[English] 日本語
Yorodumi
- PDB-3iyg: Ca model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3iyg
TitleCa model of bovine TRiC/CCT derived from a 4.0 Angstrom cryo-EM map
Descriptor(T-complex protein 1 subunit ...) x 7
KeywordsCHAPERONE / TRiC/CCT / Asymmetric / Cryo-EM / subunit arrangement / ATP-binding / Chaperone / Isopeptide bond / Nucleotide-binding / Phosphoprotein / Disulfide bond
Specimen sourceBos taurus / mammal / bovine / ウシ /
MethodElectron microscopy (4 Å resolution / Particle / Single particle)
AuthorsCong, Y. / Baker, M.L. / Ludtke, S.J. / Frydman, J. / Chiu, W.
CitationProc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972

Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 4967-4972 Yorodumi Papers
4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.
Yao Cong / Matthew L Baker / Joanita Jakana / David Woolford / Erik J Miller / Stefanie Reissmann / Ramya N Kumar / Alyssa M Redding-Johanson / Tanveer S Batth / Aindrila Mukhopadhyay / Steven J Ludtke / Judith Frydman / Wah Chiu

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 28, 2009 / Release: Mar 16, 2010
RevisionDateData content typeGroupProviderType
1.0Mar 16, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

-
Structure visualization

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


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
Q: T-complex protein 1 subunit theta
G: T-complex protein 1 subunit gamma
Z: T-complex protein 1 subunit zeta
D: T-complex protein 1 subunit delta
B: T-complex protein 1 subunit beta
E: T-complex protein 1 subunit
A: T-complex protein 1 subunit alpha
H: T-complex protein 1 subunit eta


Theoretical massNumber of molelcules
Total (without water)451,9498
Polyers451,9498
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
T-complex protein 1 subunit ... , 7 types, 7 molecules QGZDBAH

#1: Polypeptide(L)T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta / Coordinate model: Cα atoms only


Mass: 55833.926 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3ZCI9

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / Coordinate model: Cα atoms only


Mass: 57486.273 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3T0K2

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta / CCT-zeta-1 / Coordinate model: Cα atoms only


Mass: 56602.305 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3MHL7

Cellular component

Molecular function

Biological process

#4: Polypeptide(L)T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Coordinate model: Cα atoms only


Mass: 56057.941 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q2T9X2

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta / Coordinate model: Cα atoms only


Mass: 55107.234 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q3ZBH0

Cellular component

Molecular function

Biological process

  • 'de novo' protein folding (GO: 0006458)
  • binding of sperm to zona pellucida (GO: 0007339)
  • chaperone mediated protein folding independent of cofactor (GO: 0051086)
  • chaperone-mediated protein complex assembly (GO: 0051131)
  • chaperone-mediated protein folding (GO: 0061077)
  • positive regulation of establishment of protein localization to telomere (GO: 1904851)
  • positive regulation of protein localization to Cajal body (GO: 1904871)
  • positive regulation of telomerase activity (GO: 0051973)
  • positive regulation of telomerase RNA localization to Cajal body (GO: 1904874)
  • positive regulation of telomere maintenance via telomerase (GO: 0032212)
  • protein stabilization (GO: 0050821)
  • scaRNA localization to Cajal body (GO: 0090666)
  • toxin transport (GO: 1901998)
#7: Polypeptide(L)T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha / Coordinate model: Cα atoms only


Mass: 57495.387 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q32L40

Cellular component

Molecular function

Biological process

#8: Polypeptide(L)T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / Coordinate model: Cα atoms only


Mass: 56614.234 Da / Num. of mol.: 1 / Source: (natural) Bos taurus / References: UniProt: Q2NKZ1

Cellular component

Molecular function

Biological process

-
Polypeptide(L) , 1 types, 1 molecules E

#6: Polypeptide(L)T-complex protein 1 subunit / Coordinate model: Cα atoms only


Mass: 56751.703 Da / Num. of mol.: 1 / Source: (natural) Bos taurus

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

-
Sample preparation

ComponentName: bovine TRiC (also called CCT) / Type: COMPLEX
Molecular weightValue: 1 deg. / Units: MEGADALTONS / Experimental value: NO
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Temp: 101 K / Humidity: 95 % / Details: vitrification using ethane as cryogen / Method: two-side blotting for 1 second before plunging

-
Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Aug 1, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 4.1 mm / Astigmatism: objective lens astigmatism correction / Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Specimen holder type: side entry / Temperature: 101 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM
EM imaging opticsEnergyfilter name: in-column omega energy filter / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV

-
Processing

EM software
IDNameCategory
1CootMODEL FITTING
2ModellerMODEL FITTING
3UCSF ChimeraMODEL FITTING
4EMANRECONSTRUCTION
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: C2
3D reconstructionMethod: Projection matching / Resolution: 4 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 101000 / Nominal pixel size: 1.2 / Actual pixel size: 1.2
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 ( Details about the particle: A recently developed 2-D fast rotational matching (FRM2D) algorithm for image alignment, available in EMAN 1.8, was adopted in the refinement steps )
Symmetry type: POINT
Atomic model buildingDetails: METHOD--Local refinement, Flexible fitting REFINEMENT PROTOCOL--Local refinement, Flexible fitting
Ref protocol: FLEXIBLE FIT / Ref space: REAL
Number of atoms included #LASTProtein: 4134 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4134

+
About Yorodumi

-
News

-
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

-
Yorodumi

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