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- PDB-7trg: The beta-tubulin folding intermediate I -

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Basic information

Entry
Database: PDB / ID: 7trg
TitleThe beta-tubulin folding intermediate I
Components
  • (T-complex protein 1 subunit ...) x 8
  • Tubulin beta chain
KeywordsCHAPERONE / Human chaperonin TRiC with beta-tubulin folding intermediate I
Function / homology
Function and homology information


odontoblast differentiation / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / cytoskeleton-dependent intracellular transport / 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 / : ...odontoblast differentiation / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / cytoskeleton-dependent intracellular transport / 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 / GTPase activating protein binding / RHOBTB1 GTPase cycle / WD40-repeat domain binding / natural killer cell mediated cytotoxicity / nuclear envelope lumen / regulation of synapse organization / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / MHC class I protein binding / chaperone-mediated protein complex assembly / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / RHOBTB2 GTPase cycle / beta-tubulin binding / microtubule-based process / heterochromatin / intercellular bridge / spindle assembly / : / positive regulation of telomere maintenance via telomerase / protein folding chaperone / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / acrosomal vesicle / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / mRNA 5'-UTR binding / structural constituent of cytoskeleton / response to virus / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / mitotic spindle / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / unfolded protein binding / melanosome / protein folding / G-protein beta-subunit binding / mitotic cell cycle / microtubule cytoskeleton / cell body / secretory granule lumen / ficolin-1-rich granule lumen / Potential therapeutics for SARS / microtubule / cytoskeleton / protein stabilization / cilium / cadherin binding / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein-containing complex / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
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 ...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) / 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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Tubulin beta chain / 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 Å
AuthorsZhao, Y. / Frydman, J. / Chiu, W.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM074074 United States
National Institutes of Health/Office of the DirectorP41GM103832 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
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
DepositionJan 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin beta chain
B: T-complex protein 1 subunit theta
C: T-complex protein 1 subunit eta
D: T-complex protein 1 subunit epsilon
E: T-complex protein 1 subunit beta
F: T-complex protein 1 subunit delta
G: T-complex protein 1 subunit alpha
H: T-complex protein 1 subunit gamma
I: T-complex protein 1 subunit zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)528,66933
Polymers524,3859
Non-polymers4,28424
Water1448
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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Protein , 1 types, 1 molecules A

#1: Protein Tubulin beta chain / Tubulin beta-5 chain


Mass: 49717.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Folded N domain and C terminal E hook tail / Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB, TUBB5, OK/SW-cl.56 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P07437

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T-complex protein 1 subunit ... , 8 types, 8 molecules BCDEFGHI

#2: 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.: 1
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
#3: Protein T-complex protein 1 subunit eta / TCP-1-eta / CCT-eta / HIV-1 Nef-interacting protein


Mass: 60579.719 Da / Num. of mol.: 1
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
#4: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 59749.957 Da / Num. of mol.: 1
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
#5: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 57567.141 Da / Num. of mol.: 1
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
#6: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


Mass: 57996.113 Da / Num. of mol.: 1
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
#7: Protein T-complex protein 1 subunit alpha / TCP-1-alpha / CCT-alpha


Mass: 60418.477 Da / Num. of mol.: 1
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 gamma / TCP-1-gamma / CCT-gamma / hTRiC5


Mass: 60613.855 Da / Num. of mol.: 1
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
#9: 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.: 1
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

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Non-polymers , 4 types, 32 molecules

#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#12: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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

ComponentName: Closed form human TRiC in complex with beta-tubulin under ATP/AlF3condition.
Type: COMPLEX / Entity ID: #1, #9, #2-#4, #6-#8, #5 / Source: RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper) / Strain: High Five / Cell: ovarian cells
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid1
250 mMPotassium chlorideKCl1
35 mMMagnesium ChlorideMgCl21
41 mMDithiothreitol1
560 mMSodium nitrateNaF1
610 mMAluminium nitrateAl(NO3)31
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
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: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 1.21 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.20.1_4487refinement
PHENIX1.20.1_4487refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 110984 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.84 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334103
ELECTRON MICROSCOPYf_angle_d0.583946055
ELECTRON MICROSCOPYf_chiral_restr0.04285477
ELECTRON MICROSCOPYf_plane_restr0.00345886
ELECTRON MICROSCOPYf_dihedral_angle_d6.77394737

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