[English] 日本語
Yorodumi
- PDB-6qb8: Human CCT:mLST8 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qb8
TitleHuman CCT:mLST8 complex
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / CCT / folding / WD40 / mLST8
Function / homology
Function and homology information


zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly / chaperonin-containing T-complex / : / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC ...zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly / chaperonin-containing T-complex / : / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC / binding of sperm to zona pellucida / Folding of actin by CCT/TriC / Prefoldin mediated transfer of substrate to CCT/TriC / RHOBTB1 GTPase cycle / WD40-repeat domain binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / beta-tubulin binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / RHOBTB2 GTPase cycle / heterochromatin / : / positive regulation of telomere maintenance via telomerase / protein folding chaperone / acrosomal vesicle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / response to virus / azurophil granule lumen / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / unfolded protein binding / melanosome / G-protein beta-subunit binding / protein folding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cilium / cadherin binding / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit ...GROEL; domain 1 / GroEL-like equatorial domain / GROEL; domain 2 / TCP-1-like chaperonin intermediate domain / GroEL / GroEL / T-complex protein 1, alpha subunit / T-complex protein 1, eta subunit / T-complex protein 1, theta subunit / T-complex protein 1, zeta subunit / T-complex protein 1, delta subunit / T-complex protein 1, gamma subunit / T-complex protein 1, epsilon subunit / T-complex protein 1, beta subunit / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / T-complex protein 1 subunit alpha / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit gamma / T-complex protein 1 subunit theta / T-complex protein 1 subunit delta / T-complex protein 1 subunit beta / T-complex protein 1 subunit eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsCuellar, J. / Santiago, C. / Ludlam, W.G. / Bueno-Carrasco, M.T. / Valpuesta, J.M. / Willardson, B.M.
Funding support United States, Spain, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)EY012287 United States
Spanish Ministry of Science, Innovation, and UniversitiesBFU2016-75984 Spain
S2013/MIT2807 Spain
CitationJournal: Nat Commun / Year: 2019
Title: Structural and functional analysis of the role of the chaperonin CCT in mTOR complex assembly.
Authors: Jorge Cuéllar / W Grant Ludlam / Nicole C Tensmeyer / Takuma Aoba / Madhura Dhavale / César Santiago / M Teresa Bueno-Carrasco / Michael J Mann / Rebecca L Plimpton / Aman Makaju / Sarah ...Authors: Jorge Cuéllar / W Grant Ludlam / Nicole C Tensmeyer / Takuma Aoba / Madhura Dhavale / César Santiago / M Teresa Bueno-Carrasco / Michael J Mann / Rebecca L Plimpton / Aman Makaju / Sarah Franklin / Barry M Willardson / José M Valpuesta /
Abstract: The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two ...The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two of the subunits of these complexes are mLST8 and Raptor, β-propeller proteins that stabilize the mTOR kinase and recruit substrates, respectively. Here we report that the eukaryotic chaperonin CCT plays a key role in mTORC assembly and signaling by folding both mLST8 and Raptor. A high resolution (4.0 Å) cryo-EM structure of the human mLST8-CCT intermediate isolated directly from cells shows mLST8 in a near-native state bound to CCT deep within the folding chamber between the two CCT rings, and interacting mainly with the disordered N- and C-termini of specific CCT subunits of both rings. These findings describe a unique function of CCT in mTORC assembly and a distinct binding site in CCT for mLST8, far from those found for similar β-propeller proteins.
History
DepositionDec 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4489
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
a: T-complex protein 1 subunit alpha
b: T-complex protein 1 subunit beta
d: T-complex protein 1 subunit delta
e: T-complex protein 1 subunit epsilon
g: T-complex protein 1 subunit gamma
h: T-complex protein 1 subunit eta
q: T-complex protein 1 subunit theta
z: T-complex protein 1 subunit zeta
A: T-complex protein 1 subunit alpha
B: T-complex protein 1 subunit beta
D: T-complex protein 1 subunit delta
E: T-complex protein 1 subunit epsilon
G: T-complex protein 1 subunit gamma
H: T-complex protein 1 subunit eta
Q: T-complex protein 1 subunit theta
Z: T-complex protein 1 subunit zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)947,76518
Polymers946,91116
Non-polymers8542
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area47880 Å2
ΔGint-205 kcal/mol
Surface area319240 Å2
MethodPISA

-
Components

-
T-complex protein 1 subunit ... , 8 types, 16 molecules aAbBdDeEgGhHqQzZ

#1: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


Mass: 60418.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCP1, CCT1, CCTA / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P17987
#2: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57567.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT2, 99D8.1, CCTB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P78371
#3: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


Mass: 57996.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT4, CCTD, SRB / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P50991
#4: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 59749.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P48643
#5: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / hTRiC5


Mass: 60482.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P49368
#6: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / HIV-1 Nef-interacting protein


Mass: 59443.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT7, CCTH, NIP7-1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q99832
#7: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta / Chaperonin containing T-complex polypeptide 1 subunit 8 / Renal carcinoma ...TCP-1-theta / CCT-theta / Chaperonin containing T-complex polypeptide 1 subunit 8 / Renal carcinoma antigen NY-REN-15


Mass: 59691.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ, KIAA0002 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P50990
#8: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / HTR3 / Tcp20


Mass: 58106.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P40227

-
Non-polymers , 1 types, 2 molecules

#9: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: CCT:mLST8 complex / Type: COMPLEX
Details: we have characterized the complex between the eukaryotic chaperonin CCT (1 MDa; formed by two copies of eight homologous subunits) and its substrate mLST8 (mammalian Lethal with SEC13 ...Details: we have characterized the complex between the eukaryotic chaperonin CCT (1 MDa; formed by two copies of eight homologous subunits) and its substrate mLST8 (mammalian Lethal with SEC13 protein 8, also called Gbeta-like protein)
Entity ID: #1-#8 / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293T
Buffer solutionpH: 7.5
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 7 sec. / Electron dose: 36 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 5576
EM imaging opticsEnergyfilter name: GIF Quantum LS
Image scansMovie frames/image: 40

-
Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2Xmipp3image acquisitionauto-picking
4CTFFIND4CTF correction
7iMODFITmodel fitting
9RELION2initial Euler assignment
10RELION2final Euler assignment
11RELION2classification
12RELION23D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1769600
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 452000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 5GW5 / Initial refinement model-ID: 1 / PDB-ID: 5GW5

5gw5

/ Source name: PDB / Type: experimental model

IDPdb chain-ID
1A
2G
3Z
4Q
5H
6E
7B
8D
9a
10g
11z
12q
13h
14e
15b
16e

+
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