[English] 日本語
Yorodumi
- PDB-4c3p: Structure of dephosphorylated Aurora A (122-403) bound to TPX2 an... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c3p
TitleStructure of dephosphorylated Aurora A (122-403) bound to TPX2 and AMPPCP
Components
  • AURORA KINASE A
  • TARGETING PROTEIN FOR XKLP2
KeywordsTRANSFERASE / ACTIVATION / ALLOSTERY / CELL CYCLE / CANCER
Function / homology
Function and homology information


activation of protein kinase activity / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / importin-alpha family protein binding / microtubule nucleation ...activation of protein kinase activity / Interaction between PHLDA1 and AURKA / regulation of centrosome cycle / axon hillock / negative regulation of microtubule depolymerization / spindle assembly involved in female meiosis I / cilium disassembly / spindle pole centrosome / importin-alpha family protein binding / microtubule nucleation / chromosome passenger complex / histone H3S10 kinase activity / positive regulation of oocyte maturation / mitotic centrosome separation / pronucleus / germinal vesicle / protein localization to centrosome / meiotic spindle / 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 / mitotic spindle assembly / negative regulation of protein binding / intercellular bridge / regulation of G2/M transition of mitotic cell cycle / liver regeneration / protein serine/threonine/tyrosine kinase activity / centriole / 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 / regulation of signal transduction by p53 class mediator / AURKA Activation by TPX2 / protein serine/threonine kinase activator activity / mitotic spindle organization / regulation of cytokinesis / 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 / peptidyl-serine phosphorylation / regulation of protein stability / kinetochore / response to wounding / G2/M transition of mitotic cell cycle / spindle / spindle pole / mitotic spindle / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / protein autophosphorylation / microtubule cytoskeleton / midbody / basolateral plasma membrane / molecular adaptor activity / Regulation of TP53 Activity through Phosphorylation / 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 / apoptotic process / ubiquitin protein ligase binding / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / glutamatergic synapse / 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 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsZorba, A. / Kutter, S. / Kern, D.
CitationJournal: Elife / Year: 2014
Title: Molecular Mechanism of Aurora a Kinase Autophosphorylation and its Allosteric Activation by Tpx2.
Authors: Zorba, A. / Buosi, V. / Kutter, S. / Kern, N. / Pontiggia, F. / Cho, Y.J. / Kern, D.
History
DepositionAug 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: 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 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AURORA KINASE A
B: TARGETING PROTEIN FOR XKLP2
D: AURORA KINASE A
E: TARGETING PROTEIN FOR XKLP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3407
Polymers75,2334
Non-polymers1,1063
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10200 Å2
ΔGint-56.4 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.927, 86.717, 153.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein AURORA KINASE A / AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR- ...AURORA 2 / AURORA/IPL1-RELATED KINASE 1 / ARK-1 / AURORA-RELAT ED KINASE 1 / HARK1 / BREAST TUMOR-AMPLIFIED KINASE / SERINE/THREONIN E- PROTEIN KINASE 15 / SERINE/THREONINE-PROTEIN KINASE 6 / SERINE/THR EONINE-PROTEIN KINASE AURORA-A / AURORA A KINASE


Mass: 32689.459 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 121-403
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O14965, non-specific serine/threonine protein kinase
#2: Protein/peptide TARGETING PROTEIN FOR XKLP2 / DIFFERENTIALLY EXPRESSED IN CANCEROUS AND NON-CANCEROUS LUN G CELLS 2 / DIL-2 / HEPATOCELLULAR ...DIFFERENTIALLY EXPRESSED IN CANCEROUS AND NON-CANCEROUS LUN G CELLS 2 / DIL-2 / HEPATOCELLULAR CARCINOMA-ASSOCIATED ANTIGEN 519 / PROTEIN FLS353 / RESTRICTED EXPRESSION PROLIFERATION-ASSOCIATED PR OTEIN 100 / P100 / TARGETING PROTEIN FOR XKLP2 / TPX2


Mass: 4927.110 Da / Num. of mol.: 2 / Fragment: AURORA A KINASE BINDING DOMAIN, RESIDUES 1-43
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ULW0
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP AND TPX2(1-43) WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE HANGING DROP OBTAINED BY COMBINING 300UM DEP A(122-403) WITH 1.5MM ...Details: CRYSTALS OF DEPHOSPHORYLATED A(122-403) IN COMPLEX WITH AMPPCP AND TPX2(1-43) WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE HANGING DROP OBTAINED BY COMBINING 300UM DEP A(122-403) WITH 1.5MM AMPPCP AND 300UM TPX2(1-43) WITH 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M BISTRIS PH5.5, 25% PEG3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.21433
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 17, 2012
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.21433 Å / Relative weight: 1
ReflectionResolution: 2.69→47.5 Å / Num. obs: 19139 / % possible obs: 100 % / Observed criterion σ(I): 2.3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.26 / Net I/σ(I): 8
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OL7

1ol7


Resolution: 2.69→47.48 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.882 / SU B: 14.978 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.402 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28857 1035 5.4 %RANDOM
Rwork0.20066 ---
obs0.20526 18104 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.69→47.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 67 21 4662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194760
X-RAY DIFFRACTIONr_bond_other_d0.0020.024517
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9826448
X-RAY DIFFRACTIONr_angle_other_deg0.786310394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0325553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.43922.807228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87315826
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1041540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021144
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.694→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 88 -
Rwork0.284 1293 -
obs--100 %

+
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