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- PDB-7nvn: Human TRiC complex in closed state with nanobody and tubulin bound -

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Basic information

Entry
Database: PDB / ID: 7nvn
TitleHuman TRiC complex in closed state with nanobody and tubulin bound
Components
  • (T-complex protein 1 subunit ...) x 8
  • Nanobody
  • Tubulin beta-2A chain
KeywordsCHAPERONE / TRiC / CCT / ATP hydrolysis / type II chaperonin / protein folding / tubulin
Function / homology
Function and homology information


Post-chaperonin tubulin folding pathway / positive regulation of establishment of protein localization to telomere / zona pellucida receptor complex / Cilium Assembly / positive regulation of protein localization to Cajal body / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly ...Post-chaperonin tubulin folding pathway / positive regulation of establishment of protein localization to telomere / zona pellucida receptor complex / Cilium Assembly / positive regulation of protein localization to Cajal body / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Carboxyterminal post-translational modifications of tubulin / scaRNA localization to Cajal body / positive regulation of telomerase RNA localization to Cajal body / tubulin complex assembly / chaperonin-containing T-complex / : / Intraflagellar transport / BBSome-mediated cargo-targeting to cilium / Sealing of the nuclear envelope (NE) by ESCRT-III / Formation of tubulin folding intermediates by CCT/TriC / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Assembly and cell surface presentation of NMDA receptors / RHOBTB1 GTPase cycle / WD40-repeat domain binding / COPI-dependent Golgi-to-ER retrograde traffic / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / Recycling pathway of L1 / RHO GTPases activate IQGAPs / chaperone-mediated protein complex assembly / heterochromatin / RHOBTB2 GTPase cycle / intercellular bridge / Hedgehog 'off' state / Activation of AMPK downstream of NMDARs / COPI-mediated anterograde transport / : / positive regulation of telomere maintenance via telomerase / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / protein folding chaperone / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / ATP-dependent protein folding chaperone / PKR-mediated signaling / cerebral cortex development / response to virus / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mRNA 5'-UTR binding / HCMV Early Events / neuron migration / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / unfolded protein binding / melanosome / G-protein beta-subunit binding / protein folding / extracellular vesicle / mitotic cell cycle / microtubule cytoskeleton / cell body / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / cytoskeleton / protein stabilization / cilium / cadherin binding / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / Golgi apparatus / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytosol / cytoplasm
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) / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
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 / Tubulin beta-2A chain / T-complex protein 1 subunit eta
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsKelly, J.J. / Chi, G. / Bulawa, C. / Paavilainen, V.O. / Bountra, C. / Huiskonen, J.T. / Yue, W.
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Snapshots of actin and tubulin folding inside the TRiC chaperonin.
Authors: John J Kelly / Dale Tranter / Els Pardon / Gamma Chi / Holger Kramer / Lotta Happonen / Kelly M Knee / Jay M Janz / Jan Steyaert / Christine Bulawa / Ville O Paavilainen / Juha T Huiskonen / Wyatt W Yue /
Abstract: The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, ...The integrity of a cell's proteome depends on correct folding of polypeptides by chaperonins. The chaperonin TCP-1 ring complex (TRiC) acts as obligate folder for >10% of cytosolic proteins, including he cytoskeletal proteins actin and tubulin. Although its architecture and how it recognizes folding substrates are emerging from structural studies, the subsequent fate of substrates inside the TRiC chamber is not defined. We trapped endogenous human TRiC with substrates (actin, tubulin) and cochaperone (PhLP2A) at different folding stages, for structure determination by cryo-EM. The already-folded regions of client proteins are anchored at the chamber wall, positioning unstructured regions toward the central space to achieve their native fold. Substrates engage with different sections of the chamber during the folding cycle, coupled to TRiC open-and-close transitions. Further, the cochaperone PhLP2A modulates folding, acting as a molecular strut between substrate and TRiC chamber. Our structural snapshots piece together an emerging model of client protein folding within TRiC.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 11, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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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
N: Nanobody
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: Nanobody
q: T-complex protein 1 subunit theta
z: T-complex protein 1 subunit zeta
T: Tubulin beta-2A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,034,48867
Polymers1,025,92119
Non-polymers8,56848
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area152260 Å2
ΔGint-772 kcal/mol
Surface area285260 Å2
MethodPISA

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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: 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 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
#4: 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: Homo sapiens (human) / References: UniProt: P48643
#5: 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
#6: 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
#9: 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

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Antibody / Protein , 2 types, 3 molecules NnT

#10: Protein Tubulin beta-2A chain / Tubulin beta class IIa


Mass: 49921.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13885
#7: Antibody Nanobody


Mass: 14412.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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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
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

Component
IDNameTypeEntity IDParent-IDSource
1Human type II chaperonin TRiC/CCT complex with nanobody Nb18 and tubulin boundCOMPLEX#1-#100MULTIPLE SOURCES
2Human type II chaperonin TRiC/CCT complexCOMPLEX#1-#3, #5-#6, #8-#101NATURAL
3NanobodyCOMPLEX#71RECOMBINANT
4T-complex protein 1 subunit epsilonCOMPLEX#41RECOMBINANT
Molecular weight
IDEntity assembly-IDUnitsExperimental value
11MEGADALTONSNO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Lama glama (llama)9844
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Homo sapiens (human)9606
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93758 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 73.26 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003669953
ELECTRON MICROSCOPYf_angle_d0.609794470
ELECTRON MICROSCOPYf_chiral_restr0.042811206
ELECTRON MICROSCOPYf_plane_restr0.003912067
ELECTRON MICROSCOPYf_dihedral_angle_d23.686726443

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