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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
DescriptorTubulin alpha-1B chain
Tubulin beta chain
Targeting protein for Xklp2
KeywordsCELL CYCLE / mitosis / GanGTP / nucleation
Specimen sourceHomo sapiens / human
Sus scrofa / mammal / Pig / イノシシ, いのしし, ニホンイノシシ, ブタ / image: Sus scrofa domestica
MethodElectron microscopy (3.3 Å resolution / Helical array / Helical)
AuthorsZhang, R. / Nogales, E.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural insight into TPX2-stimulated microtubule assembly.
Rui Zhang / Johanna Roostalu / Thomas Surrey / Eva Nogales

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 5, 2017 / Release: Nov 22, 2017

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Structure visualization

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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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Polypeptide(L) , 3 types, 14 molecules ACEJLKBDFH...

#1: Polypeptide(L)
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 / References: UniProt: Q2XVP4
#2: Polypeptide(L)
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source: (natural) Sus scrofa / References: UniProt: P02554
#3: Polypeptide(L)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 / References: UniProt: Q9ULW0

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Non-polymers , 3 types, 24 molecules

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


Mass: 523.180 Da / Num. of mol.: 6 / Formula: C10H16N5O14P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Formula: Mg
#6: Chemical
ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP (energy-carrying molecule analogue) *YM


Mass: 521.208 Da / Num. of mol.: 6 / Formula: C11H18N5O13P3

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Experimental details

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Experiment

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

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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
239606Homo sapiens
Source (recombinant)Organism: Spodoptera aff. frugiperda 2 RZ-2014 / 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 FIELD / 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
IDNameCategoryImage processing IDImaging IDFitting ID
1AppionPARTICLE SELECTION1
2SerialEMIMAGE ACQUISITION1
4CTFFINDCTF CORRECTION1
7CootMODEL FITTING1
9EMANINITIAL EULER ASSIGNMENT1
10FREALIGNFINAL EULER ASSIGNMENT1
12FREALIGNRECONSTRUCTION1
13REFMACMODEL REFINEMENT1
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
Refine
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLOverall ESU RStereochemistry target valuesSolvent model details
131.217-3.83-0.200.017.03-0.47-3.190.739HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.396900.396903.30212.80191280100.0032.9230.5301.625MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
ELECTRON MICROSCOPY
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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