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- PDB-9s72: Human CCT in Closed Conformation -

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Basic information

Entry
Database: PDB / ID: 9s72
TitleHuman CCT in Closed Conformation
Components(T-complex protein 1 subunit ...) x 8
KeywordsCHAPERONE / Chaperonins / Cryoelectron Microscopy / Closed conformation
Function / homology
Function and homology information


positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / zona pellucida receptor complex / tubulin complex assembly / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC / Folding of actin by CCT/TriC ...positive regulation of establishment of protein localization to telomere / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / zona pellucida receptor complex / tubulin complex assembly / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / BBSome-mediated cargo-targeting to cilium / Formation of tubulin folding intermediates by CCT/TriC / 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 / RHOBTB2 GTPase cycle / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / beta-tubulin binding / positive regulation of telomere maintenance via telomerase / heterochromatin / protein folding chaperone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / ATP-dependent protein folding chaperone / : / mRNA 3'-UTR binding / response to virus / mRNA 5'-UTR binding / azurophil granule lumen / melanosome / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / protein folding / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cadherin binding / ubiquitin protein ligase binding / centrosome / Neutrophil degranulation / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 / : / : ...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 / ALUMINUM FLUORIDE / 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: 2.71 Å
AuthorsGutierrez-Seijo, J. / Cuervo, A. / Cuellar, J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-137175NB-I00 Spain
CitationJournal: Methods Mol Biol / Year: 2026
Title: CryoEM Strategies for Elucidating the Closed State Architecture of CCT.
Authors: Jorge Gutiérrez-Seijo / Ana Cuervo / Sergio Pipaón / David Gil-Cantero / Carmen Majano / César Santiago / José María Valpuesta / Jorge Cuéllar /
Abstract: Cryo-electron microscopy (CryoEM) has emerged as a state-of-the-art technique in structural biology, thanks to advances in sample preparation, high-voltage electron microscopy, direct electron ...Cryo-electron microscopy (CryoEM) has emerged as a state-of-the-art technique in structural biology, thanks to advances in sample preparation, high-voltage electron microscopy, direct electron detectors, and sophisticated image processing software. In this study, we investigate the eukaryotic chaperonin CCT, a ~1 MDa hetero-oligomeric complex essential for the folding of key substrates such as actin, tubulin, and WD40 family members. While several open-state structures of CCT have been resolved, the highest-resolution reconstructions have been obtained in the closed state. This is primarily due to the increased structural rigidity of the complex when its apical domains become immobilized in this conformation. However, the pseudo-symmetric arrangement of subunits in the closed state poses challenges for subunit identification. Here, we present a workflow for obtaining a high-resolution CryoEM structure of closed CCT, achieved without the use of nanobodies, substrates, or any tools designed to increase CCT asymmetry. Our results demonstrate that subunit assignment and atomic modeling are achievable by exploiting subunit-intrinsic structural features alone.
History
DepositionAug 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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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
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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)955,74164
Polymers947,17316
Non-polymers8,56848
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

#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 natural source / Source: (natural) 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P78371
#3: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P49368
#4: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50991
#5: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P48643
#6: 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P40227
#7: 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 natural source / Source: (natural) Homo sapiens (human) / 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: 59691.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P50990

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Non-polymers , 4 types, 73 molecules

#9: 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
#10: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 83.977 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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 in closed state / Type: COMPLEX / Entity ID: #1-#8 / Source: NATURAL
Molecular weightValue: 0.947 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK 293
Buffer solutionpH: 7.4
SpecimenConc.: 0.7 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 28.79 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2

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Processing

EM software
IDNameVersionCategory
1Xmipp3particle selection
2EPU3.9.1image acquisition
4Gctf3CTF correction
7Coot1.1.14model fitting
9cryoSPARC4initial Euler assignment
10RELION5initial Euler assignment
11cryoSPARC4final Euler assignment
12RELION5classification
13cryoSPARC43D reconstruction
14DeepEMhancer0.173D reconstruction
15PHENIX1.20.1_4487:model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3095579
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.71 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 105562 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00465008
ELECTRON MICROSCOPYf_angle_d0.83887704
ELECTRON MICROSCOPYf_dihedral_angle_d5.0638925
ELECTRON MICROSCOPYf_chiral_restr0.04910507
ELECTRON MICROSCOPYf_plane_restr0.00711260

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