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- PDB-8shp: CCT G beta 5 complex closed state 13 -

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Basic information

Entry
Database: PDB / ID: 8shp
TitleCCT G beta 5 complex closed state 13
Components
  • (T-complex protein 1 subunit ...) x 8
  • Guanine nucleotide-binding protein subunit beta-5
  • Phosducin-like protein
KeywordsCHAPERONE / CCT / Gb5 / complex / open
Function / homology
Function and homology information


heterotrimeric G-protein complex assembly / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / 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 ...heterotrimeric G-protein complex assembly / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / 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 / chaperonin-containing T-complex / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / cell projection organization / regulation of G protein-coupled receptor signaling pathway / Prefoldin mediated transfer of substrate to CCT/TriC / positive regulation of smoothened signaling pathway / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / G protein-coupled dopamine receptor signaling pathway / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / : / 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 / visual perception / GTPase activator activity / positive regulation of GTPase activity / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / cilium / Thromboxane signalling through TP receptor / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / mRNA 5'-UTR binding / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / azurophil granule lumen / GPER1 signaling / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / unfolded protein binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / melanosome / protein folding / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / presynapse / protein-folding chaperone binding / Ca2+ pathway / cell body / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / Extra-nuclear estrogen signaling / cytoskeleton / protein stabilization / cadherin binding / G protein-coupled receptor signaling pathway / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / Golgi apparatus / signal transduction / ATP hydrolysis activity / RNA binding
Similarity search - Function
Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / 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 ...Phosducin / Phosducin, N-terminal domain superfamily / : / Phosducin, thioredoxin-like domain / Phosducin / 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 / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / Thioredoxin-like superfamily / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Guanine nucleotide-binding protein subunit beta-5 / 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 ...ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Guanine nucleotide-binding protein subunit beta-5 / 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 / Phosducin-like protein / T-complex protein 1 subunit eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsWang, S. / Sass, M. / Willardson, B.M. / Shen, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)R01 EY012287 United States
CitationJournal: Mol Cell / Year: 2023
Title: Visualizing the chaperone-mediated folding trajectory of the G protein β5 β-propeller.
Authors: Shuxin Wang / Mikaila I Sass / Yujin Kwon / W Grant Ludlam / Theresa M Smith / Ethan J Carter / Nathan E Gladden / Margot Riggi / Janet H Iwasa / Barry M Willardson / Peter S Shen /
Abstract: The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, ...The Chaperonin Containing Tailless polypeptide 1 (CCT) complex is an essential protein folding machine with a diverse clientele of substrates, including many proteins with β-propeller domains. Here, we determine the structures of human CCT in complex with its accessory co-chaperone, phosducin-like protein 1 (PhLP1), in the process of folding Gβ, a component of Regulator of G protein Signaling (RGS) complexes. Cryoelectron microscopy (cryo-EM) and image processing reveal an ensemble of distinct snapshots that represent the folding trajectory of Gβ from an unfolded molten globule to a fully folded β-propeller. These structures reveal the mechanism by which CCT directs Gβ folding through initiating specific intermolecular contacts that facilitate the sequential folding of individual β sheets until the propeller closes into its native structure. This work directly visualizes chaperone-mediated protein folding and establishes that CCT orchestrates folding by stabilizing intermediates through interactions with surface residues that permit the hydrophobic core to coalesce into its folded state.
History
DepositionApr 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: Guanine nucleotide-binding protein subunit beta-5
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, N-terminally processed
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, N-terminally processed
q: T-complex protein 1 subunit theta
z: T-complex protein 1 subunit zeta
P: Phosducin-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,013,54966
Polymers1,004,98118
Non-polymers8,56848
Water34219
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 , 2 types, 2 molecules NP

#1: Protein Guanine nucleotide-binding protein subunit beta-5 / Gbeta5 / Transducin beta chain 5


Mass: 43619.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: O14775
#10: Protein Phosducin-like protein / PHLP


Mass: 34322.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: Q13371

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

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


Mass: 58243.172 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P17987
#3: Protein T-complex protein 1 subunit beta / TCP-1-beta / CCT-beta


Mass: 56490.855 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P78371
#4: Protein T-complex protein 1 subunit delta / TCP-1-delta / CCT-delta / Stimulator of TAR RNA-binding


Mass: 56242.168 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P50991
#5: Protein T-complex protein 1 subunit epsilon / TCP-1-epsilon / CCT-epsilon


Mass: 59618.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P48643
#6: Protein T-complex protein 1 subunit gamma / TCP-1-gamma / CCT-gamma / hTRiC5


Mass: 58837.996 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P49368
#7: Protein T-complex protein 1 subunit eta, N-terminally processed


Mass: 57939.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: Q99832
#8: 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: 58427.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P50990
#9: Protein T-complex protein 1 subunit zeta / TCP-1-zeta / Acute morphine dependence-related protein 2 / CCT-zeta-1 / HTR3 / Tcp20


Mass: 57719.613 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293T / Tissue: Kidney / References: UniProt: P40227

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Non-polymers , 4 types, 67 molecules

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


Mass: 427.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / 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
#13: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: AlF3
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: CCT-Gb5-PhLP1 in closed state 13 / Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: Kidney / Tissue: Kidney
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293T
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMsodium chlorideNaCl1
220 mMN-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acidHEPES1
310 %3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonateCHAPS1
410 mMD-desthiobiotinD-desthiobiotin1
51 mMTris Carboxy Ethyl PhospheneTCEP1
65 mMmagnesium chlorideMgCl21
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was monodisperse
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 40.42 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
10cryoSPARC4.2.1initial Euler assignment
11cryoSPARC4.2.1final Euler assignment
13cryoSPARC4.2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43246 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00468826
ELECTRON MICROSCOPYf_angle_d0.53192921
ELECTRON MICROSCOPYf_dihedral_angle_d5.4749550
ELECTRON MICROSCOPYf_chiral_restr0.04211052
ELECTRON MICROSCOPYf_plane_restr0.00311863

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