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- PDB-5m54: Mechanism of microtubule minus-end recognition and protection by ... -

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Basic information

Entry
Database: PDB / ID: 5m54
TitleMechanism of microtubule minus-end recognition and protection by CAMSAP proteins
Components
  • Calmodulin-regulated spectrin-associated protein 1
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsMOTOR PROTEIN / CAMSAP / CKK / Microtubule / Tubulin / motor protein
Function / homologyTubulin/FtsZ, GTPase domain superfamily / Tubulin C-terminal domain / Beta tubulin, autoregulation binding site / CKK domain / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Calmodulin-regulated spectrin-associated protein, CH domain / Tubulin, C-terminal / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Calmodulin-regulated spectrin-associated protein ...Tubulin/FtsZ, GTPase domain superfamily / Tubulin C-terminal domain / Beta tubulin, autoregulation binding site / CKK domain / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Calmodulin-regulated spectrin-associated protein, CH domain / Tubulin, C-terminal / CAMSAP, spectrin and Ca2+/calmodulin-binding region / Calmodulin-regulated spectrin-associated protein / Recycling pathway of L1 / CH domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / CKK domain superfamily / Tubulin/FtsZ family, GTPase domain / Microtubule-binding calmodulin-regulated spectrin-associated / Tubulin/FtsZ, C-terminal / CAMSAP CH domain / Spectrin-binding region of Ca2+-Calmodulin / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Calponin homology (CH) domain profile. / CKK domain profile. / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / MHC class II antigen presentation / Separation of Sister Chromatids / Resolution of Sister Chromatid Cohesion / Regulation of PLK1 Activity at G2/M Transition / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Loss of Nlp from mitotic centrosomes / PRC-barrel-like superfamily / Tubulin/FtsZ, GTPase domain / Recruitment of NuMA to mitotic centrosomes / Beta tubulin / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases Activate Formins / Hedgehog 'on' state / Recruitment of mitotic centrosome proteins and complexes / RHO GTPases activate IQGAPs / Tubulin / Alpha tubulin / Calponin homology domain / Hedgehog 'off' state / Cilium Assembly / Anchoring of the basal body to the plasma membrane / Intraflagellar transport / microtubule minus-end binding / regulation of cell morphogenesis / spectrin binding / positive regulation of axon guidance / regulation of microtubule polymerization / cytoplasmic microtubule / cytoskeleton organization / recycling endosome / cellular response to interleukin-4 / microtubule-based process / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton / neuron projection development / double-stranded RNA binding / microtubule / microtubule binding / calmodulin binding / GTPase activity / myelin sheath / GTP binding / ubiquitin protein ligase binding / protein heterodimerization activity / cytosol / cytoplasm / Tubulin alpha chain / Tubulin alpha-1B chain / Calmodulin-regulated spectrin-associated protein 1 / Tubulin beta-2B chain
Function and homology information
Specimen sourceHomo sapiens (human)
Bos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8 Å resolution
AuthorsAkhmanova, A. / Moores, C.A. / Baldus, M. / Steinmetz, M.O. / Topf, M. / Roberts, A.J. / Grant, B.J. / Scarabelli, G. / Joseph, A.-J. / van Hooff, J.J.E. / Houben, K. / Hua, S. / Luo, Y. / Stangier, M.M. / Jiang, K. / Atherton, J.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: A structural model for microtubule minus-end recognition and protection by CAMSAP proteins.
Authors: 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

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Structure visualization

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Assembly

Deposited unit
C: Calmodulin-regulated spectrin-associated protein 1
D: Tubulin alpha chain
E: Tubulin beta-2B chain
A: Tubulin alpha chain
B: Tubulin beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,09313
Polyers206,4045
Non-polymers3,6898
Water1448
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)16920
ΔGint (kcal/M)-83
Surface area (Å2)69970
MethodPISA

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Components

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Protein/peptide , 3 types, 5 molecules CDAEB

#1: Protein/peptide Calmodulin-regulated spectrin-associated protein 1


Mass: 13506.602 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: CAMSAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5T5Y3
#2: Protein/peptide Tubulin alpha chain


Mass: 48638.793 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4C1, UniProt: P81947*PLUS
#3: Protein/peptide Tubulin beta-2B chain


Mass: 47809.746 Da / Num. of mol.: 2 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856

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Non-polymers , 5 types, 16 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


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 / Paclitaxel
#8: Water ChemComp-HOH / water


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1Complex of two tubulin dimers with bound CAMSAP1-CKK domainCOMPLEX1, 2, 30MULTIPLE SOURCES
2TubulinCOMPLEX2,31NATURAL
3CAMSAP1-CKK domainCOMPLEX11RECOMBINANT
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
129913Bos taurus (cattle)
239606Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Details: 20e-/A2 used in final reconstuctions / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategory
10SPIDERinitial Euler assignment
11FREALIGNfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 5954
Details: Gold-standard noise substitution test used to assess for over fitting (Chen et al., 2013)
Symmetry type: POINT
Atomic model buildingRef protocol: OTHER
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415021
ELECTRON MICROSCOPYf_angle_d0.72520423
ELECTRON MICROSCOPYf_dihedral_angle_d3.7019018
ELECTRON MICROSCOPYf_chiral_restr0.0462225
ELECTRON MICROSCOPYf_plane_restr0.0072752

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