[English] 日本語
Yorodumi
- EMDB-0495: hTRiC-hPFD Class4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0495
TitlehTRiC-hPFD Class4
Map datahTRiC-hPFD Class4
Sample
  • Complex: hTRiC-hPFD
    • Complex: hTRiC
      • Protein or peptide: x 8 types
    • Complex: hPFD
      • Protein or peptide: x 6 types
KeywordsTRiC/CCT / PFD / CryoEM / Molecular Chaperone / Protein folding / CHAPERONE
Function / homology
Function and homology information


RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / 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 / RNA polymerase II core complex assembly ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / 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 / RNA polymerase II core complex assembly / tubulin complex assembly / chaperonin-containing T-complex / RPAP3/R2TP/prefoldin-like 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 / Prefoldin mediated transfer of substrate to CCT/TriC / negative regulation of amyloid fibril formation / protein folding chaperone complex / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / : / microtubule-based process / 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 / tubulin binding / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / negative regulation of canonical Wnt signaling pathway / cilium / mRNA 5'-UTR binding / transcription corepressor activity / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / azurophil granule lumen / G-protein beta-subunit binding / unfolded protein binding / melanosome / protein folding / retina development in camera-type eye / amyloid-beta binding / protein-folding chaperone binding / cell body / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cadherin binding / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / regulation of DNA-templated transcription / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / T-complex protein 1, alpha subunit ...Prefoldin subunit 3 / Prefoldin, subunit 4 / Prefoldin subunit 2 / Prefoldin beta-like / Prefoldin alpha-like / Prefoldin alpha subunit, archaea-type / Prefoldin subunit / Prefoldin subunit / Prefoldin / 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
Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 / T-complex protein 1 subunit beta ...Prefoldin subunit 6 / Prefoldin subunit 1 / 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 / Prefoldin subunit 3 / T-complex protein 1 subunit beta / Prefoldin subunit 5 / T-complex protein 1 subunit eta / Prefoldin subunit 4 / Prefoldin subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsGestaut DR / Roh SH
Funding support United States, European Union, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM074074 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)F32GM103124 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM103832 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM079429 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P01NS092525 United States
European Research Council (ERC)AdvG #233226European Union
European Research Council (ERC)AdvG #670821European Union
CitationJournal: Cell / Year: 2019
Title: The Chaperonin TRiC/CCT Associates with Prefoldin through a Conserved Electrostatic Interface Essential for Cellular Proteostasis.
Authors: Daniel Gestaut / Soung Hun Roh / Boxue Ma / Grigore Pintilie / Lukasz A Joachimiak / Alexander Leitner / Thomas Walzthoeni / Ruedi Aebersold / Wah Chiu / Judith Frydman /
Abstract: Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the ...Maintaining proteostasis in eukaryotic protein folding involves cooperation of distinct chaperone systems. To understand how the essential ring-shaped chaperonin TRiC/CCT cooperates with the chaperone prefoldin/GIMc (PFD), we integrate cryoelectron microscopy (cryo-EM), crosslinking-mass-spectrometry and biochemical and cellular approaches to elucidate the structural and functional interplay between TRiC/CCT and PFD. We find these hetero-oligomeric chaperones associate in a defined architecture, through a conserved interface of electrostatic contacts that serves as a pivot point for a TRiC-PFD conformational cycle. PFD alternates between an open "latched" conformation and a closed "engaged" conformation that aligns the PFD-TRiC substrate binding chambers. PFD can act after TRiC bound its substrates to enhance the rate and yield of the folding reaction, suppressing non-productive reaction cycles. Disrupting the TRiC-PFD interaction in vivo is strongly deleterious, leading to accumulation of amyloid aggregates. The supra-chaperone assembly formed by PFD and TRiC is essential to prevent toxic conformations and ensure effective cellular proteostasis.
History
DepositionJan 23, 2019-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6nrd
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0495.png

Downloads & links

-
Map

FileDownload / File: emd_0495.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhTRiC-hPFD Class4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 240 pix.
= 408. Å		1.7 Å/pix.
x 240 pix.
= 408. Å		1.7 Å/pix.
x 240 pix.
= 408. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum-1.1301266 - 2.3742108
Average (Standard dev.)0.000000000046929 (±0.14745198)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 408.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.71.71.7
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z408.000408.000408.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-1.1302.3740.000

-
Supplemental data

-
Additional map: hTRiC-hPFD Class4, unfiltered sum map

Fileemd_0495_additional.map
AnnotationhTRiC-hPFD Class4, unfiltered sum map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: hTRiC-hPFD Class4, half map 1

Fileemd_0495_half_map_1.map
AnnotationhTRiC-hPFD Class4, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: hTRiC-hPFD Class4, half map 2

Fileemd_0495_half_map_2.map
AnnotationhTRiC-hPFD Class4, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : hTRiC-hPFD

EntireName: hTRiC-hPFD
Components
  • Complex: hTRiC-hPFD
    • Complex: hTRiC
      • Protein or peptide: T-complex protein 1 subunit alpha
      • Protein or peptide: T-complex protein 1 subunit beta
      • Protein or peptide: T-complex protein 1 subunit gamma
      • Protein or peptide: T-complex protein 1 subunit delta
      • Protein or peptide: T-complex protein 1 subunit epsilon
      • Protein or peptide: T-complex protein 1 subunit zeta
      • Protein or peptide: T-complex protein 1 subunit eta
      • Protein or peptide: T-complex protein 1 subunit theta
    • Complex: hPFD
      • Protein or peptide: Prefoldin subunit 1
      • Protein or peptide: Prefoldin subunit 2
      • Protein or peptide: Prefoldin subunit 3
      • Protein or peptide: Prefoldin subunit 4
      • Protein or peptide: Prefoldin subunit 5
      • Protein or peptide: Prefoldin subunit 6

+
Supramolecule #1: hTRiC-hPFD

SupramoleculeName: hTRiC-hPFD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #2: hTRiC

SupramoleculeName: hTRiC / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: hPFD

SupramoleculeName: hPFD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #9-#14
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: T-complex protein 1 subunit alpha

MacromoleculeName: T-complex protein 1 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.061055 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEHP AAKVLCELAD LQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS GYRLACKEAV RYINENLIVN TDELGRDCLI NAAKTSMSSK I IGINGDFF ...String:
MEGPLSVFGD RSTGETIRSQ NVMAAASIAN IVKSSLGPVG LDKMLVDDIG DVTITNDGAT ILKLLEVEHP AAKVLCELAD LQDKEVGDG TTSVVIIAAE LLKNADELVK QKIHPTSVIS GYRLACKEAV RYINENLIVN TDELGRDCLI NAAKTSMSSK I IGINGDFF ANMVVDAVLA IKYTDIRGQP RYPVNSVNIL KAHGRSQMES MLISGYALNC VVGSQGMPKR IVNAKIACLD FS LQKTKMK LGVQVVITDP EKLDQIRQRE SDITKERIQK ILATGANVIL TTGGIDDMCL KYFVEAGAMA VRRVLKRDLK RIA KASGAT ILSTLANLEG EETFEAAMLG QAEEVVQERI CDDELILIKN TKARTSASII LRGANDFMCD EMERSLHDAL CVVK RVLES KSVVPGGGAV EAALSIYLEN YATSMGSREQ LAIAEFARSL LVIPNTLAVN AAQDSTDLVA KLRAFHNEAQ VNPER KNLK WIGLDLSNGK PRDNKQAGVF EPTIVKVKSL KFATEAAITI LRIDDLIKLH

UniProtKB: T-complex protein 1 subunit alpha

+
Macromolecule #2: T-complex protein 1 subunit beta

MacromoleculeName: T-complex protein 1 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.736742 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: ADEERAETAR LTSFIGAIAI GDLVKSTLGP KGMDKILLSS GRDASLMVTN DGATILKNIG VDNPAAKVLV DMSRVQDDEV GDGTTSVTV LAAELLREAE SLIAKKIHPQ TIIAGWREAT KAAREALLSS AVDHGSDEVK FRQDLMNIAG TTLSSKLLTH H KDHFTKLA ...String:
ADEERAETAR LTSFIGAIAI GDLVKSTLGP KGMDKILLSS GRDASLMVTN DGATILKNIG VDNPAAKVLV DMSRVQDDEV GDGTTSVTV LAAELLREAE SLIAKKIHPQ TIIAGWREAT KAAREALLSS AVDHGSDEVK FRQDLMNIAG TTLSSKLLTH H KDHFTKLA VEAVLRLKGS GNLEAIHIIK KLGGSLADSY LDEGFLLDKK IGVNQPKRIE NAKILIANTG MDTDKIKIFG SR VRVDSTA KVAEIEHAEK EKMKEKVERI LKHGINCFIN RQLIYNYPEQ LFGAAGVMAI EHADFAGVER LALVTGGEIA STF DHPELV KLGSCKLIEE VMIGEDKLIH FSGVALGEAC TIVLRGATQQ ILDEAERSLH DALCVLAQTV KDSRTVYGGG CSEM LMAHA VTQLANRTPG KEAVAMESYA KALRMLPTII ADNAGYDSAD LVAQLRAAHS EGNTTAGLDM REGTIGDMAI LGITE SFQV KRQVLLSAAE AAEVILRVDN IIKAA

UniProtKB: T-complex protein 1 subunit beta

+
Macromolecule #3: T-complex protein 1 subunit gamma

MacromoleculeName: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.165945 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: NTKRESGRKV QSGNINAAKT IADIIRTCLG PKSMMKMLLD PMGGIVMTND GNAILREIQV QHPAAKSMIE ISRTQDEEVG DGTTSVIIL AGEMLSVAEH FLEQQMHPTV VISAYRKALD DMISTLKKIS IPVDISDSDM MLNIINSSIT TKAISRWSSL A CNIALDAV ...String:
NTKRESGRKV QSGNINAAKT IADIIRTCLG PKSMMKMLLD PMGGIVMTND GNAILREIQV QHPAAKSMIE ISRTQDEEVG DGTTSVIIL AGEMLSVAEH FLEQQMHPTV VISAYRKALD DMISTLKKIS IPVDISDSDM MLNIINSSIT TKAISRWSSL A CNIALDAV KMVQFEENGR KEIDIKKYAR VEKIPGGIIE DSCVLRGVMI NKDVTHPRMR RYIKNPRIVL LDSSLEYKKG ES QTDIEIT REEDFTRILQ MEEEYIQQLC EDIIQLKPDV VITEKGISDL AQHYLMRANI TAIRRVRKTD NNRIARACGA RIV SRPEEL REDDVGTGAG LLEIKKIGDE YFTFITDCKD PKACTILLRG ASKEILSEVE RNLQDAMQVC RNVLLDPQLV PGGG ASEMA VAHALTEKSK AMTGVEQWPY RAVAQALEVI PRTLIQNCGA STIRLLTSLR AKHTQENCET WGVNGETGTL VDMKE LGIW EPLAVKLQTY KTAVETAVLL LRIDDIVSG

UniProtKB: T-complex protein 1 subunit gamma

+
Macromolecule #4: T-complex protein 1 subunit delta

MacromoleculeName: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.6365 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: DRDKPAQIRF SNISAAKAVA DAIRTSLGPK GMDKMIQDGK GDVTITNDGA TILKQMQVLH PAARMLVELS KAQDIEAGDG TTSVVIIAG SLLDSCTKLL QKGIHPTIIS ESFQKALEKG IEILTDMSRP VELSDRETLL NSATTSLNSK VVSQYSSLLS P MSVNAVMK ...String:
DRDKPAQIRF SNISAAKAVA DAIRTSLGPK GMDKMIQDGK GDVTITNDGA TILKQMQVLH PAARMLVELS KAQDIEAGDG TTSVVIIAG SLLDSCTKLL QKGIHPTIIS ESFQKALEKG IEILTDMSRP VELSDRETLL NSATTSLNSK VVSQYSSLLS P MSVNAVMK VIDPATATSV DLRDIKIVKK LGGTIDDCEL VEGLVLTQKV SNSGITRVEK AKIGLIQFCL SAPKTDMDNQ IV VSDYAQM DRVLREERAY ILNLVKQIKK TGCNVLLIQK SILRDALSDL ALHFLNKMKI MVIKDIERED IEFICKTIGT KPV AHIDQF TADMLGSAEL AEEVNLNGSG KLLKITGCAS PGKTVTIVVR GSNKLVIEEA ERSIHDALCV IRCLVKKRAL IAGG GAPEI ELALRLTEYS RTLSGMESYC VRAFADAMEV IPSTLAENAG LNPISTVTEL RNRHAQGEKT AGINVRKGGI SNILE ELVV QPLLVSVSAL TLATETVRSI LKIDDVVNTR

UniProtKB: T-complex protein 1 subunit delta

+
Macromolecule #5: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.989797 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: KSRLMGLEAL KSHIMAAKAV ANTMRTSLGP NGLDKMMVDK DGDVTVTNDG ATILSMMDVD HQIAKLMVEL SKSQDDEIGD GTTGVVVLA GALLEEAEQL LDRGIHPIRI ADGYEQAARV AIEHLDKISD SVLVDIKDTE PLIQTAKTTL GSKVVNSCHR Q MAEIAVNA ...String:
KSRLMGLEAL KSHIMAAKAV ANTMRTSLGP NGLDKMMVDK DGDVTVTNDG ATILSMMDVD HQIAKLMVEL SKSQDDEIGD GTTGVVVLA GALLEEAEQL LDRGIHPIRI ADGYEQAARV AIEHLDKISD SVLVDIKDTE PLIQTAKTTL GSKVVNSCHR Q MAEIAVNA VLTVADMERR DVDFELIKVE GKVGGRLEDT KLIKGVIVDK DFSHPQMPKK VEDAKIAILT CPFEPPKPKT KH KLDVTSV EDYKALQKYE KEKFEEMIQQ IKETGANLAI CQWGFDDEAN HLLLQNNLPA VRWVGGPEIE LIAIATGGRI VPR FSELTA EKLGFAGLVQ EISFGTTKDK MLVIEQCKNS RAVTIFIRGG NKMIIEEAKR SLHDALCVIR NLIRDNRVVY GGGA AEISC ALAVSQEADK CPTLEQYAMR AFADALEVIP MALSENSGMN PIQTMTEVRA RQVKEMNPAL GIDCLHKGTN DMKQQ HVIE TLIGKKQQIS LATQMVRMIL KIDDIRKPGE SEE

UniProtKB: T-complex protein 1 subunit epsilon

+
Macromolecule #6: T-complex protein 1 subunit zeta

MacromoleculeName: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.445008 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITGD GTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK VHAELADVLT E AVVDSILA ...String:
AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITGD GTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK VHAELADVLT E AVVDSILA IKKQDEPIDL FMIEIMEMKH KSETDTSLIR GLVLDHGARH PDMKKRVEDA YILTCNVSLE YEKTEVNSGF FY KSAEERE KLVKAERKFI EDRVKKIIEL KRKVCGDSDK GFVVINQKGI DPFSLDALSK EGIVALRRAK RRNMERLTLA CGG VALNSF DDLSPDCLGH AGLVYEYTLG EEKFTFIEKC NNPRSVTLLI KGPNKHTLTQ IKDAVRDGLR AVKNAIDDGC VVPG AGAVE VAMAEALIKH KPSVKGRAQL GVQAFADALL IIPKVLAQNS GFDLQETLVK IQAEHSESGQ LVGVDLNTGE PMVAA EVGV WDNYCVKKQL LHSCTVIATN ILLVDEIMRA G

UniProtKB: T-complex protein 1 subunit zeta

+
Macromolecule #7: T-complex protein 1 subunit eta

MacromoleculeName: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.369867 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: GTDSSQGIPQ LVSNISACQV IAEAVRTTLG PRGMDKLIVD GRGKATISND GATILKLLDV VHPAAKTLVD IAKSQDAEVG DGTTSVTLL AAEFLKQVKP YVEEGLHPQI IIRAFRTATQ LAVNKIKEIA VTVKKADKVE QRKLLEKCAM TALSSKLISQ Q KAFFAKMV ...String:
GTDSSQGIPQ LVSNISACQV IAEAVRTTLG PRGMDKLIVD GRGKATISND GATILKLLDV VHPAAKTLVD IAKSQDAEVG DGTTSVTLL AAEFLKQVKP YVEEGLHPQI IIRAFRTATQ LAVNKIKEIA VTVKKADKVE QRKLLEKCAM TALSSKLISQ Q KAFFAKMV VDAVMMLDDL LQLKMIGIKK VQGGALEDSQ LVAGVAFKKT FSYAGFEMQP KKYHNPKIAL LNVELELKAE KD NAEIRVH TVEDYQAIVD AEWNILYDKL EKIHHSGAKV VLSKLPIGDV ATQYFADRDM FCAGRVPEED LKRTMMACGG SIQ TSVNAL SADVLGRCQV FEETQIGGER YNFFTGCPKA KTCTFILRGG AEQFMEETER SLHDAIMIVR RAIKNDSVVA GGGA IEMEL SKYLRDYSRT IPGKQQLLIG AYAKALEIIP RQLCDNAGFD ATNILNKLRA RHAQGGTWYG VDINNEDIAD NFEAF VWEP AMVRINALTA ASEAACLIVS VDETIKNPRS

UniProtKB: T-complex protein 1 subunit eta

+
Macromolecule #8: T-complex protein 1 subunit theta

MacromoleculeName: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.102406 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MLKEGAKHFS GLEEAVYRNI QACKELAQTT RTAYGPNGMN KMVINHLEKL FVTNDAATIL RELEVQHPAA KMIVMASHMQ EQEVGDGTN FVLVFAGALL ELAEELLRIG LSVSEVIEGY EIACRKAHEI LPNLVCCSAK NLRDIDEVSS LLRTSIMSKQ Y GNEVFLAK ...String:
MLKEGAKHFS GLEEAVYRNI QACKELAQTT RTAYGPNGMN KMVINHLEKL FVTNDAATIL RELEVQHPAA KMIVMASHMQ EQEVGDGTN FVLVFAGALL ELAEELLRIG LSVSEVIEGY EIACRKAHEI LPNLVCCSAK NLRDIDEVSS LLRTSIMSKQ Y GNEVFLAK LIAQACVSIF PDSGHFNVDN IRVCKILGSG ISSSSVLHGM VFKKETEGDV TSVKDAKIAV YSCPFDGMIT ET KGTVLIK TAEELMNFSK GEENLMDAQV KAIADTGANV VVTGGKVADM ALHYANKYNI MLVRLNSKWD LRRLCKTVGA TAL PRLTPP VLEEMGHCDS VYLSEVGDTQ VVVFKHEKED GAISTIVLRG STDNLMDDIE RAVDDGVNTF KVLTRDKRLV PGGG ATEIE LAKQITSYGE TCPGLEQYAI KKFAEAFEAI PRALAENSGV KANEVISKLY AVHQEGNKNV GLDIEAEVPA VKDML EAGI LDTYLGKYWA IKLATNAAVT VLRVDQIIMA

UniProtKB: T-complex protein 1 subunit theta

+
Macromolecule #9: Prefoldin subunit 1

MacromoleculeName: Prefoldin subunit 1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.522427 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
AFTELQAKVI DTQQKVKLAD IQIEQLNRTK KHAHLTDTEI MTLVDETNMY EGVGRMFILQ SKEAIHSQLL EKQKIAEEKI KELEQKKSY LERSVKEAED NIREMLMA

UniProtKB: Prefoldin subunit 1

+
Macromolecule #10: Prefoldin subunit 2

MacromoleculeName: Prefoldin subunit 2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.862538 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
SAEQVIAGFN RLRQEQRGLA SKAAELEMEL NEHSLVIDTL KEVDETRKCY RMVGGVLVER TVKEVLPALE NNKEQIQKII ETLTQQLQA KGKELNEFRE KHNI

UniProtKB: Prefoldin subunit 2

+
Macromolecule #11: Prefoldin subunit 3

MacromoleculeName: Prefoldin subunit 3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.558005 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
VLKKLDEQYQ KYKFMELNLA QKKRRLKGQI PEIKQTLEIL KYMQKKKEST NSMETRFLLA DNLYCKASVP PTDKMCLWLG ANVMLEYDI DEAQALLEKN LSTATKNLDS LEEDLDFLRD QFTTTEVNMA RVY

UniProtKB: Prefoldin subunit 3

+
Macromolecule #12: Prefoldin subunit 4

MacromoleculeName: Prefoldin subunit 4 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.142691 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
DQQKINKFAR NTSRITELKE EIEVKKKQLQ NLEDACDDIM LADDDCLMIP YQIGDVFISH SQEETQEMLE EAKKNLQEEI DALESRVES IQRVLADLKV QLYAK

UniProtKB: Prefoldin subunit 4

+
Macromolecule #13: Prefoldin subunit 5

MacromoleculeName: Prefoldin subunit 5 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.579903 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
NLPQLEMLKN QLDQEVEFLS TSIAQLKVVQ TKYVEAKDCL NVLNKSNEGK ELLVPLTSSM YVPGKLHDVE HVLIDVGTGY YVEKTAEDA KDFFKRKIDF LTKQMEKIQP ALQEKHAMKQ AVMEMMSQ

UniProtKB: Prefoldin subunit 5

+
Macromolecule #14: Prefoldin subunit 6

MacromoleculeName: Prefoldin subunit 6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.775323 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString:
VEKYQQLQKD LSKSMSGRQK LEAQLTENNI VKEELALLDG SNVVFKLLGP VLVKQELGEA RATVGKRLDY ITAEIKRYES QLRDLERQS EQQRETLAQL QQE

UniProtKB: Prefoldin subunit 6

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9580
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more