[English] 日本語
Yorodumi
- EMDB-2674: Cryo-EM map of p150 CAP-Gly-microtubule complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2674
TitleCryo-EM map of p150 CAP-Gly-microtubule complex
Map dataReconstruction of p150glued(1-105), filtered to 12 angstrom to visualise the decoration.
Sample
  • Sample: Microtubule complexed with p150glued (1-105), filtered to 12 angstrom
  • Protein or peptide: p150glued, microtubule
Keywordsmicrotubule / dynactin / +TIPs / p150 / CAP-Gly
Function / homology
Function and homology information


centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / microtubule anchoring at centrosome / ventral spinal cord development / maintenance of synapse structure / melanosome transport / nuclear membrane disassembly / positive regulation of microtubule nucleation ...centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / microtubule anchoring at centrosome / ventral spinal cord development / maintenance of synapse structure / melanosome transport / nuclear membrane disassembly / positive regulation of microtubule nucleation / microtubule plus-end / XBP1(S) activates chaperone genes / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / non-motile cilium assembly / retrograde transport, endosome to Golgi / nuclear migration / motor behavior / microtubule associated complex / neuromuscular process / neuromuscular junction development / intercellular bridge / cell leading edge / establishment of mitotic spindle orientation / COPI-mediated anterograde transport / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / regulation of mitotic spindle organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of microtubule polymerization / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / neuron projection maintenance / MHC class II antigen presentation / centriole / AURKA Activation by TPX2 / tubulin binding / ciliary basal body / tau protein binding / mitotic spindle / kinetochore / spindle pole / spindle / neuron cellular homeostasis / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Signaling by ALK fusions and activated point mutants / nuclear envelope / mitotic cell cycle / nervous system development / cell cortex / microtubule binding / microtubule / neuron projection / axon / cell division / neuronal cell body / centrosome / protein kinase binding / membrane / cytosol / cytoplasm
Similarity search - Function
Dynein associated protein / Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsWang Q / Crevenna AH / Kunze I / Mizuno N
CitationJournal: Proc Natl Acad Sci U S A / Year: 2014
Title: Structural basis for the extended CAP-Gly domains of p150(glued) binding to microtubules and the implication for tubulin dynamics.
Authors: Qianmin Wang / Alvaro H Crevenna / Ines Kunze / Naoko Mizuno /
Abstract: p150(glued) belongs to a group of proteins accumulating at microtubule plus ends (+TIPs). It plays a key role in initiating retrograde transport by recruiting and tethering endosomes and dynein to ...p150(glued) belongs to a group of proteins accumulating at microtubule plus ends (+TIPs). It plays a key role in initiating retrograde transport by recruiting and tethering endosomes and dynein to microtubules. p150(glued) contains an N-terminal microtubule-binding cytoskeleton-associated protein glycine-rich (CAP-Gly) domain that accelerates tubulin polymerization. Although this copolymerization is well-studied using light microscopic techniques, structural consequences of this interaction are elusive. Here, using electron-microscopic and spectroscopic approaches, we provide a detailed structural view of p150(glued) CAP-Gly binding to microtubules and tubulin. Cryo-EM 3D reconstructions of p150(glued)-CAP-Gly complexed with microtubules revealed the recognition of the microtubule surface, including tubulin C-terminal tails by CAP-Gly. These binding surfaces differ from other retrograde initiation proteins like EB1 or dynein, which could facilitate the simultaneous attachment of all accessory components. Furthermore, the CAP-Gly domain, with its basic extensions, facilitates lateral and longitudinal interactions of tubulin molecules by covering the tubulin acidic tails. This shielding effect of CAP-Gly and its basic extensions may provide a molecular basis of the roles of p150(glued) in microtubule dynamics.
History
DepositionJun 12, 2014-
Header (metadata) releaseJul 23, 2014-
Map releaseAug 6, 2014-
UpdateAug 13, 2014-
Current statusAug 13, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2674-125...

Downloads & links

-
Map

FileDownload / File: emd_2674.map.gz / Format: CCP4 / Size: 646.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of p150glued(1-105), filtered to 12 angstrom to visualise the decoration.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 60 pix.
= 132.6 Å		2.21 Å/pix.
x 60 pix.
= 132.6 Å		2.21 Å/pix.
x 47 pix.
= 103.87 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-24.265134809999999 - 34.65099335
Average (Standard dev.)1.0 (±10.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions604760
Spacing604760
CellA: 103.87 Å / B: 132.6 Å / C: 132.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.212.212.21
M x/y/z476060
origin x/y/z0.0000.0000.000
length x/y/z103.870132.600132.600
α/β/γ90.00090.00090.000
start NX/NY/NZ0-51-100
NX/NY/NZ82103201
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS476060
D min/max/mean-24.26534.6511.000

-
Supplemental data

-
Sample components

-
Entire : Microtubule complexed with p150glued (1-105), filtered to 12 angstrom

EntireName: Microtubule complexed with p150glued (1-105), filtered to 12 angstrom
Components
  • Sample: Microtubule complexed with p150glued (1-105), filtered to 12 angstrom
  • Protein or peptide: p150glued, microtubule

-
Supramolecule #1000: Microtubule complexed with p150glued (1-105), filtered to 12 angstrom

SupramoleculeName: Microtubule complexed with p150glued (1-105), filtered to 12 angstrom
type: sample / ID: 1000 / Oligomeric state: One CAP-Gly bound to tubulin monomer / Number unique components: 1

-
Macromolecule #1: p150glued, microtubule

MacromoleculeName: p150glued, microtubule / type: protein_or_peptide / ID: 1 / Name.synonym: dynactin1 / Oligomeric state: polymer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human
Molecular weightExperimental: 10 KDa / Theoretical: 10 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria) / Recombinant strain: gold / Recombinant plasmid: pEC vector (in house vector)
SequenceUniProtKB: Dynactin subunit 1 / InterPro: CAP Gly-rich domain, Dynein associated protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 6.8 / Details: 80 mM Pipes, 1 mM MgCl2, 1 mM EGTA
GridDetails: 300 mesh Quantifoil grid, glow discharged
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 5 seconds with force 2, before plunging

-
Electron microscopy

MicroscopeFEI TECNAI 20
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateMay 22, 2012
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 220 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 67873 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsThe particles were aligned using SPIDER and helical symmetry was applied using IHRSR.
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.98 Å
Applied symmetry - Helical parameters - Δ&Phi: 129 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: Spider, EMAN, IHRSR, bsoft
CTF correctionDetails: Phases of individual images are flipped.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more