[English] 日本語
- PDB-5m5c: Mechanism of microtubule minus-end recognition and protection by ... -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5m5c
TitleMechanism of microtubule minus-end recognition and protection by CAMSAP proteins
DescriptorCalmodulin-regulated spectrin-associated protein 1
Tubulin alpha-1B chain
Tubulin beta-2B chain
KeywordsTRANSPORT PROTEIN / CAMSAP CKK Microtubule Tubulin
Specimen sourceHomo sapiens / human
Bos taurus / mammal / Bovine / ウシ /
MethodElectron microscopy (4.8 Å resolution / Filament / Single particle)
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 21, 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

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


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)210,13713

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)18230
ΔGint (kcal/M)-87
Surface area (Å2)69320


Polypeptide(L) , 3 types, 5 molecules CDAEB

#1: Polypeptide(L)Calmodulin-regulated spectrin-associated protein 1

Mass: 13550.654 Da / Num. of mol.: 1 / Fragment: UNP residues 1472-1589 / Mutation: N1492A / Source: (gene. exp.) Homo sapiens / References: UniProt: Q5T5Y3

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)Tubulin alpha chain

Mass: 48638.793 Da / Num. of mol.: 2 / Source: (natural) Bos taurus / References: UniProt: F2Z4C1
#3: Polypeptide(L)Tubulin beta-2B chain

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

Cellular component

Molecular function

Biological process

Non-polymers , 5 types, 16 molecules


Mass: 523.180 Da / Num. of mol.: 2 / Formula: C10H16N5O14P3
#5: ChemicalChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Formula: Mg

Mass: 443.201 Da / Num. of mol.: 2 / Formula: C10H15N5O11P2
#7: ChemicalChemComp-TA1 / TAXOL

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

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

Experimental details


EM experimentAggregation state: FILAMENT / Reconstruction method: SINGLE PARTICLE

Sample preparation

IDNameTypeEntity IDParent IDSource
1Complex of two tubulin dimers with bound CAMSAP1-N1492A MUTANT CKK domainCOMPLEX1,2,30MULTIPLE SOURCES
2tubulin dimerCOMPLEX2,31NATURAL
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
329913Bos taurus
139606homo sapiens
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: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategoryImaging IDFitting IDImage processing ID
Particle selectionNumber of particles selected: 4144
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 6530
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_d0.00415018
ELECTRON MICROSCOPYf_angle_d0.78820419
ELECTRON MICROSCOPYf_dihedral_angle_d4.0359016
ELECTRON MICROSCOPYf_chiral_restr0.0492225
ELECTRON MICROSCOPYf_plane_restr0.0072751

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more