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- PDB-8i1u: Human TRiC-PhLP2A complex in the closed state -

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Basic information

Entry
Database: PDB / ID: 8i1u
TitleHuman TRiC-PhLP2A complex in the closed state
Components
  • (T-complex protein 1 subunit ...) x 8
  • Phosducin-like protein 3
KeywordsCHAPERONE / chaperonin complex / cochaperone
Function / homology
Function and homology information


negative regulation of chaperone-mediated protein folding / perinucleolar compartment / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex ...negative regulation of chaperone-mediated protein folding / perinucleolar compartment / zona pellucida receptor complex / scaRNA localization to Cajal body / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / Formation of tubulin folding intermediates by CCT/TriC / vascular endothelial growth factor receptor 2 binding / binding of sperm to zona pellucida / Prefoldin mediated transfer of substrate to CCT/TriC / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / beta-tubulin binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / heterochromatin / RHOBTB2 GTPase cycle / chaperone-mediated protein folding / protein folding chaperone / regulation of peptidyl-tyrosine phosphorylation / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of endothelial cell proliferation / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / response to virus / mRNA 5'-UTR binding / cilium / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / positive regulation of angiogenesis / azurophil granule lumen / melanosome / unfolded protein binding / protein folding / cell body / actin cytoskeleton organization / angiogenesis / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / protein stabilization / cytoskeleton / cadherin binding / centrosome / apoptotic process / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Thioredoxin-like superfamily
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 / Phosducin-like protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsRoh, S.H. / Park, J. / Kim, H. / Lim, S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Human TRiC-PhLP2A complex in the closed state
Authors: Roh, S.H. / Park, J. / Lim, S. / Kim, H.
History
DepositionJan 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
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
Q: Phosducin-like protein 3
R: Phosducin-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,011,04266
Polymers1,002,47418
Non-polymers8,56848
Water0
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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T-complex protein 1 subunit ... , 8 types, 16 molecules AIBJCKDLEMFNGOHP

#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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TCP1, CCT1, CCTA / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT2, 99D8.1, CCTB / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT3, CCTG, TRIC5 / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT4, CCTD, SRB / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT5, CCTE, KIAA0098 / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT6A, CCT6, CCTZ / Production host: Trichoplusia ni (cabbage looper) / 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT7, CCTH, NIP7-1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q99832
#8: Protein T-complex protein 1 subunit theta / TCP-1-theta / CCT-theta / Chaperonin containing T-complex polypeptide 1 subunit 8


Mass: 59691.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCT8, C21orf112, CCTQ / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P50990

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Protein , 1 types, 2 molecules QR

#9: Protein Phosducin-like protein 3 / HTPHLP / PhPL3 / Viral IAP-associated factor 1 / VIAF-1


Mass: 27650.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCL3, PhLP2A, VIAF1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2J4

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Non-polymers , 3 types, 48 molecules

#10: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine 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
#11: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 83.977 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION

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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: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of TRiC/CCT-PhLP2A treated with ATP-AlFxCOMPLEX#1-#90RECOMBINANT
2Human TRiC/CCT complexCOMPLEX#1-#81RECOMBINANT
3PhLP2A (PDCL3)COMPLEX#91RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
11Trichoplusia ni (cabbage looper)7111high fivepFastbac-dual
22Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMsodium chlorideNaClSodium chloride1
21 mMDTTC4H10O2S21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / 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: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 1368
Image scansWidth: 4096 / Height: 4096

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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
4cryoSPARC3.2.0CTF correctioncryoSPARC was used for the CTF correction
7UCSF Chimera1.15model fitting
9PHENIX1.19model refinementPhenix was used for refinement
10Coot0.9.6model refinement
11cryoSPARC3.2.0initial Euler assignment
12cryoSPARC3.2.0final Euler assignment
13cryoSPARC3.2.0classification
14cryoSPARC3.2.03D reconstruction
CTF correctionDetails: CTF correction was performed for every micrographs / Type: NONE
Particle selectionNum. of particles selected: 282298
Details: The initial particle selection after 2D class classification
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21028 / Algorithm: FOURIER SPACE / 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_d0.00368425
ELECTRON MICROSCOPYf_angle_d0.61592396
ELECTRON MICROSCOPYf_dihedral_angle_d5.8599484
ELECTRON MICROSCOPYf_chiral_restr0.04410998
ELECTRON MICROSCOPYf_plane_restr0.00411789

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