[English] 日本語
Yorodumi
- PDB-6vpi: TPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + D25... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vpi
TitleTPX2 residues 7-20 fused to Aurora A residues 116-389 C247V + D256N + C319V triple mutant disulfide homodimer in complex with AMP-PNP
ComponentsTPX2 fragment - Aurora A kinase domain fusion
KeywordsTRANSFERASE / Ser/Thr kinase
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 / liver regeneration / regulation of cytokinesis / 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 / Serine/threonine-protein kinase, active site ...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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / MALONIC ACID / Aurora kinase A / Targeting protein for Xklp2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLim, D.C. / Yaffe, M.B.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES015339 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES028374 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES020466 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM104047 United States
CitationJournal: Sci.Signal. / Year: 2020
Title: Redox priming promotes Aurora A activation during mitosis.
Authors: Lim, D.C. / Joukov, V. / Rettenmaier, T.J. / Kumagai, A. / Dunphy, W.G. / Wells, J.A. / Yaffe, M.B.
History
DepositionFeb 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5575
Polymers33,8981
Non-polymers6594
Water4,197233
1
A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules

A: TPX2 fragment - Aurora A kinase domain fusion
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,11310
Polymers67,7952
Non-polymers1,3188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area7270 Å2
ΔGint-78 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.292, 85.292, 128.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-907-

HOH

-
Components

#1: Protein TPX2 fragment - Aurora A kinase domain fusion / Targeting protein for Xklp2 / Aurora kinase A / Differentially expressed in cancerous and non- ...Targeting protein for Xklp2 / Aurora kinase A / 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 / 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: 33897.742 Da / Num. of mol.: 1 / Fragment: kinase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: TPX2, C20orf1, C20orf2, DIL2, HCA519, AURKA, AIK, AIRK1, ARK1, AURA, AYK1, BTAK, IAK1, STK15, STK6
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2
References: UniProt: Q9ULW0, UniProt: O14965, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.25 % / Mosaicity: 0.359 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.336 M sodium malonate pH 7.5, 0.348 M sodium malonate pH 6.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 16, 2015 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→23.33 Å / Num. obs: 32094 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.026 / Rrim(I) all: 0.054 / Χ2: 0.988 / Net I/σ(I): 13.9 / Num. measured all: 126757
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.70.61715620.790.3550.7140.90497.5
2.03-2.073.90.53615800.8230.3030.6180.88598.4
2.07-2.113.90.45115700.8690.2530.5190.94498.7
2.11-2.153.90.39315710.9050.2210.4520.98698.8
2.15-2.23.90.36416060.9270.2030.4180.94898.8
2.2-2.2540.28515890.9460.160.3281.0198.7
2.25-2.3140.25415880.9580.1430.2930.98399.3
2.31-2.3740.20816230.9680.1160.2390.98599.1
2.37-2.4440.19215770.9760.1080.221.03999
2.44-2.5240.15715980.9840.0880.181.02398.9
2.52-2.6140.13516010.9880.0760.1551.08499.1
2.61-2.7140.11115930.9910.0620.1271.09998.7
2.71-2.8440.08716200.9930.0480.11.03898.7
2.84-2.9940.06716050.9960.0380.0770.9998.4
2.99-3.1740.05416180.9980.030.0621.02998.3
3.17-3.4240.03916080.9980.0220.0450.96397.9
3.42-3.7640.0316260.9990.0160.0341.0298
3.76-4.340.02216330.9990.0120.0250.98497.8
4.3-5.413.90.019165810.010.0210.91897.5
5.41-23.333.90.01816680.9990.0090.0210.91191.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL5

1ol5


Resolution: 2→23.26 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.25
RfactorNum. reflection% reflection
Rfree0.215 1995 6.23 %
Rwork0.186 --
obs0.1878 32025 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 120.3 Å2 / Biso mean: 41.7298 Å2 / Biso min: 20.54 Å2
Refinement stepCycle: final / Resolution: 2→23.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 40 233 2558
Biso mean--72.43 49.54 -
Num. residues----278
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.29861390.26222094223398
2.05-2.110.29971400.23442102224299
2.11-2.170.26981420.23392126226899
2.17-2.240.26511410.22522130227199
2.24-2.320.22981420.22262137227999
2.32-2.410.28241430.22322138228199
2.41-2.520.23771420.22222138228099
2.52-2.650.22841430.22912139228299
2.65-2.820.261390.22192143228299
2.82-3.040.23431430.21722160230398
3.04-3.340.25921440.19372156230098
3.34-3.820.20381440.15782160230498
3.82-4.810.14931460.13172192233898
4.81-23.260.18131470.17062215236293
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)
10.2525-0.52810.16091.7288-0.10930.5624-0.0693-0.0455-0.05160.2590.06860.09510.0744-0.0170.00180.3288-0.01020.03730.1969-0.02560.2474-28.263-4.4126.94
20.0250.01530.01590.01110.0170.0469-0.14430.2448-0.1379-0.30040.1644-0.0664-0.20430.16090.00010.3394-0.0082-0.010.4247-0.07350.3801-17.69819.13937.645
30.33080.4340.07031.7770.22871.1453-0.00380.04260.0671-0.0729-0.00860.0199-0.161-0.0513-00.3010.0074-0.0260.2074-0.02380.2564-26.3214.46412.217
40.0756-0.12270.05130.1999-0.07420.1227-0.1884-0.2831-0.19320.62390.16790.4621-0.1036-0.28660.00130.7361-0.01760.21640.43810.0020.5268-35.413-11.00538.616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 126:287 )A126 - 287
2X-RAY DIFFRACTION2( CHAIN A AND RESID 288:307 )A288 - 307
3X-RAY DIFFRACTION3( CHAIN A AND RESID 308:389 )A308 - 389
4X-RAY DIFFRACTION4( CHAIN A AND RESID 7:20 )A7 - 20

+
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