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- EMDB-4154: Mechanism of microtubule minus-end recognition and protection by ... -

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Basic information

Entry
Database: EMDB / ID: 4154
TitleMechanism of microtubule minus-end recognition and protection by CAMSAP proteins
SampleComplex of two tubulin dimers with bound CAMSAP3-CKK domain
SourceBos taurus / mammal / ウシ /
Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Map dataCAMSAP3 CKK decorated 13pf microtubule asymmetric unit
Methodsingle particle reconstruction, at 5.3 Å resolution
AuthorsAkhmanova A / Moores CA
CitationNat. Struct. Mol. Biol., 2017, 24, 931-943

Nat. Struct. Mol. Biol., 2017, 24, 931-943 Yorodumi Papers
A structural model for microtubule minus-end recognition and protection by CAMSAP proteins.
Joseph Atherton / Kai Jiang / Marcel M Stangier / Yanzhang Luo / Shasha Hua / Klaartje Houben / Jolien J E van Hooff / Agnel-Praveen Joseph / Guido Scarabelli / Barry J Grant / Anthony J Roberts / Maya Topf / Michel O Steinmetz / Marc Baldus / Carolyn A Moores / Anna Akhmanova

Validation ReportPDB-ID: 5m50

SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2016 / Header (metadata) release: Nov 30, 2016 / Map release: Oct 4, 2017 / Last update: Nov 15, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0314
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0314
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5m50
  • Surface level: 0.0314
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_4154.map.gz (map file in CCP4 format, 2743 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
95 pix
1.53 Å/pix.
= 145.73 Å
88 pix
1.53 Å/pix.
= 134.992 Å
82 pix
1.53 Å/pix.
= 125.788 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

(generated in cubic-lattice coordinate)

Voxel sizeX=Y=Z: 1.534 Å
Density
Contour Level:0.0314 (by author), 0.0314 (movie #1):
Minimum - Maximum-0.039573725 - 0.12910078
Average (Standard dev.)0.0059765955 (0.016930932)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions888295
Origin000
Limit878194
Spacing828895
CellA: 125.788 Å / B: 134.992 Å / C: 145.73001 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5341.5341.534
M x/y/z828895
origin x/y/z0.0000.0000.000
length x/y/z125.788134.992145.730
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS828895
D min/max/mean-0.0400.1290.006

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Supplemental data

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Sample components

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Entire Complex of two tubulin dimers with bound CAMSAP3-CKK domain

EntireName: Complex of two tubulin dimers with bound CAMSAP3-CKK domain
Number of components: 11

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Component #1: protein, Complex of two tubulin dimers with bound CAMSAP3-CKK domain

ProteinName: Complex of two tubulin dimers with bound CAMSAP3-CKK domain
Recombinant expression: No

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Component #2: protein, tubulin

ProteinName: tubulin / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #3: protein, CAMSAP3-CKK domain

ProteinName: CAMSAP3-CKK domain / Recombinant expression: No
SourceSpecies: Mus musculus / mammal / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: protein, Tubulin alpha chain

ProteinName: Tubulin alpha chain / Recombinant expression: No
MassTheoretical: 48.769988 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #5: protein, Tubulin beta-2B chain

ProteinName: Tubulin beta-2B chain / Recombinant expression: No
MassTheoretical: 47.940945 kDa
SourceSpecies: Bos taurus / mammal / ウシ /

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Component #6: protein, Calmodulin-regulated spectrin-associated protein 3

ProteinName: Calmodulin-regulated spectrin-associated protein 3 / Recombinant expression: No
MassTheoretical: 13.431391 kDa
Source (engineered)Expression System: Mus musculus / mammal / ハツカネズミ, はつかねずみ /

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Component #7: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #8: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #9: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Component #10: ligand, TAXOL

LigandName: TAXOL / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.853906 kDa

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Component #11: ligand, water

LigandName: water / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

Specimen statefilament
Sample solutionBuffer solution: BRB80 / pH: 6.8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image acquisition

Image acquisitionDetails: 25e-/A2 used in final reconstuctions

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6530
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Gold-standard noise substitution test used to asses for over fitting (Chen et al., 2013)
Euler angles: Projection matching in Fourier space

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Atomic model buiding

Output model

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