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- PDB-1ol5: Structure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 a... -

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Basic information

Entry
Database: PDB / ID: 1ol5
TitleStructure of Aurora-A 122-403, phosphorylated on Thr287, Thr288 and bound to TPX2 1-43
Components
  • RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100
  • SERINE/THREONINE KINASE 6
KeywordsTRANSFERASE/CELL CYCLE / TRANSFERASE-CELL CYCLE COMPLEX / CELL CYCLE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex ...importin-alpha family protein binding / Interaction between PHLDA1 and AURKA / activation of protein kinase activity / regulation of centrosome cycle / negative regulation of microtubule depolymerization / axon hillock / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / chromosome passenger complex / microtubule nucleation / 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 / mitotic spindle assembly / spindle midzone / intercellular bridge / 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 / regulation of mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / molecular function activator activity / AURKA Activation by TPX2 / regulation of cytokinesis / liver regeneration / 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 / molecular adaptor activity / 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
Similarity search - Function
TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / Aurora kinase A / Aurora kinase / Phosphorylase Kinase; domain 1 ...TPX2 / Aurora-A binding / TPX2, C-terminal / TPX2 central domain / Targeting protein for Xklp2 (TPX2) domain / Aurora-A binding / Cell cycle regulated microtubule associated protein / 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
ADENOSINE-5'-DIPHOSPHATE / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsBayliss, R. / Conti, E.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural Basis of Aurora-A Activation by Tpx2 at the Mitotic Spindle
Authors: Bayliss, R. / Sardon, T. / Vernos, I. / Conti, E.
History
DepositionAug 6, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 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
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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SERINE/THREONINE KINASE 6
B: RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5499
Polymers37,7612
Non-polymers7887
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.630, 81.720, 83.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsFOR THE HETERO-ASSEMBLY DESCRIBED BY REMARK 350

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein SERINE/THREONINE KINASE 6 / AURORA-A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / ...AURORA-A / SERINE/THREONINE KINASE 15 / AURORA/IPL1-RELATED KINASE 1 / AURORA-RELATED KINASE 1 / HARK1 / BREAST-TUMOR-AMPLIFIED KINASE


Mass: 32849.418 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 122-403
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR287, THR288 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CODONPLUS RIL / References: UniProt: O14965, EC: 2.7.1.37
#2: Protein/peptide RESTRICTED EXPRESSION PROLIFERATION ASSOCIATED PROTEIN 100 / TPX2 / PROTEIN FLS353 / DIL-2 / P100 / TARGETING PROTEIN FOR XKLP2 / HEPATOCELLULAR CARCINOMA- ...TPX2 / PROTEIN FLS353 / DIL-2 / P100 / TARGETING PROTEIN FOR XKLP2 / HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 519


Mass: 4911.110 Da / Num. of mol.: 1 / Fragment: N-TERMINAL, RESIDUES 1-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULW0

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-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.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 55.3 %
Crystal growpH: 6.5 / Details: 18% (W/V) PEG8000, 100 MM MES PH 6.5, 200 MM MGSO4
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 %(w/v)PEG80001reservoir
2100 mMMES1reservoirpH6.5
3200 mM1reservoirMgSO4
420 mg/mlprotein1drop
52 mMATPgammaS1drop
60.2 mM1dropMgSO4
720 %PEG80001drop
8100 mMMES1droppH6.5
9200 mM1dropMgSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorDate: Apr 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 14609 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 5.6 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 5.1
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 1.1 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: UNPHOSPHORYLATED AURORA/TPX2

Resolution: 2.5→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -5 %RANDOM
Rwork0.194 ---
obs0.194 14609 100 %-
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2418 0 45 144 2607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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