[English] 日本語
Yorodumi
- EMDB-1960: Symmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1960
TitleSymmetry-free cryo-EM map of TRiC in the nucleotide-free (apo) state
Map datasymmetry-free apo-TRiC 3D reconstruction
SampleBovine TRiC/CCT in the nucleotide-free (apo) state:
bovine TRiC
KeywordsTRiC/CCT / chaperonin / cryo-EM / protein folding
Function / homologyChaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 1. / T-complex protein 1, beta subunit / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / Chaperonin Cpn60/TCP-1 family / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 2. ...Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 1. / T-complex protein 1, beta subunit / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like apical domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like equatorial domain superfamily / Chaperonin Cpn60/TCP-1 family / TCP-1/cpn60 chaperonin family / Chaperonins TCP-1 signature 2. / Chaperonins TCP-1 signature 3. / Association of TriC/CCT with target proteins during biosynthesis / Neutrophil degranulation / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / scaRNA localization to Cajal body / positive regulation of establishment of protein localization to telomere / zona pellucida receptor complex / chaperonin-containing T-complex / positive regulation of telomerase RNA localization to Cajal body / binding of sperm to zona pellucida / 'de novo' protein folding / toxin transport / protein binding involved in protein folding / chaperone-mediated protein complex assembly / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / positive regulation of telomerase activity / cell body / unfolded protein binding / protein stabilization / microtubule / myelin sheath / ubiquitin protein ligase binding / ATP binding / T-complex protein 1 subunit beta
Function and homology information
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / 10.5 Å resolution
AuthorsCong Y / Schroder GF / Meyer AS / Jakana J / Ma B / Dougherty MT / Schmid MF / Reissmann S / Levitt M / Ludtke SL / Frydman J / Chiu W
CitationJournal: EMBO J. / Year: 2012
Title: Symmetry-free cryo-EM structures of the chaperonin TRiC along its ATPase-driven conformational cycle.
Authors: Yao Cong / Gunnar F Schröder / Anne S Meyer / Joanita Jakana / Boxue Ma / Matthew T Dougherty / Michael F Schmid / Stefanie Reissmann / Michael Levitt / Steven L Ludtke / Judith Frydman / Wah Chiu
Validation ReportPDB-ID: 4a0o

SummaryFull reportAbout validation report
DateDeposition: Sep 3, 2011 / Header (metadata) release: Feb 6, 2012 / Map release: Feb 6, 2012 / Last update: Mar 20, 2013

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4a0o
  • Surface level: 1.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_1960.map.gz (map file in CCP4 format, 11665 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.4 Å/pix.
= 345.6 Å
144 pix
2.4 Å/pix.
= 345.6 Å
144 pix
2.4 Å/pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.4 Å
Density
Contour Level:1.13 (by author), 1.13 (movie #1):
Minimum - Maximum-0.42493957 - 2.51474524
Average (Standard dev.)0.07473919 (0.28258339)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
CellA=B=C: 345.6 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.42.42.4
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
D min/max/mean-0.4252.5150.075

-
Supplemental data

-
Sample components

-
Entire Bovine TRiC/CCT in the nucleotide-free (apo) state

EntireName: Bovine TRiC/CCT in the nucleotide-free (apo) state / Number of components: 1 / Oligomeric State: 16-mer
MassTheoretical: 1000 kDa / Experimental: 1000 kDa

-
Component #1: protein, bovine TRiC

ProteinName: bovine TRiC / a.k.a: TRiC or CCT / Oligomeric Details: 16-mer / Recombinant expression: No
MassTheoretical: 1000 kDa / Experimental: 1000 kDa
SourceSpecies: Bos taurus (cattle)
Source (natural)Organ or tissue: Testes

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml
Support film200-mesh Quantifoil holey grid
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 101 K / Humidity: 100 % / Method: Two-side blotting for 1 second before plunging / Details: Vitrification instrument: FEI vitrobot

-
Electron microscopy imaging

ImagingMicroscope: JEOL 3200FSC / Date: Oct 20, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal) / Astigmatism: objective lens astigmatism correction / Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3000 nm / Energy filter: JEOL in-column omega energy filter / Energy window: 0-20 eV
Specimen HolderHolder: Side entry / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 101 K
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 700 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 47151 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: EMAN1.8 / CTF correction: each micrograph
Details: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps
Resolution: 10.5 Å / Resolution method: FSC 0.5

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
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

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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