[English] 日本語
Yorodumi
- PDB-5lxm: Crystal structure of Aurora-A bound to a hydrocarbon-stapled prot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lxm
TitleCrystal structure of Aurora-A bound to a hydrocarbon-stapled proteomimetic of TPX2
Components
  • Aurora kinase A
  • Targeting protein for Xklp2
KeywordsTRANSFERASE / Protein kinase / Proteomimetic / Stapled helix peptide / Mitosis
Function / homology
Function and homology information


Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / microtubule nucleation / importin-alpha family protein binding / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity ...Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / microtubule nucleation / importin-alpha family protein binding / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / histone H3S10 kinase activity / chromosome passenger complex / positive regulation of oocyte maturation / pronucleus / mitotic centrosome separation / meiotic spindle / germinal vesicle / protein localization to centrosome / anterior/posterior axis specification / centrosome localization / spindle organization / neuron projection extension / activation of protein kinase activity / intercellular bridge / positive regulation of mitochondrial fission / mitotic spindle pole / SUMOylation of DNA replication proteins / mitotic spindle assembly / spindle midzone / regulation of mitotic spindle organization / regulation of G2/M transition of mitotic cell cycle / protein serine/threonine/tyrosine kinase activity / centriole / AURKA Activation by TPX2 / positive regulation of mitotic nuclear division / positive regulation of mitotic cell cycle / mitotic spindle organization / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ciliary basal body / regulation of cytokinesis / regulation of signal transduction by p53 class mediator / negative regulation of protein binding / molecular function activator activity / liver regeneration / 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 / kinetochore / response to wounding / spindle pole / spindle / G2/M transition of mitotic cell cycle / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / peptidyl-serine phosphorylation / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / microtubule / molecular adaptor activity / postsynaptic density / non-specific serine/threonine protein kinase / protein kinase activity / protein heterodimerization activity / protein phosphorylation / cell division / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / nucleoplasm / ATP binding / nucleus / cytosol
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 / Transferase(Phosphotransferase) 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 / 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 / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsMcIntyre, P.J. / Bayliss, R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/K016903/1 United Kingdom
Cancer Research UKC24461/A12772 United Kingdom
CitationJournal: ACS Chem. Biol. / Year: 2016
Title: A TPX2 Proteomimetic Has Enhanced Affinity for Aurora-A Due to Hydrocarbon Stapling of a Helix.
Authors: Rennie, Y.K. / McIntyre, P.J. / Akindele, T. / Bayliss, R. / Jamieson, A.G.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id
Revision 2.0Sep 4, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aurora kinase A
D: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,57012
Polymers37,1992
Non-polymers1,37110
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-39 kcal/mol
Surface area13510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.780, 79.780, 140.260
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AD

#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: 32836.508 Da / Num. of mol.: 1 / Mutation: C290A, 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/peptide Targeting protein for Xklp2 / Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular ...Differentially expressed in cancerous and non-cancerous lung cells 2 / DIL-2 / Hepatocellular carcinoma-associated antigen 519 / Hepatocellular carcinoma-associated antigen 90 / Protein fls353 / Restricted expression proliferation-associated protein 100 / p100


Mass: 4362.501 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9ULW0

-
Non-polymers , 9 types, 87 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-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#10: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: MORPHEUS Crystallization Screen condition C1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→61.98 Å / Num. obs: 31554 / % possible obs: 99.4 % / Redundancy: 9.6 % / Net I/σ(I): 9.94

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.2data extraction
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CEG

4ceg


Resolution: 2.08→61.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.13
RfactorNum. reflection% reflection
Rfree0.2429 1602 5.08 %
Rwork0.1996 --
obs0.2018 31526 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 169.8 Å2 / Biso mean: 74.378 Å2 / Biso min: 37.48 Å2
Refinement stepCycle: final / Resolution: 2.08→61.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 85 77 2582
Biso mean--96.19 66.44 -
Num. residues----301
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)
12.50611.65270.9431.43980.16789.26840.66061.43770.1701-1.033-0.42750.0909-1.58240.2503-0.19141.24020.45790.05471.01770.03680.460644.3288-0.46054.9321
27.414-2.23992.40454.606-0.10567.2480.14880.78240.3781-0.3136-0.19340.0927-1.6278-0.74130.15190.9790.20530.13080.65150.04240.366245.4526-1.92746.1031
34.0051-1.0571-3.69424.8779-0.58615.67510.43280.8040.0535-0.792-0.5265-0.2232-0.8537-0.48890.09190.6390.18940.05270.8040.00830.346647.7404-14.5042.2049
43.0054-1.9471-2.7794.129-2.15418.05590.07690.00120.1690.6573-0.08720.1588-0.85310.16780.00290.71230.11130.04850.647-0.05770.380844.269-9.772917.1404
56.97280.1431.33724.6476-3.22128.8121-0.03850.8399-0.89830.3546-0.11450.51680.0636-1.42660.12260.36250.01890.07280.4838-0.14510.514641.1669-26.615916.4901
67.3088-6.5604-6.32735.92136.57268.2372-0.23560.0219-0.0580.49810.1933-0.03840.03040.0752-0.0530.55410.05650.06110.5171-0.04250.355946.3099-19.135714.3136
75.788-3.2392-2.43573.465-0.26855.07740.35871.1181-0.1583-0.0895-0.468-0.0572-0.32470.31080.14010.39440.0421-0.0440.8374-0.12250.30754.8994-23.30016.6908
87.0177-1.5462-1.36363.789-1.61632.8578-0.42410.0854-0.37720.4294-0.04890.0865-0.20260.07120.42530.51480.03880.03850.5528-0.03340.358556.3319-26.87718.7879
99.6347-4.3188-3.13398.22050.55063.3593-0.4598-0.37341.02831.39120.2501-1.0344-0.1340.80450.22560.83440.0766-0.1420.6983-0.00970.444563.8247-22.757527.3874
108.0292.8623-3.66244.1471-3.11426.3059-0.5826-1.202-0.47221.02630.25230.20630.10750.1610.29150.96240.27510.17350.62160.07480.49451.1755-32.496131.0889
113.2405-2.235-3.81454.1690.36299.1654-0.37650.9076-1.52390.72120.00930.88960.8306-0.9730.46010.6314-0.07370.2150.4023-0.13160.623944.8878-34.875719.733
122.8199-1.4471-2.13076.2261-4.09826.59690.87172.7928-0.4633-3.23330.3918-2.2087-2.81330.1009-1.47911.0472-0.01780.34651.1517-0.00540.666655.0643-8.9193-5.8914
132.2457-1.32242.37546.681-0.75333.23090.05210.6747-0.0416-0.4256-0.68061.38140.5661-0.68150.50410.94830.2431-0.02751.7635-0.21360.626836.1666-11.3314-3.6083
146.5902-6.5617-6.81378.95966.01796.88460.4102-0.6725-0.7575-0.2491-1.0850.5542-0.2808-1.61720.65340.49460.141-0.02941.2702-0.21370.464548.0302-26.0654-6.7796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 126 through 145 )A126 - 145
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 171 )A146 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 201 )A172 - 201
4X-RAY DIFFRACTION4chain 'A' and (resid 202 through 229 )A202 - 229
5X-RAY DIFFRACTION5chain 'A' and (resid 230 through 250 )A230 - 250
6X-RAY DIFFRACTION6chain 'A' and (resid 251 through 269 )A251 - 269
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 292 )A270 - 292
8X-RAY DIFFRACTION8chain 'A' and (resid 293 through 324 )A293 - 324
9X-RAY DIFFRACTION9chain 'A' and (resid 325 through 343 )A325 - 343
10X-RAY DIFFRACTION10chain 'A' and (resid 344 through 363 )A344 - 363
11X-RAY DIFFRACTION11chain 'A' and (resid 364 through 392 )A364 - 392
12X-RAY DIFFRACTION12chain 'D' and (resid 6 through 10 )D6 - 10
13X-RAY DIFFRACTION13chain 'D' and (resid 11 through 30 )D11 - 30
14X-RAY DIFFRACTION14chain 'D' and (resid 31 through 43 )D31 - 43

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more