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- PDB-5g15: Structure Aurora A (122-403) bound to activating monobody Mb1 and... -

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Basic information

Entry
Database: PDB / ID: 5g15
TitleStructure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP
Components
  • AURORA A KINASE
  • MB1 MONOBODY
KeywordsTRANSFERASE / AURORA A / MONOBODY / AMPPCP / KINASE / ACTIVATION / ALLOSTERY / CELL CYCLE / CANCER
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 / mitotic centrosome separation / histone H3S10 kinase activity ...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 / mitotic centrosome separation / histone H3S10 kinase activity / pronucleus / germinal vesicle / meiotic spindle / protein localization to centrosome / anterior/posterior axis specification / neuron projection extension / spindle organization / centrosome localization / positive regulation of mitochondrial fission / mitotic spindle pole / spindle midzone / SUMOylation of DNA replication proteins / negative regulation of protein binding / regulation of G2/M transition of mitotic cell cycle / centriole / liver regeneration / 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 / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / 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 / peptidyl-serine phosphorylation / kinetochore / response to wounding / spindle / G2/M transition of mitotic cell cycle / spindle pole / Regulation of PLK1 Activity at G2/M Transition / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / microtubule cytoskeleton / protein autophosphorylation / midbody / Regulation of TP53 Activity through Phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynaptic density / ciliary basal body / protein heterodimerization activity / negative regulation of gene expression / cell division / protein serine kinase activity / protein serine/threonine kinase activity / ubiquitin protein ligase binding / apoptotic process / centrosome / protein kinase binding / negative regulation of apoptotic process / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Aurora kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsZorba, A. / Kutter, S. / Kern, D. / Koide, S. / Koide, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Allosteric modulation of a human protein kinase with monobodies.
Authors: Zorba, A. / Nguyen, V. / Koide, A. / Hoemberger, M. / Zheng, Y. / Kutter, S. / Kim, C. / Koide, S. / Kern, D.
History
DepositionMar 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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 A KINASE
B: MB1 MONOBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1818
Polymers43,2672
Non-polymers9146
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-74.7 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.339, 91.361, 143.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2110-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein AURORA A KINASE / 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/THREO -PROTEIN KINASE 15 / SERINE/THREONINE-PROTEIN KINASE 6 / SERINE/ THREONINE-PROTEIN KINASE AURORA-A / AURORA A KINASE


Mass: 32689.459 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 122-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Antibody MB1 MONOBODY


Mass: 10577.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PET28A / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)

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Non-polymers , 4 types, 151 molecules

#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.86 Å3/Da / Density % sol: 57.04 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER ...Details: AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER THE DAY OF CRYSTALLIZATION IN CONCENTRATIONS OF 100-120MM IN STORAGE BUFFER. CRYSTALS OF AURA IN COMPLEX WITH AMPPCP AND ACTIVATING MONOBODY, MB1, WERE OBTAINED BY COMBINING 0.5UL OF [300UM AURA WITH 5MM AMPPCP AND 300UM MB1] WITH 0.5UL OF MOTHER LIQUOR (0.1M MES SODIUM SALT PH 6.50, 0.2M AMMONIUM SULFATE, 4% (V/V) 1,3-PROPANEDIOL, 30% (W/V) PEG8000). CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE SITTING DROP METHOD. THE CRYSTALS WERE WASHED WITH MOTHER LIQUOR AND FLASH FROZEN IN LIQUID NITROGEN IN PREPARATION FOR DATA COLLECTION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99992
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2015
RadiationMonochromator: DOUBLE-CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 2.06→58.13 Å / Num. obs: 30879 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 7.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.3
Reflection shellResolution: 2.06→2.12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.21 / Mean I/σ(I) obs: 1.8 / % possible all: 99.5

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Processing

Software
NameVersionClassification
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
REFMAC5.8.0135refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4C3R AND 3K2M

4c3r

3k2m


Resolution: 2.06→77.1 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.946 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.27388 1052 3.4 %RANDOM
Rwork0.22687 ---
obs0.22853 29755 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.133 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.06→77.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2873 0 52 145 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193019
X-RAY DIFFRACTIONr_bond_other_d0.0020.022809
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.9834113
X-RAY DIFFRACTIONr_angle_other_deg1.04636472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40222.857140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37915503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6111523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213337
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02717
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9143.1891418
X-RAY DIFFRACTIONr_mcbond_other2.8953.1871417
X-RAY DIFFRACTIONr_mcangle_it4.454.7641771
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.5363.61600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.064→2.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 81 -
Rwork0.425 2170 -
obs--99.08 %

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