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- PDB-5m50: Mechanism of microtubule minus-end recognition and protection by ... -

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Basic information

Database: PDB / ID: 5m50
TitleMechanism of microtubule minus-end recognition and protection by CAMSAP proteins
  • Calmodulin-regulated spectrin-associated protein 3
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsSTRUCTURAL PROTEIN / CAMSAP CKK Microtubule Tubulin / Structural protein
Specimen sourceMus musculus / mammal / House mouse /
Bos taurus / mammal / Cattle /
MethodElectron microscopy (5.3 Å resolution / Filament / Single particle) / Transmission electron microscopy
AuthorsAkhmanova, A. / Moores, C.A. / Baldus, M. / Steinmetz, M.O. / Topf, M. / Roberts, A.J. / Grant, B.J. / Scarabelli, G. / Joseph, A.-P. / van Hooff, J.J.E. / Houben, K. / Hua, S. / Luo, Y. / Stangier, M.M. / Jiang, K. / Atherton, J.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Oct 20, 2016 / Release: Oct 4, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 4, 2017Structure modelrepositoryInitial release
1.1Oct 18, 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

Structure visualization

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Deposited unit
D: Tubulin alpha chain
E: Tubulin beta-2B chain
A: Tubulin alpha chain
B: Tubulin beta-2B chain
C: Calmodulin-regulated spectrin-associated protein 3
hetero molecules

Theoretical massNumber of molelcules
Total (without water)210,54213

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)17760
ΔGint (kcal/M)-80
Surface area (Å2)68240


Protein/peptide , 3 types, 5 molecules DAEBC

#1: Protein/peptide Tubulin alpha chain

Mass: 48769.988 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#2: Protein/peptide Tubulin beta-2B chain

Mass: 47940.945 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt: Q6B856
#3: Protein/peptide Calmodulin-regulated spectrin-associated protein 3 / Protein Nezha

Mass: 13431.391 Da / Num. of mol.: 1 / Source: (gene. exp.) Mus musculus / Gene: Camsap3, Kiaa1543 / Production host: Escherichia coli / References: UniProt: Q80VC9

Non-polymers , 5 types, 16 molecules


Mass: 523.180 Da / Num. of mol.: 2 / Formula: C10H16N5O14P3 / : Guanosine triphosphate / Comment: GTP (energy-carrying molecule) *YM
#5: Chemical ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg / : Magnesium
#6: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE

Mass: 443.201 Da / Num. of mol.: 2 / Formula: C10H15N5O11P2 / : Guanosine diphosphate / Comment: GDP (energy-carrying molecule) *YM
#7: Chemical ChemComp-TA1 / TAXOL

Mass: 853.906 Da / Num. of mol.: 2 / Formula: C47H51NO14
#8: Water ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 8 / Formula: H2O / : Water

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

Sample preparation

IDNameTypeEntity IDParent IDSource
1Complex of two tubulin dimers with bound CAMSAP3-CKK domainCOMPLEX1, 2, 30MULTIPLE SOURCES
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129913Bos taurus
2310090Mus musculus
Source (recombinant)Organism: Escherichia coli
Buffer solutionDetails: BRB80 / pH: 6.8
SpecimenDetails: 13pf Microtubules / Embedding 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

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 25 e/Å2 / Details: 25e-/A2 used in final reconstuctions / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
3D reconstructionResolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6530
Details: Gold-standard noise substitution test used to asses for over fitting (Chen et al., 2013)
Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415009
ELECTRON MICROSCOPYf_angle_d0.77720402
ELECTRON MICROSCOPYf_dihedral_angle_d3.9979009
ELECTRON MICROSCOPYf_chiral_restr0.0482222
ELECTRON MICROSCOPYf_plane_restr0.0072752

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