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- PDB-7ylw: yeast TRiC-plp2-tubulin complex at S3 closed TRiC state -

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Basic information

Entry
Database: PDB / ID: 7ylw
Titleyeast TRiC-plp2-tubulin complex at S3 closed TRiC state
Components
  • (T-complex protein 1 subunit ...) x 8
  • Phosducin-like protein 2
  • Tubulin beta chain
KeywordsCHAPERONE / TRiC/CCT / tubulin / phosducin-like protein
Function / homology
Function and homology information


cellular response to pheromone / : / Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperonin-containing T-complex / : / negative regulation of signal transduction / Neutrophil degranulation / ATP-dependent protein folding chaperone / structural constituent of cytoskeleton ...cellular response to pheromone / : / Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperonin-containing T-complex / : / negative regulation of signal transduction / Neutrophil degranulation / ATP-dependent protein folding chaperone / structural constituent of cytoskeleton / G-protein beta/gamma-subunit complex binding / microtubule cytoskeleton organization / unfolded protein binding / protein folding / mitotic cell cycle / actin binding / actin cytoskeleton organization / microtubule / regulation of cell cycle / GTPase activity / GTP binding / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
: / 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 ...: / 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) / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 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 / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / 3-Layer(bba) Sandwich / Helix Hairpins / Thioredoxin-like superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon ...ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta / Phosducin-like protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsHan, W.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Sci Adv / Year: 2023
Title: Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT.
Authors: Wenyu Han / Mingliang Jin / Caixuan Liu / Qiaoyu Zhao / Shutian Wang / Yifan Wang / Yue Yin / Chao Peng / Yanxing Wang / Yao Cong /
Abstract: The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron ...The cytoskeletal proteins tubulin and actin are the obligate substrates of TCP-1 ring complex/Chaperonin containing TCP-1 (TRiC/CCT), and their folding involves co-chaperone. Through cryo-electron microscopy analysis, we present a more complete picture of TRiC-assisted tubulin/actin folding along TRiC adenosine triphosphatase cycle, under the coordination of co-chaperone plp2. In the open S1/S2 states, plp2 and tubulin/actin engaged within opposite TRiC chambers. Notably, we captured an unprecedented TRiC-plp2-tubulin complex in the closed S3 state, engaged with a folded full-length -tubulin and loaded with a guanosine triphosphate, and a plp2 occupying opposite rings. Another closed S4 state revealed an actin in the intermediate folding state and a plp2. Accompanying TRiC ring closure, plp2 translocation could coordinate substrate translocation on the CCT6 hemisphere, facilitating substrate stabilization and folding. Our findings reveal the folding mechanism of the major cytoskeletal proteins tubulin/actin under the coordination of the biogenesis machinery TRiC and plp2 and extend our understanding of the links between cytoskeletal proteostasis and related human diseases.
History
DepositionJul 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
T: Tubulin beta chain
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
p: Phosducin-like protein 2
q: T-complex protein 1 subunit theta
z: T-complex protein 1 subunit zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,061,66665
Polymers1,052,74318
Non-polymers8,92347
Water25214
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

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


Mass: 60557.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: TCP1, CCT1, YDR212W, YD8142.13, YD8142B.04 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12612
#2: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57276.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCT2, BIN3, TCP2, YIL142W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39076
#3: Protein T-complex protein 1 subunit delta


Mass: 57682.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT4 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39078
#4: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 61995.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCT5, TCP5, YJR064W, J1752 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40413
#5: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma


Mass: 65423.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: fusion protein of T-complex protein 1 subunit gamma,rep-His-CBP and T-complex protein 1 subunit gamma
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCT3, BIN2, TCP3, YJL014W, J1336 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39077
#6: Protein T-complex protein 1 subunit eta


Mass: 59802.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CCT7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P42943
#7: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta


Mass: 61735.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCT8, YJL008C, J1374 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P47079
#9: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / CCT-zeta


Mass: 59997.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CCT6, TCP20, TCP6, YDR188W, YD9395.21 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P39079

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Protein , 2 types, 2 molecules Tp

#8: Protein Tubulin beta chain


Mass: 50967.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TUB2, GI527_G0002040 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PXT5
#10: Protein Phosducin-like protein 2 / Viral IAP-associated factor 1 homolog


Mass: 32836.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PLP2, VIAF1, YOR281C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12017

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Non-polymers , 5 types, 61 molecules

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


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#12: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#14: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1yeast TRiC-plp2-tubulin complex at C3 closed TRiC stateCOMPLEX#1-#4, #6-#100MULTIPLE SOURCES
2TRiC, tubulin beta chainCOMPLEX#1-#91NATURAL
3plp2COMPLEX#101RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae (brewer's yeast)4932
32Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Eschericia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 2500 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 38 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28063 / Symmetry type: POINT

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