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- PDB-5ocu: Molecular basis of human kinesin-8 function and inhibition -

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Basic information

Entry
Database: PDB / ID: 5ocu
TitleMolecular basis of human kinesin-8 function and inhibition
DescriptorKinesin-like protein KIF18A
Tubulin alpha chain
Tubulin beta chain
KeywordsTRANSPORT PROTEIN / Cytoskeleton / Motor protein / Kinesin
Specimen sourceHomo sapiens / human
Bos taurus / mammal / Bovine / ウシ /
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 (5.2 Å resolution / Filament / Helical)
AuthorsLocke, J. / Joseph, A.P. / Topf, M. / Moores, C.A.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, E9539-E9548

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, E9539-E9548 Yorodumi Papers
Structural basis of human kinesin-8 function and inhibition.
Julia Locke / Agnel Praveen Joseph / Alejandro Peña / Martin M Möckel / Thomas U Mayer / Maya Topf / Carolyn A Moores

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 3, 2017 / Release: Oct 25, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 25, 2017Structure modelrepositoryInitial release
1.1Nov 8, 2017Structure modelDatabase referencescitation / citation_author_citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
1.2Nov 15, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
K: Kinesin-like protein KIF18A
A: Tubulin alpha chain
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,66910
Polyers142,2293
Non-polymers2,4417
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Polypeptide(L) , 3 types, 3 molecules KAB

#1: Polypeptide(L)Kinesin-like protein KIF18A / Marrow stromal KIF18A / MS-KIF18A


Mass: 42213.938 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens / References: UniProt: Q8NI77
#2: Polypeptide(L)Tubulin alpha chain


Mass: 50107.238 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#3: Polypeptide(L)Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 1 / Source: (natural) Sus scrofa / References: UniProt: P02554

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Non-polymers , 6 types, 7 molecules

#4: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg
#5: ChemicalChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP (energy-carrying molecule analogue) *YM


Mass: 506.196 Da / Num. of mol.: 1 / Formula: C10H17N6O12P3
#6: ChemicalChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn
#7: ChemicalChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / GTP *YM


Mass: 523.180 Da / Num. of mol.: 1 / Formula: C10H16N5O14P3
#8: ChemicalChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / GDP *YM


Mass: 443.201 Da / Num. of mol.: 1 / Formula: C10H15N5O11P2
#9: ChemicalChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 1 / Formula: C47H51NO14

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
113-Protofilament microtuble-bound human Kinesin-8 motor domain neck-linker with AMPPNPCOMPLEX1, 2, 30MULTIPLE SOURCES
2Kinesin-8 motor domain neck-linkerCOMPLEX11RECOMBINANT
3Tubulin, alphaCOMPLEX21NATURAL
4Tubulin, betaCOMPLEX31NATURAL
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129606Homo sapiens
139913Bos taurus
249823Sus scrofa
Source (recombinant)Organism: Escherichia coli BL21(DE3)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300 / Details: FEI Polara
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus min: 500 nm / Calibrated defocus max: 3500 nm / Cs: 2.3 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingAverage exposure time: 2 sec. / Electron dose: 5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum
Image scansDimension width: 3840 / Dimension height: 3712 / Movie frames/image: 5

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Processing

EM software
IDNameVersionCategoryImaging IDImage processing IDFitting ID
2SerialEMIMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7ChimeraMODEL FITTING1
9SPIDERINITIAL EULER ASSIGNMENT1
10SPIDERFINAL EULER ASSIGNMENT1
11SPIDERCLASSIFICATION1
12FREALIGNRECONSTRUCTION1
13Flex-EMMODEL REFINEMENT1
14Flex-EMMODEL FITTING
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0 deg. / Axial rise/subunit: 81 Å / Axial symmetry: C1
3D reconstructionResolution: 5.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 70473 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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