / postsynaptic density / protein autophosphorylation / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / non-specific serine/threonine protein kinase / protein kinase activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / cell division / negative regulation of gene expression / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / apoptotic process / ubiquitin protein ligase binding / chromatin / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding
Similarity search - Function
Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Aurora kinase A / Helix-loop-helix DNA-binding domain / Aurora kinase / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. ...Transcription regulator Myc / Transcription regulator Myc, N-terminal / Myc amino-terminal region / Aurora kinase A / Helix-loop-helix DNA-binding domain / Aurora kinase / Helix-loop-helix DNA-binding domain superfamily / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / N-myc proto-oncogene protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRichards, M.W. / Burgess, S.G. / Bayliss, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structural Basis of N-Myc Binding by Aurora-A and its Destabilization by Kinase Inhibitors
Authors: Richards, M. / Burgess, S. / Poon, E. / Carstensen, A. / Eilers, M. / Chesler, L. / Bayliss, R.
History
DepositionMar 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Structure summary
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AURORA KINASE A
B: N-MYC PROTO-ONCOGENE PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6185
Polymers40,1422
Non-polymers4763
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-39.2 kcal/mol
Surface area13380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.520, 86.520, 92.210
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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 / AURORA-A


Mass: 32964.637 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 122-403 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein N-MYC PROTO-ONCOGENE PROTEIN / CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 37 / BHLHE37 / N-MYC


Mass: 7177.783 Da / Num. of mol.: 1 / Mutation: YES / Source method: obtained synthetically / Details: N-TERMINAL BIOTIN GROUP / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P04198
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES PRESENT ARE 122-403 OF AURORA-A. GA AT N- TERMINUS REMAINS FROM A PROTEASE CLEAVAGE ...RESIDUES PRESENT ARE 122-403 OF AURORA-A. GA AT N- TERMINUS REMAINS FROM A PROTEASE CLEAVAGE SEQUENCE. C290 AND C393 ARE MUTATED TO ALANINE. RESIDUES PRESENT ARE 28-89 WITH A SERINE RESIDUE APPENDED AT THE N-TERMINUS.

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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: 2.49 Å3/Da / Density % sol: 50.6 % / Description: NONE
Crystal growpH: 9 / Details: 100 MM BICINE PH 9.0, 20% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.72→74.93 Å / Num. obs: 42854 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Biso Wilson estimate: 25.63 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CEG

4ceg


Resolution: 1.72→74.929 Å / SU ML: 0.15 / σ(F): 1.35 / Phase error: 18.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 2010 4.7 %
Rwork0.1762 --
obs0.1771 42820 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.09 Å2
Refinement stepCycle: LAST / Resolution: 1.72→74.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 29 197 2564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052456
X-RAY DIFFRACTIONf_angle_d1.0433344
X-RAY DIFFRACTIONf_dihedral_angle_d13.746900
X-RAY DIFFRACTIONf_chiral_restr0.044363
X-RAY DIFFRACTIONf_plane_restr0.007422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.76310.24141330.22122912X-RAY DIFFRACTION100
1.7631-1.81070.23191570.20992837X-RAY DIFFRACTION100
1.8107-1.8640.22181560.19822844X-RAY DIFFRACTION100
1.864-1.92420.21571450.18972926X-RAY DIFFRACTION100
1.9242-1.9930.22731260.18722853X-RAY DIFFRACTION100
1.993-2.07280.19441390.17982922X-RAY DIFFRACTION100
2.0728-2.16710.22171530.17892888X-RAY DIFFRACTION100
2.1671-2.28140.22631130.17542926X-RAY DIFFRACTION100
2.2814-2.42430.21751280.18432917X-RAY DIFFRACTION100
2.4243-2.61150.20631840.18752859X-RAY DIFFRACTION100
2.6115-2.87430.21951320.18772957X-RAY DIFFRACTION100
2.8743-3.29020.18251500.17972918X-RAY DIFFRACTION100
3.2902-4.14530.16071530.16022953X-RAY DIFFRACTION100
4.1453-74.99970.18821410.1653098X-RAY DIFFRACTION100

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