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- EMDB-21937: KIF14[391-755] - ADP in complex with a microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-21937
TitleKIF14[391-755] - ADP in complex with a microtubule
Map dataMain map. Locally refined single unit. Not helically averaged. Composite map from the localdeblur map and the 7 A low pass filtered map.
Sample
  • Complex: Kif14[391-755] - ADP in complex with a microtubule
    • Complex: KIF14[391-755] - ADP
      • Protein or peptide: Kinesin-like protein KIF14
    • Organelle or cellular component: Microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsKIF14 / kinesin / motility / microtubule / tubulin / MOTOR PROTEIN
Function / homology
Function and homology information


cerebellar granular layer structural organization / regulation of cell maturation / cerebellar Purkinje cell layer structural organization / RHO GTPases activate CIT / negative regulation of integrin activation / RND2 GTPase cycle / RND1 GTPase cycle / cell proliferation in forebrain / regulation of Rap protein signal transduction / cerebellar cortex development ...cerebellar granular layer structural organization / regulation of cell maturation / cerebellar Purkinje cell layer structural organization / RHO GTPases activate CIT / negative regulation of integrin activation / RND2 GTPase cycle / RND1 GTPase cycle / cell proliferation in forebrain / regulation of Rap protein signal transduction / cerebellar cortex development / olfactory bulb development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Flemming body / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / microtubule motor activity / regulation of myelination / kinesin complex / mitotic metaphase chromosome alignment / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / activation of protein kinase activity / microtubule-based movement / positive regulation of cytokinesis / regulation of G1/S transition of mitotic cell cycle / spindle midzone / regulation of cell adhesion / regulation of neuron apoptotic process / regulation of G2/M transition of mitotic cell cycle / regulation of cell migration / tubulin binding / substrate adhesion-dependent cell spreading / hippocampus development / regulation of cell growth / PDZ domain binding / establishment of protein localization / structural constituent of cytoskeleton / cerebral cortex development / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / midbody / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / microtubule / cell division / GTPase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / GTP binding / protein kinase binding / ATP hydrolysis activity / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. ...Kinesin-associated / Kinesin-associated / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / SMAD/FHA domain superfamily / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin beta chain / Kinesin-like protein KIF14 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesMus musculus (house mouse) / Sus scrofa (pig)
Methodhelical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBenoit MPMH / Asenjo AB
Funding support United States, Canada, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM113164 United States
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN/04103-2015 Canada
Canadian Cancer Society Research Institute703405 Canada
Fonds de Recherche du Quebec-Sante (FRSQ)Chercheure-Boursiere Junior 1, Junior 2 Awards Canada
Canadian Institutes of Health Research (CIHR)New Investigator Award Canada
Simons FoundationSF349247 United States
NYSTAR United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Agouron InstituteF00316 United States
National Institutes of Health/Office of the DirectorOD019994 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of mechano-chemical coupling by the mitotic kinesin KIF14.
Authors: Matthieu P M H Benoit / Ana B Asenjo / Mohammadjavad Paydar / Sabin Dhakal / Benjamin H Kwok / Hernando Sosa /
Abstract: KIF14 is a mitotic kinesin whose malfunction is associated with cerebral and renal developmental defects and several cancers. Like other kinesins, KIF14 couples ATP hydrolysis and microtubule binding ...KIF14 is a mitotic kinesin whose malfunction is associated with cerebral and renal developmental defects and several cancers. Like other kinesins, KIF14 couples ATP hydrolysis and microtubule binding to the generation of mechanical work, but the coupling mechanism between these processes is still not fully clear. Here we report 20 high-resolution (2.7-3.9 Å) cryo-electron microscopy KIF14-microtubule structures with complementary functional assays. Analysis procedures were implemented to separate coexisting conformations of microtubule-bound monomeric and dimeric KIF14 constructs. The data provide a comprehensive view of the microtubule and nucleotide induced KIF14 conformational changes. It shows that: 1) microtubule binding, the nucleotide species, and the neck-linker domain govern the transition between three major conformations of the motor domain; 2) an undocked neck-linker prevents the nucleotide-binding pocket to fully close and dampens ATP hydrolysis; 3) 13 neck-linker residues are required to assume a stable docked conformation; 4) the neck-linker position controls the hydrolysis rather than the nucleotide binding step; 5) the two motor domains of KIF14 dimers adopt distinct conformations when bound to the microtubule; and 6) the formation of the two-heads-bound-state introduces structural changes in both motor domains of KIF14 dimers. These observations provide the structural basis for a coordinated chemo-mechanical kinesin translocation model.
History
DepositionMay 9, 2020-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00973
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.00973
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  • Surface view with fitted model
  • Atomic models: PDB-6wwj
  • Surface level: 0.00973
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wwj
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21937.png

Downloads & links

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Map

FileDownload / File: emd_21937.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map. Locally refined single unit. Not helically averaged. Composite map from the localdeblur map and the 7 A low pass filtered map.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 416 pix.
= 345.696 Å		0.83 Å/pix.
x 416 pix.
= 345.696 Å		0.83 Å/pix.
x 416 pix.
= 345.696 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.831 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.00973 / Movie #1: 0.00973
Minimum - Maximum-0.005662297 - 0.077268496
Average (Standard dev.)0.000115180796 (±0.0015088652)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 345.69598 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8310.8310.831
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z345.696345.696345.696
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-0.0060.0770.000

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Supplemental data

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Mask #1

Fileemd_21937_msk_1.map
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Additional map: Helical reconstruction half map 1 (gold standard).

Fileemd_21937_additional_1.map
AnnotationHelical reconstruction half map 1 (gold standard).
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Additional map: Helical reconstruction.

Fileemd_21937_additional_2.map
AnnotationHelical reconstruction.
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Additional map: Helical reconstruction half map 2 (gold standard).

Fileemd_21937_additional_3.map
AnnotationHelical reconstruction half map 2 (gold standard).
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Additional map: Localdeblur map - used to make the composite...

Fileemd_21937_additional_4.map
AnnotationLocaldeblur map - used to make the composite map. Locally refined single unit. Not helically averaged.
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Additional map: 7 A low pass filtered localdeblur map -...

Fileemd_21937_additional_5.map
Annotation7 A low pass filtered localdeblur map - used to make the composite map. Locally refined single unit. Not helically averaged.
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Half map: Half map 1 (gold standard). Locally refined single...

Fileemd_21937_half_map_1.map
AnnotationHalf map 1 (gold standard). Locally refined single unit. Not helically averaged.
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Half map: Half map 2 (gold standard). Locally refined single...

Fileemd_21937_half_map_2.map
AnnotationHalf map 2 (gold standard). Locally refined single unit. Not helically averaged.
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Sample components

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Entire : Kif14[391-755] - ADP in complex with a microtubule

EntireName: Kif14[391-755] - ADP in complex with a microtubule
Components
  • Complex: Kif14[391-755] - ADP in complex with a microtubule
    • Complex: KIF14[391-755] - ADP
      • Protein or peptide: Kinesin-like protein KIF14
    • Organelle or cellular component: Microtubule
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Kif14[391-755] - ADP in complex with a microtubule

SupramoleculeName: Kif14[391-755] - ADP in complex with a microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: KIF14[391-755] - ADP

SupramoleculeName: KIF14[391-755] - ADP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: Microtubule

SupramoleculeName: Microtubule / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
Molecular weightTheoretical: 49.999887 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Kinesin-like protein KIF14

MacromoleculeName: Kinesin-like protein KIF14 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 41.196445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPLGSNSQVT VAVRVRPFSK REKTEKASQV VFTNGEEITV EHPDMKQVYS FIYDVSFWSF DECHPGYASQ TTVYETLAAP LLDRAFEGY NTCLFAYGQT GSGKSYTMMG LNEEPGIIPR FCEDLFAQIA KKQTSEVSYH LEMSFFEVYN EKIHDLLVCK G ENGQRKQP ...String:
GPLGSNSQVT VAVRVRPFSK REKTEKASQV VFTNGEEITV EHPDMKQVYS FIYDVSFWSF DECHPGYASQ TTVYETLAAP LLDRAFEGY NTCLFAYGQT GSGKSYTMMG LNEEPGIIPR FCEDLFAQIA KKQTSEVSYH LEMSFFEVYN EKIHDLLVCK G ENGQRKQP LRAREHPVSG PYVEGLSMNV VSSYSDIQSW LELGNKQRAT AATGMNDKSS RSHSVFTLVM TQTKTEVVEG EE HDHRITS RINLVDLAGS ERCSTAHSSG QRLKEGVSIN KSLLTLGKVI SALSEQANGK RVFIPYREST LTWLLKESLG GNS KTAMIA TVSPAASNIE ETLSTLRYAT QARLIVNIAK VNEDMNAKLI RELK

UniProtKB: Kinesin-like protein KIF14

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
Component:
ConcentrationName
80.0 mMK-PIPES
20.0 uMPaclitaxel
5.0 mMMagnesium chloride
1.0 mMEGTA
4.0 mMADP
GridModel: UltrAuFoil / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Average electron dose: 70.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 60168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 5.46 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.09 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1)
Details: 2 half datasets containing one distinct half of each filament were refined independently.
Number images used: 171108
Segment selectionDetails: manual picking of filaments
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6wwj:
KIF14[391-755] - ADP in complex with a microtubule

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