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- EMDB-9541: Structure of TRiC-AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-9541
TitleStructure of TRiC-AMP-PNP
Map dataYeast TRiC-AMP-PNP at 4.6 angstroms resolution
Sample
  • Complex: Yeast TRiC-AMP-PNP
    • Complex: T-complex protein 1 subunit alpha
    • Complex: T-complex protein 1 subunit beta
    • Complex: T-complex protein 1 subunit delta
    • Complex: T-complex protein 1 subunit epsilon
    • Complex: T-complex protein 1 subunit gamma
    • Complex: T-complex protein 1 subunit eta
    • Complex: T-complex protein 1 subunit theta
    • Complex: T-complex protein 1 subunit zeta
    • 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 delta
    • Protein or peptide: T-complex protein 1 subunit epsilon
    • Protein or peptide: T-complex protein 1 subunit gamma
    • Protein or peptide: T-complex protein 1 subunit eta
    • Protein or peptide: T-complex protein 1 subunit theta
    • Protein or peptide: T-complex protein 1 subunit zeta
KeywordsChaperonin / Yeast / CHAPERONE
Function / homology
Function and homology information


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 ...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
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. ...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
T-complex protein 1 subunit alpha / T-complex protein 1 subunit beta / T-complex protein 1 subunit gamma / T-complex protein 1 subunit delta / T-complex protein 1 subunit zeta / T-complex protein 1 subunit epsilon / T-complex protein 1 subunit eta / T-complex protein 1 subunit theta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsZang Y / Jin M
Funding support China, 4 items
OrganizationGrant numberCountry
CAS Pilot Strategic Science and Technology Projects BXDB08030201 China
National Natural Science Foundation of China31270771 China
National Natural Science Foundation of China31222016 China
National Basic Research Program of China2013CB910401 China
CitationJournal: Nat Struct Mol Biol / Year: 2016
Title: Staggered ATP binding mechanism of eukaryotic chaperonin TRiC (CCT) revealed through high-resolution cryo-EM.
Authors: Yunxiang Zang / Mingliang Jin / Huping Wang / Zhicheng Cui / Liangliang Kong / Caixuan Liu / Yao Cong /
Abstract: The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide ...The eukaryotic chaperonin TRiC (or CCT) assists in the folding of 10% of cytosolic proteins. Here we present two cryo-EM structures of Saccharomyces cerevisiae TRiC in a newly identified nucleotide partially preloaded (NPP) state and in the ATP-bound state, at 4.7-Å and 4.6-Å resolution, respectively. Through inner-subunit eGFP tagging, we identified the subunit locations in open-state TRiC and found that the CCT2 subunit pair forms an unexpected Z shape. ATP binding induces a dramatic conformational change on the CCT2 side, thereby suggesting that CCT2 plays an essential role in TRiC allosteric cooperativity. Our structural and biochemical data reveal a staggered ATP binding mechanism of TRiC with preloaded nucleotide on the CCT6 side of NPP-TRiC and demonstrate that TRiC has evolved into a complex that is structurally divided into two sides. This work offers insight into how the TRiC nucleotide cycle coordinates with its mechanical cycle in preparing folding intermediates for further productive folding.
History
DepositionSep 27, 2016-
Header (metadata) releaseOct 26, 2016-
Map releaseOct 26, 2016-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.921
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.921
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gw5
  • Surface level: 0.921
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9541.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast TRiC-AMP-PNP at 4.6 angstroms resolution
Voxel sizeX=Y=Z: 1.318 Å
Density
Contour LevelBy AUTHOR: 0.921 / Movie #1: 0.921
Minimum - Maximum-1.5845709 - 3.335837
Average (Standard dev.)0.028204367 (±0.16525468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 337.408 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z337.408337.408337.408
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-1.5853.3360.028

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Supplemental data

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Sample components

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Entire : Yeast TRiC-AMP-PNP

EntireName: Yeast TRiC-AMP-PNP
Components
  • Complex: Yeast TRiC-AMP-PNP
    • Complex: T-complex protein 1 subunit alpha
    • Complex: T-complex protein 1 subunit beta
    • Complex: T-complex protein 1 subunit delta
    • Complex: T-complex protein 1 subunit epsilon
    • Complex: T-complex protein 1 subunit gamma
    • Complex: T-complex protein 1 subunit eta
    • Complex: T-complex protein 1 subunit theta
    • Complex: T-complex protein 1 subunit zeta
    • 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 delta
    • Protein or peptide: T-complex protein 1 subunit epsilon
    • Protein or peptide: T-complex protein 1 subunit gamma
    • Protein or peptide: T-complex protein 1 subunit eta
    • Protein or peptide: T-complex protein 1 subunit theta
    • Protein or peptide: T-complex protein 1 subunit zeta

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Supramolecule #1: Yeast TRiC-AMP-PNP

SupramoleculeName: Yeast TRiC-AMP-PNP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Yeast TRiC ATP-binding state
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 960 KDa

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Supramolecule #2: T-complex protein 1 subunit alpha

SupramoleculeName: T-complex protein 1 subunit alpha / type: complex / ID: 2 / Parent: 1

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Supramolecule #3: T-complex protein 1 subunit beta

SupramoleculeName: T-complex protein 1 subunit beta / type: complex / ID: 3 / Parent: 1

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Supramolecule #4: T-complex protein 1 subunit delta

SupramoleculeName: T-complex protein 1 subunit delta / type: complex / ID: 4 / Parent: 1

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Supramolecule #5: T-complex protein 1 subunit epsilon

SupramoleculeName: T-complex protein 1 subunit epsilon / type: complex / ID: 5 / Parent: 1

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Supramolecule #6: T-complex protein 1 subunit gamma

SupramoleculeName: T-complex protein 1 subunit gamma / type: complex / ID: 6 / Parent: 1

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Supramolecule #7: T-complex protein 1 subunit eta

SupramoleculeName: T-complex protein 1 subunit eta / type: complex / ID: 7 / Parent: 1

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Supramolecule #8: T-complex protein 1 subunit theta

SupramoleculeName: T-complex protein 1 subunit theta / type: complex / ID: 8 / Parent: 1

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Supramolecule #9: T-complex protein 1 subunit zeta

SupramoleculeName: T-complex protein 1 subunit zeta / type: complex / ID: 9 / Parent: 1

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 60.557566 KDa
SequenceString: 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

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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: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.276254 KDa
SequenceString: 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

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Macromolecule #3: T-complex protein 1 subunit delta

MacromoleculeName: T-complex protein 1 subunit delta / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 57.68241 KDa
SequenceString: 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

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Macromolecule #4: T-complex protein 1 subunit epsilon

MacromoleculeName: T-complex protein 1 subunit epsilon / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 61.995004 KDa
SequenceString: 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

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Macromolecule #5: T-complex protein 1 subunit gamma

MacromoleculeName: T-complex protein 1 subunit gamma / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 58.889094 KDa
SequenceString: 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

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Macromolecule #6: T-complex protein 1 subunit eta

MacromoleculeName: T-complex protein 1 subunit eta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 59.802438 KDa
SequenceString: 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

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Macromolecule #7: T-complex protein 1 subunit theta

MacromoleculeName: T-complex protein 1 subunit theta / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 61.735102 KDa
SequenceString: 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

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Macromolecule #8: T-complex protein 1 subunit zeta

MacromoleculeName: T-complex protein 1 subunit zeta / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 59.997559 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 18000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.005 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 18000
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 / Average exposure time: 7.6 sec. / Average electron dose: 38.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 126441
Startup modelType of model: OTHER
Details: A previous asymmetric bovine apo-TRiC structure, but eight-fold symmetrized (C8 symmetry, but no symmetry was imposed between thetwo rings) and low-pass filtered to 60 angstroms.
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67990

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5gw5:
Structure of TRiC-AMP-PNP

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