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- PDB-7wu7: Prefoldin-tubulin-TRiC complex -

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Basic information

Entry
Database: PDB / ID: 7wu7
TitlePrefoldin-tubulin-TRiC complex
Components
  • (Prefoldin subunit ...) x 6
  • (T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / chapronin complex
Function / homology
Function and homology information


RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly / RPAP3/R2TP/prefoldin-like complex / BBSome-mediated cargo-targeting to cilium / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / RNA polymerase II core complex assembly / Prefoldin mediated transfer of substrate to CCT/TriC / chaperonin-containing T-complex / negative regulation of amyloid fibril formation / protein folding chaperone complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / microtubule-based process / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / protein folding chaperone / : / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / tubulin binding / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / negative regulation of canonical Wnt signaling pathway / mRNA 5'-UTR binding / cilium / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transcription corepressor activity / G-protein beta-subunit binding / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / retina development in camera-type eye / amyloid-beta binding / protein-folding chaperone binding / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cadherin binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / T-complex protein 1, alpha subunit ...Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / 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
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 ...ADENOSINE-5'-DIPHOSPHATE / Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 / T-complex protein 1 subunit beta / Prefoldin subunit 5 / T-complex protein 1 subunit eta / Prefoldin subunit 4 / Prefoldin subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsGestaut, D. / Zhao, Y. / Park, J. / Ma, B. / Leitner, A. / Collier, M. / Pintilie, G. / Roh, S.-H. / Chiu, W. / Frydman, J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Cell / Year: 2022
Title: Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT.
Authors: Daniel Gestaut / Yanyan Zhao / Junsun Park / Boxue Ma / Alexander Leitner / Miranda Collier / Grigore Pintilie / Soung-Hun Roh / Wah Chiu / Judith Frydman /
Abstract: The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of ...The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
History
DepositionFeb 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Prefoldin subunit 1
2: Prefoldin subunit 2
3: Prefoldin subunit 3
4: Prefoldin subunit 4
5: Prefoldin subunit 5
6: Prefoldin subunit 6
A: T-complex protein 1 subunit alpha
B: T-complex protein 1 subunit beta
C: T-complex protein 1 subunit gamma
D: T-complex protein 1 subunit delta
E: T-complex protein 1 subunit epsilon
F: T-complex protein 1 subunit zeta
G: T-complex protein 1 subunit eta
H: T-complex protein 1 subunit theta
I: T-complex protein 1 subunit alpha
J: T-complex protein 1 subunit beta
K: T-complex protein 1 subunit gamma
L: T-complex protein 1 subunit delta
M: T-complex protein 1 subunit epsilon
N: T-complex protein 1 subunit zeta
O: T-complex protein 1 subunit eta
P: T-complex protein 1 subunit theta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,049,15426
Polymers1,047,44522
Non-polymers1,7094
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Prefoldin subunit ... , 6 types, 6 molecules 123456

#1: Protein Prefoldin subunit 1


Mass: 14234.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN1, PFD1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60925
#2: Protein Prefoldin subunit 2


Mass: 16672.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN2, PFD2, HSPC231 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UHV9
#3: Protein Prefoldin subunit 3 / HIBBJ46 / von Hippel-Lindau-binding protein 1 / VBP-1 / VHL-binding protein 1


Mass: 22658.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VBP1, PFDN3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61758
#4: Protein Prefoldin subunit 4 / Protein C-1


Mass: 16160.071 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN4, PFD4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NQP4
#5: Protein Prefoldin subunit 5 / Myc modulator 1 / c-Myc-binding protein Mm-1


Mass: 16051.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN5, MM1, PFD5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99471
#6: Protein Prefoldin subunit 6 / Protein Ke2


Mass: 14603.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFDN6, HKE2, PFD6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O15212

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

#7: 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17987
#8: 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78371
#9: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / hTRiC5


Mass: 60613.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49368
#10: 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50991
#11: 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48643
#12: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / HTR3 / Tcp20


Mass: 58166.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P40227
#13: 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 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99832
#14: 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: 59576.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ, KIAA0002 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50990

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Non-polymers , 1 types, 4 molecules

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


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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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: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex
Type: COMPLEX / Entity ID: #1-#14 / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Cell: high five / Plasmid: pFastbac-dual
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium chlorideNaCl1
21 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 3500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 11796

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1cryoSPARC3.2.0particle selectioncryoSPARC was used for 2D classification
2Topazparticle selectionTopaz was used for the particle picking
5cryoSPARC3.2.0CTF correctioncryoSPARC was used for the CTF correction
6GctfCTF correctionGctf was used for the CTF correction
9UCSF Chimera1.15model fitting
11cryoSPARC3.2.0initial Euler assignment
12cryoSPARC3.2.0final Euler assignment
13cryoSPARC3.2.0classification
14cryoSPARC3.2.03D reconstruction
15PHENIX1.19model refinementPhenix was used for refinement
16Coot0.9.6model refinement
17NAMDmodel refinementNamdinator website for MDFF
CTF correctionDetails: CTF correction was performed for every micrographs / Type: NONE
Particle selectionNum. of particles selected: 443858
Details: The initial particle selection after 2D class classification
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 194013 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6NR8

6nr8


Accession code: 6NR8 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00367787
ELECTRON MICROSCOPYf_angle_d0.78191457
ELECTRON MICROSCOPYf_dihedral_angle_d6.0479299
ELECTRON MICROSCOPYf_chiral_restr0.04710955
ELECTRON MICROSCOPYf_plane_restr0.00511729

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