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- EMDB-19043: MAP7 MTBD (microtubule binding domain) decorated Taxol stabilized... -

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Basic information

Entry
Database: EMDB / ID: EMD-19043
TitleMAP7 MTBD (microtubule binding domain) decorated Taxol stabilized microtubule (13pf) protofilament
Map dataUnsharpened map of MAP7 MTBD bound Taxol stabilized microtubule protofilament
Sample
  • Complex: Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol stabilized microtubule
    • Complex: Tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Microtubule associated protein 7 (MAP7)
      • Protein or peptide: Microtubule associated protein 7 (MAP7)
KeywordsMicrotubule associated protein 7(MAP 7) / microtubule binding domain / Taxol stabilized microtubule / cryo-EM / STRUCTURAL PROTEIN
Function / homology
Function and homology information


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 ...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 / 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 / microtubule associated complex / response to osmotic stress / COPI-mediated anterograde transport / establishment or maintenance of cell polarity / protein localization to plasma membrane / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / basolateral plasma membrane / microtubule / axon / signaling receptor binding / GTPase activity / GTP binding / perinuclear region of cytoplasm / structural molecule activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Microtubule-associated protein 7 family / : / MAP7 (E-MAP-115) family / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...Microtubule-associated protein 7 family / : / MAP7 (E-MAP-115) family / 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
Similarity search - Domain/homology
Tubulin beta chain / Ensconsin / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBangera M / Moores CA
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/R000352/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: A structural and dynamic visualization of the interaction between MAP7 and microtubules.
Authors: Agnes Adler / Mamata Bangera / J Wouter Beugelink / Salima Bahri / Hugo van Ingen / Carolyn A Moores / Marc Baldus /
Abstract: Microtubules (MTs) are key components of the eukaryotic cytoskeleton and are essential for intracellular organization, organelle trafficking and mitosis. MT tasks depend on binding and interactions ...Microtubules (MTs) are key components of the eukaryotic cytoskeleton and are essential for intracellular organization, organelle trafficking and mitosis. MT tasks depend on binding and interactions with MT-associated proteins (MAPs). MT-associated protein 7 (MAP7) has the unusual ability of both MT binding and activating kinesin-1-mediated cargo transport along MTs. Additionally, the protein is reported to stabilize MTs with its 112 amino-acid long MT-binding domain (MTBD). Here we investigate the structural basis of the interaction of MAP7 MTBD with the MT lattice. Using a combination of solid and solution-state nuclear magnetic resonance (NMR) spectroscopy with electron microscopy, fluorescence anisotropy and isothermal titration calorimetry, we shed light on the binding mode of MAP7 to MTs at an atomic level. Our results show that a combination of interactions between MAP7 and MT lattice extending beyond a single tubulin dimer and including tubulin C-terminal tails contribute to formation of the MAP7-MT complex.
History
DepositionDec 5, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19043.png

Downloads & links

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Map

FileDownload / File: emd_19043.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map of MAP7 MTBD bound Taxol stabilized microtubule protofilament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 448 pix.
= 478.016 Å		1.07 Å/pix.
x 448 pix.
= 478.016 Å		1.07 Å/pix.
x 448 pix.
= 478.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.49003446 - 1.284008
Average (Standard dev.)-0.006542572 (±0.040346976)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 478.01602 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened C1 reconstruction of MAP7 MTBD bound Taxol...

Fileemd_19043_additional_1.map
AnnotationUnsharpened C1 reconstruction of MAP7 MTBD bound Taxol stabilized 13pf microtubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map 1

Fileemd_19043_half_map_1.map
AnnotationUnsharpened half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unsharpened half map 2

Fileemd_19043_half_map_2.map
AnnotationUnsharpened half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol...

EntireName: Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol stabilized microtubule
Components
  • Complex: Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol stabilized microtubule
    • Complex: Tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta chain
    • Complex: Microtubule associated protein 7 (MAP7)
      • Protein or peptide: Microtubule associated protein 7 (MAP7)

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Supramolecule #1: Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol...

SupramoleculeName: Complex of MAP7 MTBD (microtubule binding domain) with 13pf Taxol stabilized microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 13 kDa/nm

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Supramolecule #2: Tubulin

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

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Supramolecule #3: Microtubule associated protein 7 (MAP7)

SupramoleculeName: Microtubule associated protein 7 (MAP7) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHPE QLITGKEDAA NNYARGHYTI GKEIIDLVLD RIRKLADQCT GLQGFLVFHS FGGGTGSGFT SLLMERLSVD YGKKSKLEFS IYPAPQVSTA VVEPYNSILT THTTLEHSDC AFMVDNEAIY DICRRNLDIE RPTYTNLNRL ISQIVSSITA SLRFDGALNV DLTEFQTNLV PYPRIHFPLA TYAPVISAEK AYHEQLSVAE ITNACFEPAN QMVKCDPRHG KYMACCLLYR GDVVPKDVNA AIATIKTKRS IQFVDWCPTG FKVGINYQPP TVVPGGDLAK VQRAVCMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDMAALEK DYEEVGVDSV EGEGEEEGEE Y

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKESESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSVH QLVENTDETY CIDNEALYDI CFRTLKLTTP TYGDLNHLVS ATMSGVTTCL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTSRGSQQ YRALTVPELT QQMFDAKNMM AACDPRHGRY LTVAAVFRGR MSMKEVDEQM LNVQNKNSSY FVEWIPNNVK TAVCDIPPRG LKMSATFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA DEQGEFEEEG EEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Microtubule associated protein 7 (MAP7)

MacromoleculeName: Microtubule associated protein 7 (MAP7) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VLRVDDRQRL ARERREEREK QLAAREIVWL EREERARQHY EKHLEERKKR LEEQRQKEER RRAAVEEKRR QRLEEDKERH EAVVRRTMER SQKPKQKHNR WSWGGSLHGS P

UniProtKB: Ensconsin

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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

Concentration0.5 mg/mL
BufferpH: 6.5 / Component - Name: BRB80 / Details: 80mM PIPES, 2mM MgCl2, 1mM EGTA
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: MAP7 MTBD decorated Taxol stabilized microtubules were applied to a glow discharged grid in a Vitrobot, incubated for 30 seconds at 25 degrees following which excess liquid was blotted off ...Details: MAP7 MTBD decorated Taxol stabilized microtubules were applied to a glow discharged grid in a Vitrobot, incubated for 30 seconds at 25 degrees following which excess liquid was blotted off and the grid was plunge frozen in liquid ethane..
DetailsTubulin mixed with GTP was incubated in a water bath maintained at 37 degrees for 1 hour followed by addition of Taxol and further incubation for 3 hours. Taxol stabilized microtubules were pelleted in an ultracentrifuge and resuspended in BRB80 buffer. Polymerized microtubules were incubated with MAP7 MTBD in a water bath maintained at 30 degrees for 10 minutes.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 49.93 e/Å2
Details: Movies were collected in counting mode fractionated over 50 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 217718
Startup modelType of model: EMDB MAP
EMDB ID:

25156

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 40100
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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