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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0757 | |||||||||||||||
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Title | TRiC at 0.05 mM ADP-AlFx, Conformation 2, 0.05-C2 | |||||||||||||||
![]() | TRiC at 0.05 mM ADP-AlFx, Conformation 2, 0.05-C2 | |||||||||||||||
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![]() | Chaperonin TRiC/CCT / Allosteric network / ATPase cycle / Conformational landscape / Cryo-EM / CHAPERONE | |||||||||||||||
Function / homology | ![]() Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / chaperone mediated protein folding independent of cofactor / chaperonin-containing T-complex / Neutrophil degranulation / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.45 Å | |||||||||||||||
![]() | Jin M / Cong Y | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An ensemble of cryo-EM structures of TRiC reveal its conformational landscape and subunit specificity. Authors: Mingliang Jin / Wenyu Han / Caixuan Liu / Yunxiang Zang / Jiawei Li / Fangfang Wang / Yanxing Wang / Yao Cong / ![]() Abstract: TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo- ...TRiC/CCT assists the folding of ∼10% of cytosolic proteins through an ATP-driven conformational cycle and is essential in maintaining protein homeostasis. Here, we determined an ensemble of cryo-electron microscopy (cryo-EM) structures of yeast TRiC at various nucleotide concentrations, with 4 open-state maps resolved at near-atomic resolutions, and a closed-state map at atomic resolution, revealing an extra layer of an unforeseen N-terminal allosteric network. We found that, during TRiC ring closure, the CCT7 subunit moves first, responding to nucleotide binding; CCT4 is the last to bind ATP, serving as an ATP sensor; and CCT8 remains ADP-bound and is hardly involved in the ATPase-cycle in our experimental conditions; overall, yeast TRiC consumes nucleotide in a 2-ring positively coordinated manner. Our results depict a thorough picture of the TRiC conformational landscape and its allosteric transitions from the open to closed states in more structural detail and offer insights into TRiC subunit specificity in ATP consumption and ring closure, and potentially in substrate processing. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.4 KB 20.4 KB | Display Display | ![]() |
Images | ![]() | 158.6 KB | ||
Filedesc metadata | ![]() | 7.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6kreMC ![]() 0756C ![]() 0758C ![]() 0759C ![]() 0760C ![]() 0761C ![]() 0762C ![]() 0763C ![]() 0764C ![]() 0765C ![]() 0766C ![]() 0767C ![]() 6krdC ![]() 6ks6C ![]() 6ks7C ![]() 6ks8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | TRiC at 0.05 mM ADP-AlFx, Conformation 2, 0.05-C2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.318 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : TRiC complex
Entire | Name: TRiC complex |
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Components |
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-Supramolecule #1: TRiC complex
Supramolecule | Name: TRiC complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: TRiC complex at 0.05 mM ADP-AlFx |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 960 KDa |
-Macromolecule #1: T-complex protein 1 subunit alpha
Macromolecule | Name: T-complex protein 1 subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 60.557566 KDa |
Sequence | String: MSQLFNNSRS DTLFLGGEKI SGDDIRNQNV LATMAVANVV KSSLGPVGLD KMLVDDIGDF TVTNDGATIL SLLDVQHPAG KILVELAQQ QDREIGDGTT SVVIIASELL KRANELVKNK IHPTTIITGF RVALREAIRF INEVLSTSVD TLGKETLINI A KTSMSSKI ...String: MSQLFNNSRS DTLFLGGEKI SGDDIRNQNV LATMAVANVV KSSLGPVGLD KMLVDDIGDF TVTNDGATIL SLLDVQHPAG KILVELAQQ QDREIGDGTT SVVIIASELL KRANELVKNK IHPTTIITGF RVALREAIRF INEVLSTSVD TLGKETLINI A KTSMSSKI IGADSDFFSN MVVDALLAVK TQNSKGEIKY PVKAVNVLKA HGKSATESLL VPGYALNCTV ASQAMPKRIA GG NVKIACL DLNLQKARMA MGVQINIDDP EQLEQIRKRE AGIVLERVKK IIDAGAQVVL TTKGIDDLCL KEFVEAKIMG VRR CKKEDL RRIARATGAT LVSSMSNLEG EETFESSYLG LCDEVVQAKF SDDECILIKG TSKHSSSSII LRGANDYSLD EMER SLHDS LSVVKRTLES GNVVPGGGCV EAALNIYLDN FATTVGSREQ LAIAEFAAAL LIIPKTLAVN AAKDSSELVA KLRSY HAAS QMAKPEDVKR RSYRNYGLDL IRGKIVDEIH AGVLEPTISK VKSLKSALEA CVAILRIDTM ITVDPEPPKE DPHDH UniProtKB: T-complex protein 1 subunit alpha |
-Macromolecule #2: T-complex protein 1 subunit beta
Macromolecule | Name: T-complex protein 1 subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 57.276254 KDa |
Sequence | String: MSVQIFGDQV TEERAENARL SAFVGAIAVG DLVKSTLGPK GMDKLLQSAS SNTCMVTNDG ATILKSIPLD NPAAKVLVNI SKVQDDEVG DGTTSVTVLS AELLREAEKL IDQSKIHPQT IIEGYRLASA AALDALTKAA VDNSHDKTMF REDLIHIAKT T LSSKILSQ ...String: MSVQIFGDQV TEERAENARL SAFVGAIAVG DLVKSTLGPK GMDKLLQSAS SNTCMVTNDG ATILKSIPLD NPAAKVLVNI SKVQDDEVG DGTTSVTVLS AELLREAEKL IDQSKIHPQT IIEGYRLASA AALDALTKAA VDNSHDKTMF REDLIHIAKT T LSSKILSQ DKDHFAELAT NAILRLKGST NLEHIQIIKI LGGKLSDSFL DEGFILAKKF GNNQPKRIEN AKILIANTTL DT DKVKIFG TKFKVDSTAK LAQLEKAERE KMKNKIAKIS KFGINTFINR QLIYDYPEQL FTDLGINSIE HADFEGVERL ALV TGGEVV STFDEPSKCK LGECDVIEEI MLGEQPFLKF SGCKAGEACT IVLRGATDQT LDEAERSLHD ALSVLSQTTK ETRT VLGGG CAEMVMSKAV DTEAQNIDGK KSLAVEAFAR ALRQLPTILA DNAGFDSSEL VSKLRSSIYN GISTSGLDLN NGTIA DMRQ LGIVESYKLK RAVVSSASEA AEVLLRVDNI IRARPRTANR QHM UniProtKB: T-complex protein 1 subunit beta |
-Macromolecule #3: T-complex protein 1 subunit delta
Macromolecule | Name: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 57.68241 KDa |
Sequence | String: MSAKVPSNAT FKNKEKPQEV RKANIIAARS VADAIRTSLG PKGMDKMIKT SRGEIIISND GHTILKQMAI LHPVARMLVE VSAAQDSEA GDGTTSVVIL TGALLGAAER LLNKGIHPTI IADSFQSAAK RSVDILLEMC HKVSLSDREQ LVRAASTSLS S KIVSQYSS ...String: MSAKVPSNAT FKNKEKPQEV RKANIIAARS VADAIRTSLG PKGMDKMIKT SRGEIIISND GHTILKQMAI LHPVARMLVE VSAAQDSEA GDGTTSVVIL TGALLGAAER LLNKGIHPTI IADSFQSAAK RSVDILLEMC HKVSLSDREQ LVRAASTSLS S KIVSQYSS FLAPLAVDSV LKISDENSKN VDLNDIRLVK KVGGTIDDTE MIDGVVLTQT AIKSAGGPTR KEKAKIGLIQ FQ ISPPKPD TENNIIVNDY RQMDKILKEE RAYLLNICKK IKKAKCNVLL IQKSILRDAV NDLALHFLSK LNIMVVKDIE REE IEFLSK GLGCKPIADI ELFTEDRLGS ADLVEEIDSD GSKIVRVTGI RNNNARPTVS VVIRGANNMI IDETERSLHD ALCV IRCLV KERGLIAGGG APEIEISRRL SKEARSMEGV QAFIWQEFAS ALEVIPTTLA ENAGLNSIKV VTELRSKHEN GELND GISV RRSGTTNTYE EHILQPVLVS TSAITLASEC VKSILRIDDI AFSR UniProtKB: T-complex protein 1 subunit delta |
-Macromolecule #4: T-complex protein 1 subunit epsilon
Macromolecule | Name: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 61.995004 KDa |
Sequence | String: MAARPQQPPM EMPDLSNAIV AQDEMGRPFI IVKDQGNKKR QHGLEAKKSH ILAARSVASI IKTSLGPRGL DKILISPDGE ITITNDGAT ILSQMELDNE IAKLLVQLSK SQDDEIGDGT TGVVVLASAL LDQALELIQK GIHPIKIANG FDEAAKLAIS K LEETCDDI ...String: MAARPQQPPM EMPDLSNAIV AQDEMGRPFI IVKDQGNKKR QHGLEAKKSH ILAARSVASI IKTSLGPRGL DKILISPDGE ITITNDGAT ILSQMELDNE IAKLLVQLSK SQDDEIGDGT TGVVVLASAL LDQALELIQK GIHPIKIANG FDEAAKLAIS K LEETCDDI SASNDELFRD FLLRAAKTSL GSKIVSKDHD RFAEMAVEAV INVMDKDRKD VDFDLIKMQG RVGGSISDSK LI NGVILDK DFSHPQMPKC VLPKEGSDGV KLAILTCPFE PPKPKTKHKL DISSVEEYQK LQTYEQDKFK EMIDDVKKAG ADV VICQWG FDDEANHLLL QNDLPAVRWV GGQELEHIAI STNGRIVPRF QDLSKDKLGT CSRIYEQEFG TTKDRMLIIE QSKE TKTVT CFVRGSNKMI VDEAERALHD SLCVVRNLVK DSRVVYGGGA AEVTMSLAVS EEADKQRGID QYAFRGFAQA LDTIP MTLA ENSGLDPIGT LSTLKSKQLK EKISNIGVDC LGYGSNDMKE LFVVDPFIGK KQQILLATQL CRMILKIDNV IISGKD EY UniProtKB: T-complex protein 1 subunit epsilon |
-Macromolecule #5: T-complex protein 1 subunit gamma
Macromolecule | Name: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 58.889094 KDa |
Sequence | String: MQAPVVFMNA SQERTTGRQA QISNITAAKA VADVIRTCLG PKAMLKMLLD PMGGLVLTND GHAILREIDV AHPAAKSMLE LSRTQDEEV GDGTTTVIIL AGEILAQCAP YLIEKNIHPV IIIQALKKAL TDALEVIKQV SKPVDVENDA AMKKLIQASI G TKYVIHWS ...String: MQAPVVFMNA SQERTTGRQA QISNITAAKA VADVIRTCLG PKAMLKMLLD PMGGLVLTND GHAILREIDV AHPAAKSMLE LSRTQDEEV GDGTTTVIIL AGEILAQCAP YLIEKNIHPV IIIQALKKAL TDALEVIKQV SKPVDVENDA AMKKLIQASI G TKYVIHWS EKMCELALDA VKTVRKDLGQ TVEGEPNFEI DIKRYVRVEK IPGGDVLDSR VLKGVLLNKD VVHPKMSRHI EN PRVVLLD CPLEYKKGES QTNIEIEKEE DWNRILQIEE EQVQLMCEQI LAVRPTLVIT EKGVSDLAQH YLLKGGCSVL RRV KKSDNN RIARVTGATI VNRVEDLKES DVGTNCGLFK VEMIGDEYFS FLDNCKEPKA CTIMLRGGSK DILNEIDRNL QDAM AVARN VMLSPSLSPG GGATEMAVSV KLAEKAKQLE GIQQWPYQAV ADAMECIPRT LIQNAGGDPI RLLSQLRAKH AQGNF TTGI DGDKGKIVDM VSYGIWEPEV IKQQSVKTAI ESACLLLRVD DIVSGVRKQE UniProtKB: T-complex protein 1 subunit gamma |
-Macromolecule #6: T-complex protein 1 subunit eta
Macromolecule | Name: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59.802438 KDa |
Sequence | String: MNFGSQTPTI VVLKEGTDAS QGKGQIISNI NACVAVQEAL KPTLGPLGSD ILIVTSNQKT TISNDGATIL KLLDVVHPAA KTLVDISRA QDAEVGDGTT SVTILAGELM KEAKPFLEEG ISSHLIMKGY RKAVSLAVEK INELAVDITS EKSSGRELLE R CARTAMSS ...String: MNFGSQTPTI VVLKEGTDAS QGKGQIISNI NACVAVQEAL KPTLGPLGSD ILIVTSNQKT TISNDGATIL KLLDVVHPAA KTLVDISRA QDAEVGDGTT SVTILAGELM KEAKPFLEEG ISSHLIMKGY RKAVSLAVEK INELAVDITS EKSSGRELLE R CARTAMSS KLIHNNADFF VKMCVDAVLS LDRNDLDDKL IGIKKIPGGA MEESLFINGV AFKKTFSYAG FEQQPKKFNN PK ILSLNVE LELKAEKDNA EVRVEHVEDY QAIVDAEWQL IFEKLRQVEE TGANIVLSKL PIGDLATQFF ADRNIFCAGR VSA DDMNRV IQAVGGSIQS TTSDIKPEHL GTCALFEEMQ IGSERYNLFQ GCPQAKTCTL LLRGGAEQVI AEVERSLHDA IMIV KRALQ NKLIVAGGGA TEMEVSKCLR DYSKTIAGKQ QMIINAFAKA LEVIPRQLCE NAGFDAIEIL NKLRLAHSKG EKWYG VVFE TENIGDNFAK FVWEPALVKI NALNSATEAT NLILSVDETI TNKGSESANA GMMPPQGAGR GRGMPM UniProtKB: T-complex protein 1 subunit eta |
-Macromolecule #7: T-complex protein 1 subunit theta
Macromolecule | Name: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 61.735102 KDa |
Sequence | String: MSLRLPQNPN AGLFKQGYNS YSNADGQIIK SIAAIRELHQ MCLTSMGPCG RNKIIVNHLG KIIITNDAAT MLRELDIVHP AVKVLVMAT EQQKIDMGDG TNLVMILAGE LLNVSEKLIS MGLSAVEIIQ GYNMARKFTL KELDEMVVGE ITDKNDKNEL L KMIKPVIS ...String: MSLRLPQNPN AGLFKQGYNS YSNADGQIIK SIAAIRELHQ MCLTSMGPCG RNKIIVNHLG KIIITNDAAT MLRELDIVHP AVKVLVMAT EQQKIDMGDG TNLVMILAGE LLNVSEKLIS MGLSAVEIIQ GYNMARKFTL KELDEMVVGE ITDKNDKNEL L KMIKPVIS SKKYGSEDIL SELVSEAVSH VLPVAQQAGE IPYFNVDSIR VVKIMGGSLS NSTVIKGMVF NREPEGHVKS LS EDKKHKV AVFTCPLDIA NTETKGTVLL HNAQEMLDFS KGEEKQIDAM MKEIADMGVE CIVAGAGVGE LALHYLNRYG ILV LKVPSK FELRRLCRVC GATPLPRLGA PTPEELGLVE TVKTMEIGGD RVTVFKQEQG EISRTSTIIL RGATQNNLDD IERA IDDGV AAVKGLMKPS GGKLLPGAGA TEIELISRIT KYGERTPGLL QLAIKQFAVA FEVVPRTLAE TAGLDVNEVL PNLYA AHNV TEPGAVKTDH LYKGVDIDGE SDEGVKDIRE ENIYDMLATK KFAINVATEA ATTVLSIDQI IMAKKAGGPR APQGPR PGN WDQED UniProtKB: T-complex protein 1 subunit theta |
-Macromolecule #8: T-complex protein 1 subunit zeta
Macromolecule | Name: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 59.997559 KDa |
Sequence | String: MSLQLLNPKA ESLRRDAALK VNVTSAEGLQ SVLETNLGPK GTLKMLVDGA GNIKLTKDGK VLLTEMQIQS PTAVLIARAA AAQDEITGD GTTTVVCLVG ELLRQAHRFI QEGVHPRIIT DGFEIARKES MKFLDEFKIS KTNLSNDREF LLQVARSSLL T KVDADLTE ...String: MSLQLLNPKA ESLRRDAALK VNVTSAEGLQ SVLETNLGPK GTLKMLVDGA GNIKLTKDGK VLLTEMQIQS PTAVLIARAA AAQDEITGD GTTTVVCLVG ELLRQAHRFI QEGVHPRIIT DGFEIARKES MKFLDEFKIS KTNLSNDREF LLQVARSSLL T KVDADLTE VLTPIVTDAV LSVYDAQADN LDLHMVEIMQ MQHLSPKDTT FIKGLVLDHG GRHPDMPTRV KNAYVLILNV SL EYEKTEV NSGFFYSSAD QRDKLAASER KFVDAKLKKI IDLKNEVCGM DPDKGFVIIN QKGIDPMSLD VFAKHNILAL RRA KRRNME RLQLVTGGEA QNSVEDLSPQ ILGFSGLVYQ ETIGEEKFTY VTENTDPKSC TILIKGSTHY ALAQTKDAVR DGLR AVANV LKDKNIIPGA GAFYIALSRY LRSANMNKLG AKGKTKTGIE AFAEALLVIP KTLVKNSGFD PLDVLAMVED ELDDA QDSD ETRYVGVDLN IGDSCDPTIE GIWDSYRVLR NAITGATGIA SNLLLCDELL RAGRSTLKET PQ UniProtKB: T-complex protein 1 subunit zeta |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45195 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |