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- EMDB-32823: Prefoldin-tubulin-TRiC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-32823
TitlePrefoldin-tubulin-TRiC complex
Map dataA differently local sharpened main map for the refinement
Sample
  • Complex: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex
    • Protein or peptide: x 14 types
  • Ligand: x 1 types
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 / positive regulation of protein localization to Cajal body / tubulin complex assembly / chaperone mediated protein folding independent of cofactor ...RNA polymerase I assembly / RNA polymerase III assembly / prefoldin complex / positive regulation of cytoskeleton organization / : / 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 / RPAP3/R2TP/prefoldin-like complex / RNA polymerase II core complex assembly / BBSome-mediated cargo-targeting to cilium / chaperonin-containing T-complex / Folding of actin by CCT/TriC / binding of sperm to zona pellucida / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / 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 / beta-tubulin binding / pericentriolar material / Association of TriC/CCT with target proteins during biosynthesis / chaperone-mediated protein complex assembly / heterochromatin / RHOBTB2 GTPase cycle / microtubule-based process / chaperone-mediated protein folding / protein folding chaperone / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / tubulin binding / acrosomal vesicle / mRNA 3'-UTR binding / cell projection / ATP-dependent protein folding chaperone / response to virus / negative regulation of canonical Wnt signaling pathway / mRNA 5'-UTR binding / cilium / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / transcription corepressor activity / G-protein beta-subunit binding / azurophil granule lumen / unfolded protein binding / melanosome / protein folding / retina development in camera-type eye / cell body / amyloid-beta binding / protein-folding chaperone binding / secretory granule lumen / microtubule / ficolin-1-rich granule lumen / protein stabilization / cytoskeleton / 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: 3.85 Å
AuthorsGestaut D / Zhao Y / Park J / Ma B / Leitner A / Collier M / Pintilie G / Roh S-H / Chiu W / Frydman J
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Cell / Year: 2022
Title: Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT.
Authors: Daniel Gestaut / Yanyan Zhao / Junsun Park / Boxue Ma / Alexander Leitner / Miranda Collier / Grigore Pintilie / Soung-Hun Roh / Wah Chiu / Judith Frydman /
Abstract: The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of ...The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.
History
DepositionFeb 7, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32823.png

Downloads & links

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Map

FileDownload / File: emd_32823.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA differently local sharpened main map for the refinement
Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.943
Minimum - Maximum-7.622423 - 11.117316
Average (Standard dev.)0.019353984 (±0.24627073)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: A B-factor sharpened map

Fileemd_32823_additional_1.map
AnnotationA B-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map

Fileemd_32823_half_map_1.map
AnnotationA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: A half map

Fileemd_32823_half_map_2.map
AnnotationA half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex

EntireName: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex
Components
  • Complex: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex
    • 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
    • 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
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex

SupramoleculeName: Ternary complex of TRiC/CCT, beta-tubulin, prefoldin complex
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Prefoldin subunit 1

MacromoleculeName: Prefoldin subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.234497 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAAPVDLELK KAFTELQAKV IDTQQKVKLA DIQIEQLNRT KKHAHLTDTE IMTLVDETNM YEGVGRMFIL QSKEAIHSQL LEKQKIAEE KIKELEQKKS YLERSVKEAE DNIREMLMAR RAQ

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Macromolecule #2: Prefoldin subunit 2

MacromoleculeName: Prefoldin subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.67283 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAENSGRAGK SSGSGAGKGA VSAEQVIAGF NRLRQEQRGL ASKAAELEME LNEHSLVIDT LKEVDETRKC YRMVGGVLVE RTVKEVLPA LENNKEQIQK IIETLTQQLQ AKGKELNEFR EKHNIRLMGE DEKPAAKENS EGAGAKASSA GVLVS

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Macromolecule #3: Prefoldin subunit 3

MacromoleculeName: Prefoldin subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.65893 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAVKDSCGK GEMATGNGRR LHLGIPEAVF VEDVDSFMKQ PGNETADTVL KKLDEQYQKY KFMELNLAQK KRRLKGQIPE IKQTLEILK YMQKKKESTN SMETRFLLAD NLYCKASVPP TDKVCLWLGA NVMLEYDIDE AQALLEKNLS TATKNLDSLE E DLDFLRDQ ...String:
MAAVKDSCGK GEMATGNGRR LHLGIPEAVF VEDVDSFMKQ PGNETADTVL KKLDEQYQKY KFMELNLAQK KRRLKGQIPE IKQTLEILK YMQKKKESTN SMETRFLLAD NLYCKASVPP TDKVCLWLGA NVMLEYDIDE AQALLEKNLS TATKNLDSLE E DLDFLRDQ FTTTEVNMAR VYNWDVKRRN KDDSTKNKA

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Macromolecule #4: Prefoldin subunit 4

MacromoleculeName: Prefoldin subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.160071 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAATMKKAAA EDVNVTFEDQ QKINKFARNT SRITELKEEI EVKKKQLQNL EDACDDIMLA DDDCLMIPYQ IGDVFISHSQ EETQEMLEE AKKNLQEEID ALESRVESIQ RVLADLKVQL YAKFGSNINL EADESHHHHH H

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Macromolecule #5: Prefoldin subunit 5

MacromoleculeName: Prefoldin subunit 5 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.051647 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAQSINITEL NLPQLEMLKN QLDQEVEFLS TSIAQLKVVQ TKYVEAKDCL NVLNKSNEGK ELLVPLTSSM YVPGKLHDVE HVLIDVGTG YYVEKTAEDA KDFFKRKIDF LTKQMEKIQP ALQEKHAMKQ AVMEMMSQKI Q

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Macromolecule #6: Prefoldin subunit 6

MacromoleculeName: Prefoldin subunit 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.603641 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MAELIQKKLQ GEVEKYQQLQ KDLSKSMSGR QKLEAQLTEN NIVKEELALL DGSNVVFKLL GPVLVKQELG EARATVGKRL DYITAEIKR YESQLRDLER QSEQQRETLA QLQQEFQRAQ AAKAGAPGKA

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Macromolecule #7: T-complex protein 1 subunit alpha

MacromoleculeName: T-complex protein 1 subunit alpha / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.418477 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 PESKDDKHGS YEDAVHSGAL ND

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Macromolecule #8: T-complex protein 1 subunit beta

MacromoleculeName: T-complex protein 1 subunit beta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.567141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGATI LKNIGVDNPA AKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK KIHPQTIIAG WREATKAARE ALLSSAVDHG SDEVKFRQDL M NIAGTTLS ...String:
MASLSLAPVN IFKAGADEER AETARLTSFI GAIAIGDLVK STLGPKGMDK ILLSSGRDAS LMVTNDGATI LKNIGVDNPA AKVLVDMSR VQDDEVGDGT TSVTVLAAEL LREAESLIAK KIHPQTIIAG WREATKAARE ALLSSAVDHG SDEVKFRQDL M NIAGTTLS SKLLTHHKDH FTKLAVEAVL RLKGSGNLEA IHIIKKLGGS LADSYLDEGF LLDKKIGVNQ PKRIENAKIL IA NTGMDTD KIKIFGSRVR VDSTAKVAEI EHAEKEKMKE KVERILKHGI NCFINRQLIY NYPEQLFGAA GVMAIEHADF AGV ERLALV TGGEIASTFD HPELVKLGSC KLIEEVMIGE DKLIHFSGVA LGEACTIVLR GATQQILDEA ERSLHDALCV LAQT VKDSR TVYGGGCSEM LMAHAVTQLA NRTPGKEAVA MESYAKALRM LPTIIADNAG YDSADLVAQL RAAHSEGNTT AGLDM REGT IGDMAILGIT ESFQVKRQVL LSAAEAAEVI LRVDNIIKAA PRKRVPDHHP C

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Macromolecule #9: T-complex protein 1 subunit gamma

MacromoleculeName: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.613855 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILREI QVQHPAAKSM IEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP TVVISAYRKA LDDMISTLKK ISIPVDISDS DMMLNIINSS I TTKAISRW ...String:
MMGHRPVLVL SQNTKRESGR KVQSGNINAA KTIADIIRTC LGPKSMMKML LDPMGGIVMT NDGNAILREI QVQHPAAKSM IEISRTQDE EVGDGTTSVI ILAGEMLSVA EHFLEQQMHP TVVISAYRKA LDDMISTLKK ISIPVDISDS DMMLNIINSS I TTKAISRW SSLACNIALD AVKMVQFEEN GRKEIDIKKY ARVEKIPGGI IEDSCVLRGV MINKDVTHPR MRRYIKNPRI VL LDSSLEY KKGESQTDIE ITREEDFTRI LQMEEEYIQQ LCEDIIQLKP DVVITEKGIS DLAQHYLMRA NITAIRRVRK TDN NRIARA CGARIVSRPE ELREDDVGTG AGLLEIKKIG DEYFTFITDC KDPKACTILL RGASKEILSE VERNLQDAMQ VCRN VLLDP QLVPGGGASE MAVAHALTEK SKAMTGVEQW PYRAVAQALE VIPRTLIQNC GASTIRLLTS LRAKHTQENC ETWGV NGET GTLVDMKELG IWEPLAVKLQ TYKTAVETAV LLLRIDDIVS GHKKKGDDQS RQGGAPDAGQ E

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Macromolecule #10: T-complex protein 1 subunit delta

MacromoleculeName: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.996113 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVTI TNDGATILKQ MQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS CTKLLQKGIH PTIISESFQK ALEKGIEILT DMSRPVELSD R ETLLNSAT ...String:
MPENVAPRSG ATAGAAGGRG KGAYQDRDKP AQIRFSNISA AKAVADAIRT SLGPKGMDKM IQDGKGDVTI TNDGATILKQ MQVLHPAAR MLVELSKAQD IEAGDGTTSV VIIAGSLLDS CTKLLQKGIH PTIISESFQK ALEKGIEILT DMSRPVELSD R ETLLNSAT TSLNSKVVSQ YSSLLSPMSV NAVMKVIDPA TATSVDLRDI KIVKKLGGTI DDCELVEGLV LTQKVSNSGI TR VEKAKIG LIQFCLSAPK TDMDNQIVVS DYAQMDRVLR EERAYILNLV KQIKKTGCNV LLIQKSILRD ALSDLALHFL NKM KIMVIK DIEREDIEFI CKTIGTKPVA HIDQFTADML GSAELAEEVN LNGSGKLLKI TGCASPGKTV TIVVRGSNKL VIEE AERSI HDALCVIRCL VKKRALIAGG GAPEIELALR LTEYSRTLSG MESYCVRAFA DAMEVIPSTL AENAGLNPIS TVTEL RNRH AQGEKTAGIN VRKGGISNIL EELVVQPLLV SVSALTLATE TVRSILKIDD VVNTR

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Macromolecule #11: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.749957 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVTV TNDGATILSM MDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE AEQLLDRGIH PIRIADGYEQ AARVAIEHLD KISDSVLVDI K DTEPLIQT ...String:
MASMGTLAFD EYGRPFLIIK DQDRKSRLMG LEALKSHIMA AKAVANTMRT SLGPNGLDKM MVDKDGDVTV TNDGATILSM MDVDHQIAK LMVELSKSQD DEIGDGTTGV VVLAGALLEE AEQLLDRGIH PIRIADGYEQ AARVAIEHLD KISDSVLVDI K DTEPLIQT AKTTLGSKVV NSCHRQMAEI AVNAVLTVAD MERRDVDFEL IKVEGKVGGR LEDTKLIKGV IVDKDFSHPQ MP KKVEDAK IAILTCPFEP PKPKTKHKLD VTSVEDYKAL QKYEKEKFEE MIQQIKETGA NLAICQWGFD DEANHLLLQN NLP AVRWVG GPEIELIAIA TGGRIVPRFS ELTAEKLGFA GLVQEISFGT TKDKMLVIEQ CKNSRAVTIF IRGGNKMIIE EAKR SLHDA LCVIRNLIRD NRVVYGGGAA EISCALAVSQ EADKCPTLEQ YAMRAFADAL EVIPMALSEN SGMNPIQTMT EVRAR QVKE MNPALGIDCL HKGTNDMKQQ HVIETLIGKK QQISLATQMV RMILKIDDIR KPGESEE

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Macromolecule #12: T-complex protein 1 subunit zeta

MacromoleculeName: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.16618 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK V HAELADVL ...String:
MAAVKTLNPK AEVARAQAAL AVNISAARGL QDVLRTNLGP KGTMKMLVSG AGDIKLTKDG NVLLHEMQIQ HPTASLIAKV ATAQDDITG DGTTSNVLII GELLKQADLY ISEGLHPRII TEGFEAAKEK ALQFLEEVKV SREMDRETLI DVARTSLRTK V HAELADVL TEAVVDSILA IKKQDEPIDL FMIEIMEMKH KSETDTSLIR GLVLDHGARH PDMKKRVEDA YILTCNVSLE YE KTEVNSG FFYKSAEERE KLVKAERKFI EDRVKKIIEL KRKVCGDSDK GFVVINQKGI DPFSLDALSK EGIVALRRAK RRN MERLTL ACGGVALNSF DDLSPDCLGH AGLVYEYTLG EEKFTFIEKC NNPRSVTLLI KGPNKHTLTQ IKDAVRDGLR AVKN AIDDG CVVPGAGAVE VAMAEALIKH KPSVKGRAQL GVQAFADALL IIPKVLAQNS GFDLQETLVK IQAEHSESGQ LVGVD LNTG EPMVAAEVGV WDNYCVKKQL LHSCTVIATN ILLVDEIMRA GMSFLKG

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Macromolecule #13: T-complex protein 1 subunit eta

MacromoleculeName: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.443535 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLLD VVHPAAKTLV DIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ IIIRAFRTAT QLAVNKIKEI AVTVKKADKV EQRKLLEKCA M TALSSKLI ...String:
MMPTPVILLK EGTDSSQGIP QLVSNISACQ VIAEAVRTTL GPRGMDKLIV DGRGKATISN DGATILKLLD VVHPAAKTLV DIAKSQDAE VGDGTTSVTL LAAEFLKQVK PYVEEGLHPQ IIIRAFRTAT QLAVNKIKEI AVTVKKADKV EQRKLLEKCA M TALSSKLI SQQKAFFAKM VVDAVMMLDD LLQLKMIGIK KVQGGALEDS QLVAGVAFKK TFSYAGFEMQ PKKYHNPKIA LL NVELELK AEKDNAEIRV HTVEDYQAIV DAEWNILYDK LEKIHHSGAK VVLSKLPIGD VATQYFADRD MFCAGRVPEE DLK RTMMAC GGSIQTSVNA LSADVLGRCQ VFEETQIGGE RYNFFTGCPK AKTCTFILRG GAEQFMEETE RSLHDAIMIV RRAI KNDSV VAGGGAIEME LSKYLRDYSR TIPGKQQLLI GAYAKALEII PRQLCDNAGF DATNILNKLR ARHAQGGTWY GVDIN NEDI ADNFEAFVWE PAMVRINALT AASEAACLIV SVDETIKNPR STVDAPTAAG RGRGRGRPH

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Macromolecule #14: T-complex protein 1 subunit theta

MacromoleculeName: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.576332 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDAA TILRELEVQH PAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL RIGLSVSEVI EGYEIACRKA HEILPNLVCC SAKNLRDIDE V SSLLRTSI ...String:
MALHVPKAPG FAQMLKEGAK HFSGLEEAVY RNIQACKELA QTTRTAYGPN GMNKMVINHL EKLFVTNDAA TILRELEVQH PAAKMIVMA SHMQEQEVGD GTNFVLVFAG ALLELAEELL RIGLSVSEVI EGYEIACRKA HEILPNLVCC SAKNLRDIDE V SSLLRTSI MSKQYGNEVF LAKLIAQACV SIFPDSGHFN VDNIRVCKIL GSGISSSSVL HGMVFKKETE GDVTSVKDAK IA VYSCPFD GMITETKGTV LIKTAEELMN FSKGEENLMD AQVKAIADTG ANVVVTGGKV ADMALHYANK YNIMLVRLNS KWD LRRLCK TVGATALPRL TPPVLEEMGH CDSVYLSEVG DTQVVVFKHE KEDGAISTIV LRGSTDNLMD DIERAVDDGV NTFK VLTRD KRLVPGGGAT EIELAKQITS YGETCPGLEQ YAIKKFAEAF EAIPRALAEN SGVKANEVIS KLYAVHQEGN KNVGL DIEA EVPAVKDMLE AGILDTYLGK YWAIKLATNA AVTVLRVDQI IMAKPAGGPK PPSGKKDWDD DQN

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Macromolecule #15: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloridesodium chloride
1.0 mMC4H10O2S2DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 11796 / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 443858
Details: The initial particle selection after 2D class classification
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6nr8

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 3.2.0) / Details: The final 3D classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2.0) / Number images used: 194013
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6nr8

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7wu7:
Prefoldin-tubulin-TRiC complex

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