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- EMDB-4650: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-4650
TitleNgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
Map dataNgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule (symmetrised reconstruction, asymmetric unit)
Sample
  • Complex: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
    • Complex: tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Beta1-tubulin
    • Complex: Naegleria Gruberi CKK
      • Protein or peptide: Predicted proteinProtein structure prediction
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
Function / homology
Function and homology information


odontoblast differentiation / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC ...odontoblast differentiation / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / natural killer cell mediated cytotoxicity / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / regulation of synapse organization / intercellular bridge / nuclear envelope lumen / Recycling pathway of L1 / RHOH GTPase cycle / spindle assembly / RHO GTPases activate IQGAPs / MHC class I protein binding / Hedgehog 'off' state / cytoplasmic microtubule / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / cellular response to interleukin-4 / AURKA Activation by TPX2 / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / mitotic spindle / microtubule cytoskeleton organization / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / mitotic cell cycle / cell body / microtubule binding / microtubule / Potential therapeutics for SARS / cytoskeleton / calmodulin binding / membrane raft / cell division / protein domain specific binding / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. / Microtubule-binding calmodulin-regulated spectrin-associated / PRC-barrel-like superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site ...CKK domain / Calmodulin-regulated spectrin-associated protein / CKK domain superfamily / Microtubule-binding calmodulin-regulated spectrin-associated / CKK domain profile. / Microtubule-binding calmodulin-regulated spectrin-associated / PRC-barrel-like superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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
Similarity search - Domain/homology
Tubulin beta chain / Predicted protein / Tubulin beta chain / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Naegleria gruberi (eukaryote) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAtherton JM / Luo Y / Xiang S / Yang C / Jiang K / Stangier M / Vemu A / Cook A / Wang S / Roll-Mecak A ...Atherton JM / Luo Y / Xiang S / Yang C / Jiang K / Stangier M / Vemu A / Cook A / Wang S / Roll-Mecak A / Steinmetz MO / Akhmanova A / Baldus M / Moores CA
Funding support United Kingdom, Switzerland, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/R000352/1 United Kingdom
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: Structural determinants of microtubule minus end preference in CAMSAP CKK domains.
Authors: Joseph Atherton / Yanzhang Luo / Shengqi Xiang / Chao Yang / Ankit Rai / Kai Jiang / Marcel Stangier / Annapurna Vemu / Alexander D Cook / Su Wang / Antonina Roll-Mecak / Michel O Steinmetz ...Authors: Joseph Atherton / Yanzhang Luo / Shengqi Xiang / Chao Yang / Ankit Rai / Kai Jiang / Marcel Stangier / Annapurna Vemu / Alexander D Cook / Su Wang / Antonina Roll-Mecak / Michel O Steinmetz / Anna Akhmanova / Marc Baldus / Carolyn A Moores /
Abstract: CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To ...CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity. Here we report near-atomic cryo-electron microscopy structures of HsCKK- and NgCKK-microtubule complexes, which show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit different footprints on microtubules. NMR experiments show that both HsCKK and NgCKK are remarkably rigid. However, whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many MAPs, the HsCKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition.
History
DepositionMar 1, 2019-
Header (metadata) releaseNov 27, 2019-
Map releaseNov 27, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qve
  • Surface level: 0.036
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4650.png

Downloads & links

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Map

FileDownload / File: emd_4650.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule (symmetrised reconstruction, asymmetric unit)
Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.036 / Movie #1: 0.036
Minimum - Maximum-0.11250246 - 0.24054983
Average (Standard dev.)0.00673205 (±0.0211474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin16596184
Dimensions1006495
Spacing6410095
CellA: 88.96 Å / B: 139.0 Å / C: 132.05 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z6410095
origin x/y/z0.0000.0000.000
length x/y/z88.960139.000132.050
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS96165184
NC/NR/NS6410095
D min/max/mean-0.1130.2410.007

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Supplemental data

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Additional map: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule...

Fileemd_4650_additional.map
AnnotationNgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule (C1 reconstruction)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule

EntireName: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
Components
  • Complex: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
    • Complex: tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Beta1-tubulin
    • Complex: Naegleria Gruberi CKK
      • Protein or peptide: Predicted proteinProtein structure prediction
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel

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Supramolecule #1: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule

SupramoleculeName: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: tubulin

SupramoleculeName: tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Naegleria Gruberi CKK

SupramoleculeName: Naegleria Gruberi CKK / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Naegleria gruberi (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Details: GTP / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Tissue: Embryonic Kidney
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

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Macromolecule #2: Predicted protein

MacromoleculeName: Predicted protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Naegleria gruberi (eukaryote)
Molecular weightTheoretical: 20.879051 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAHHHHHHSA ALEVLFQGPN GMILKNMKQP NKTNKLLIKN ALIHLTLAGE VNKKEREDVF EAMKEYEDTN QMIILVREVN VPAFRALYV VVTDGLNANV GSSTSTTDSN RTDNSSRSES PNIEKRSDQI LVKKIIGKGP KFLTEDVVDV FCRYDSGGKK L SKLSSRTF GVTTDVVVLK SAAIKKIKR

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Macromolecule #3: Beta1-tubulin

MacromoleculeName: Beta1-tubulin / type: protein_or_peptide / ID: 3 / Details: GDP Taxol / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Tissue: embryonic kidney
Molecular weightTheoretical: 49.717629 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / 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: 2 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 2 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM / Paclitaxel

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8 / Details: BRB20
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 / Details: dose weighted images used in final reconstructions
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28421

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6qve:
NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule

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