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- PDB-6bjc: TPX2_mini decorated GMPCPP-microtubule -

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Basic information

Entry
Database: PDB / ID: 6bjc
TitleTPX2_mini decorated GMPCPP-microtubule
Components
  • Targeting protein for Xklp2
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / mitosis / GanGTP / nucleation
Function / homologyTPX2, C-terminal / Targeting protein for Xklp2 (TPX2) / TPX2 / Beta tubulin, autoregulation binding site / Aurora-A binding / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Hedgehog 'off' state / TPX2 central domain ...TPX2, C-terminal / Targeting protein for Xklp2 (TPX2) / TPX2 / Beta tubulin, autoregulation binding site / Aurora-A binding / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / Hedgehog 'off' state / TPX2 central domain / Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Tubulin C-terminal domain / Aurora-A binding / Tubulin/FtsZ, GTPase domain / Cell cycle regulated microtubule associated protein / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Regulation of TP53 Activity through Phosphorylation / AURKA Activation by TPX2 / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Tubulin/FtsZ, C-terminal / Beta tubulin / Recycling pathway of L1 / RHO GTPases activate IQGAPs / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / Alpha tubulin / Hedgehog 'on' state / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / Tubulin / Intraflagellar transport / Cilium Assembly / importin-alpha family protein binding / regulation of mitotic spindle organization / axon hillock / intercellular bridge / mitotic spindle assembly / microtubule-based process / activation of protein kinase activity / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton / microtubule organizing center / spindle / mitotic cell cycle / spindle pole / regulation of G2/M transition of mitotic cell cycle / microtubule / regulation of signal transduction by p53 class mediator / GTPase activity / cell proliferation / cell division / GTP binding / apoptotic process / protein kinase binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm / Tubulin beta chain / Tubulin alpha-1B chain / Targeting protein for Xklp2
Function and homology information
Specimen sourceHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.3 Å resolution
AuthorsZhang, R. / Nogales, E.
CitationJournal: Elife / Year: 2017
Title: Structural insight into TPX2-stimulated microtubule assembly.
Authors: Rui Zhang / Johanna Roostalu / Thomas Surrey / Eva Nogales
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 5, 2017 / Release: Nov 22, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 22, 2017Structure modelrepositoryInitial release
1.1Oct 3, 2018Structure modelData collection / Other / Refinement descriptioncell / refine_cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
T: Targeting protein for Xklp2
E: Tubulin alpha-1B chain
F: Tubulin beta chain
J: Tubulin alpha-1B chain
H: Tubulin beta chain
L: Tubulin alpha-1B chain
G: Tubulin beta chain
K: Tubulin alpha-1B chain
I: Tubulin beta chain
P: Targeting protein for Xklp2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)778,85438
Polyers772,29614
Non-polymers6,55824
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)56120
ΔGint (kcal/M)-363
Surface area (Å2)170700

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Components

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Protein/peptide , 3 types, 14 molecules ACEJLKBDFHGITP

#1: Protein/peptide
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 6 / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: Q2XVP4
#2: Protein/peptide
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: P02554
#3: Protein/peptide Targeting protein for Xklp2 / / 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: 85811.328 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Gene: TPX2, C20orf1, C20orf2, DIL2, HCA519
Production host: Spodoptera aff. frugiperda 2 RZ-2014 (insect)
Strain (production host): sf21 / References: UniProt: Q9ULW0

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Non-polymers , 3 types, 24 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Formula: C10H16N5O14P3 / Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Formula: Mg / Magnesium
#6: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 6 / Formula: C11H18N5O13P3 / Comment: GMP-CPP (energy-carrying molecule analogue) *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1TPX2_mini decorated GMPCPP-microtubuleCOMPLEX1, 2, 30MULTIPLE SOURCES
2TubulinCOMPLEX1,21NATURAL
3Targeting protein for Xklp2COMPLEX31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganOrganism
129823brainsus scrofa (pig)
239606Homo sapiens (human)
Source (recombinant)Organism: Spodoptera aff. frugiperda 2 RZ-2014 (insect) / Strain: sf21
Buffer solutionDetails: BRB80 / pH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-1.2/1.3 4C
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 kelvins / Details: blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6 sec. / Electron dose: 27.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 4 / Number of real images: 2000

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Processing

SoftwareName: REFMAC / Version: 5.8.0091 / Classification: refinement
EM software
IDNameCategory
1Appionparticle selection
2SerialEMimage acquisition
4CTFFINDCTF correction
7Cootmodel fitting
9EMANinitial Euler assignment
10FREALIGNfinal Euler assignment
12FREALIGN3D reconstruction
13REFMACmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.74 deg. / Axial rise/subunit: 9.03 Å / Axial symmetry: C1
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 85000 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingRef protocol: AB INITIO MODEL
RefineCorrelation coeff Fo to Fc: 0.739 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS / Overall SU B: 32.923 / Overall SU ML: 0.53 / Overall ESU R: 1.625
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Solvent computationSolvent model details: PARAMETERS FOR MASK CACLULATION
Displacement parametersB iso mean: 31.217 Å2 / Aniso B11: -3.83 Å2 / Aniso B12: -0.2 Å2 / Aniso B13: 0.01 Å2 / Aniso B22: 7.03 Å2 / Aniso B23: -0.47 Å2 / Aniso B33: -3.19 Å2
Least-squares processR factor R work: 0.3969 / R factor obs: 0.3969 / Highest resolution: 3.3 Å / Lowest resolution: 212.8 Å / Number reflection obs: 191280 / Percent reflection obs: 1
Number of atoms included #1Total: 41136
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01942070
ELECTRON MICROSCOPYr_bond_other_d0.0020.02038788
ELECTRON MICROSCOPYr_angle_refined_deg1.4511.95957162
ELECTRON MICROSCOPYr_angle_other_deg0.9673.00089218
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.6564.8475882
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.09724.1981977
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.12815.0006769
ELECTRON MICROSCOPYr_dihedral_angle_4_deg12.07915.000254
ELECTRON MICROSCOPYr_chiral_restr0.0820.2006252
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.02148014
ELECTRON MICROSCOPYr_gen_planes_other0.0020.0209904
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it0.8573.11120794
ELECTRON MICROSCOPYr_mcbond_other0.8573.11120793
ELECTRON MICROSCOPYr_mcangle_it1.5894.66325954
ELECTRON MICROSCOPYr_mcangle_other1.5894.66325955
ELECTRON MICROSCOPYr_scbond_it0.6803.20021276
ELECTRON MICROSCOPYr_scbond_other0.6803.20021277
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other1.3134.74231208
ELECTRON MICROSCOPYr_long_range_B_refined3.78527.26996104
ELECTRON MICROSCOPYr_long_range_B_other3.78527.27096105
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints ncs

Refine ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Dom IDAuth asym IDEns IDNumber
1A152676
2C152676
1A252676
2E252676
1A352676
2J352676
1A452674
2L452674
1A552676
2K552676
1B652670
2D652670
1B752670
2F752670
1B852668
2H852668
1B952670
2G952670
1B1052668
2I1052668
1C1152674
2E1152674
1C1252674
2J1252674
1C1352674
2L1352674
1C1452674
2K1452674
1D1552670
2F1552670
1D1652668
2H1652668
1D1752672
2G1752672
1D1852670
2I1852670
1T192566
2P192566
1E2052672
2J2052672
1E2152672
2L2152672
1E2252672
2K2252672
1F2352666
2H2352666
1F2452670
2G2452670
1F2552668
2I2552668
1J2652674
2L2652674
1J2752676
2K2752676
1H2852674
2G2852674
1H2952672
2I2952672
1L3052674
2K3052674
1G3152674
2I3152674
Refine LS shellHighest resolution: 3.386 Å / R factor R work: 0.635 / Lowest resolution: 3.6 Å / Number reflection R free: 0 / Number reflection R work: 14319 / Total number of bins used: 20 / Percent reflection obs: 1

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