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- PDB-7ztl: Crystal structure of a covalently linked Aurora-A N-Myc complex -

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Basic information

Entry
Database: PDB / ID: 7ztl
TitleCrystal structure of a covalently linked Aurora-A N-Myc complex
Components
  • Aurora kinase A
  • N-myc proto-oncogene protein
KeywordsTRANSFERASE / Crosslink / protein-protein-complex
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 / positive regulation of oocyte maturation / spindle pole centrosome / 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 / positive regulation of oocyte maturation / spindle pole centrosome / 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 / spindle organization / embryonic digit morphogenesis / cartilage condensation / positive regulation of mitochondrial fission / 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 / positive regulation of mitotic nuclear division / AURKA Activation by TPX2 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / mitotic spindle organization / ciliary basal body / regulation of cytokinesis / negative regulation of protein binding / regulation of signal transduction by p53 class mediator / epithelial cell proliferation / molecular function activator activity / positive regulation of epithelial cell proliferation / liver regeneration / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / lung development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / regulation of protein stability / spindle microtubule / mitotic spindle / kinetochore / kinase binding / positive regulation of miRNA transcription / response to wounding / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / sequence-specific double-stranded DNA binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / DNA-binding transcription activator activity, RNA polymerase II-specific / basolateral plasma membrane / peptidyl-serine phosphorylation / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / postsynaptic density / protein dimerization activity / non-specific serine/threonine protein kinase / DNA-binding transcription factor activity, RNA polymerase II-specific / protein kinase activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / DNA-binding transcription factor activity / cell division / protein phosphorylation / negative regulation of gene expression / 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. / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-JWG / Aurora kinase A / N-myc proto-oncogene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDiebold, M. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK2243 Germany
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Crystal structure of a covalently linked Aurora-A-MYCN complex.
Authors: Diebold, M. / Schonemann, L. / Eilers, M. / Sotriffer, C. / Schindelin, H.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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)44,17711
Polymers43,0502
Non-polymers1,1279
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.614, 86.614, 91.789
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-617-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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: 35943.914 Da / Num. of mol.: 1 / Mutation: C290A, K339C, C393A
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
Production host: Escherichia coli (E. coli)
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


Mass: 7105.782 Da / Num. of mol.: 1 / Mutation: N85K / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04198

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Non-polymers , 7 types, 217 molecules

#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-JWG / 4-(3-hydroxy-3-oxopropylamino)-4-oxidanylidene-butanoic acid


Mass: 189.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M TRIS pH 8.5, 0.4 M MgCl2, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→39.17 Å / Num. obs: 31825 / % possible obs: 99.94 % / Redundancy: 19.8 % / Biso Wilson estimate: 39.88 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1551 / Rpim(I) all: 0.03537 / Net I/σ(I): 11.06
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 2.516 / Mean I/σ(I) obs: 1.28 / Num. unique obs: 3148 / CC1/2: 0.568 / Rpim(I) all: 0.5728

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5G1X

5g1x


Resolution: 1.9→39.17 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1931 1594 5.01 %
Rwork0.1634 30217 -
obs0.1649 31811 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.71 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2279 0 71 208 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082449
X-RAY DIFFRACTIONf_angle_d1.02993324
X-RAY DIFFRACTIONf_chiral_restr0.0623358
X-RAY DIFFRACTIONf_plane_restr0.0093415
X-RAY DIFFRACTIONf_dihedral_angle_d15.0906356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.34851470.30722704X-RAY DIFFRACTION99.82
1.96-2.030.24721510.23432709X-RAY DIFFRACTION99.97
2.03-2.110.2241280.20142735X-RAY DIFFRACTION99.93
2.11-2.210.2361280.18352736X-RAY DIFFRACTION100
2.21-2.330.22771280.18392713X-RAY DIFFRACTION99.93
2.33-2.470.22111320.18192753X-RAY DIFFRACTION99.97
2.47-2.660.1971920.17272667X-RAY DIFFRACTION100
2.66-2.930.21521320.17852768X-RAY DIFFRACTION99.97
2.93-3.350.23131360.17032752X-RAY DIFFRACTION100
3.35-4.220.16021610.14482781X-RAY DIFFRACTION100
4.23-39.170.16981590.14092899X-RAY DIFFRACTION99.9
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.941376468343.57915982785-0.4674824024015.982899412520.4655719687734.04229471474-0.04302231258250.202239129676-0.138754183623-0.2585843836470.184717314418-0.3519862454290.1901817181210.533104604267-0.1360958483160.2505243910080.0638347873961-0.0152633174820.377797958721-0.01938889535220.275212647771-21.931281780626.54268306483.35493285043
22.27861820184-1.54885798273-1.676352518234.483115336722.584537511092.960005737520.05826366815410.318487723522-0.0283546347321-0.543039098299-0.0525778774251-0.4113734830260.005916228499610.101188590548-0.007269757436370.326636208084-0.00898871645952-0.01594844514220.4325412918030.007022527774150.290601681812-31.883732390830.0361521431-3.57058279865
33.67662511043-0.41932931595-1.148443281731.840446726340.3789461603241.918154008910.02459647258490.243437567220.290896009671-0.2210725705660.0372174485169-0.0083709923576-0.152385455585-0.0980773779646-0.07108287270150.2870376186270.00859437473746-0.0332678715230.3303069677470.02815010375260.310923545487-40.965527951238.30827868556.39299221285
43.402663560750.892982941436-1.363349335024.38283583542-0.32113697613.045060696610.115327445106-0.02420989306480.6010800039070.03392974446930.07945631398280.194532484417-0.389194790121-0.347111342239-0.19222632640.2716558917860.0816018435599-0.005669041186790.3200161957190.004279584681260.392769992218-51.650011447644.695237595613.3491149057
59.234656425614.780154173344.379817436358.70536155097-1.994807914094.993921016530.5134456011320.125858461917-0.467947755243-0.533159097795-0.287891123325-0.4664851383530.2808169199570.557363312179-0.1433300189880.5615876970720.07141512416970.004760339440940.408898771037-0.05797172013450.462391348862-50.271230884819.365197788615.5747210102
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 126 through 172 )AA126 - 1721 - 47
22chain 'A' and (resid 173 through 204 )AA173 - 20448 - 79
33chain 'A' and (resid 205 through 324 )AA205 - 32480 - 199
44chain 'A' and (resid 325 through 389 )AA325 - 389200 - 264
55chain 'B' and (resid 72 through 89 )BI72 - 892 - 19

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