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- EMDB-31038: Intact Ypt32-TRAPPII (dimer). -

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Basic information

Entry
Database: EMDB / ID: EMD-31038
TitleIntact Ypt32-TRAPPII (dimer).
Map data
Sample
  • Complex: Intact Ypt32-TRAPPII (dimer).
    • Protein or peptide: x 11 types
Function / homology
Function and homology information


Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport ...Anchoring of the basal body to the plasma membrane / beta-glucan biosynthetic process / RAB geranylgeranylation / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPII-mediated vesicle transport / cytoplasm to vacuole targeting by the Cvt pathway / intra-Golgi vesicle-mediated transport / protein localization to phagophore assembly site / cellular bud neck / cis-Golgi network / protein-containing complex localization / phagophore assembly site / retrograde transport, endosome to Golgi / cis-Golgi network membrane / exocytosis / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / cell wall organization / macroautophagy / trans-Golgi network / recycling endosome / autophagy / protein transport / protein-containing complex assembly / mitochondrial outer membrane / early endosome / endosome / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / nucleus / cytosol / cytoplasm
Similarity search - Function
TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit ...TRAPP II complex, Trs120 / TRAPP II complex TRAPPC10, C-terminal / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit TRAPPC10/Trs130 / Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 / Trafficking protein particle complex subunit 2 / Sedlin, N-terminal conserved region / Trafficking protein particle complex subunit / Sybindin-like family / Sybindin-like family / TRAPP I complex, subunit 5 / TRAPP complex, Trs33 subunit / Bet3 family / Transport protein particle (TRAPP) component / Transport protein particle (TRAPP) component / NO signalling/Golgi transport ligand-binding domain superfamily / Longin-like domain superfamily / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
TRAPP-associated protein TCA17 / Trafficking protein particle complex II-specific subunit 65 / Trafficking protein particle complex subunit BET3 / Trafficking protein particle complex subunit 20 / GTP-binding protein YPT32/YPT11 / Trafficking protein particle complex subunit 31 / Trafficking protein particle complex subunit BET5 / Trafficking protein particle complex II-specific subunit 130 / Trafficking protein particle complex subunit 23 / Trafficking protein particle complex II-specific subunit 120 / Trafficking protein particle complex subunit 33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.31 Å
AuthorsMi CC / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Adv / Year: 2022
Title: Structural basis for assembly of TRAPPII complex and specific activation of GTPase Ypt31/32.
Authors: Chenchen Mi / Li Zhang / Guoqiang Huang / Guangcan Shao / Fan Yang / Xin You / Meng-Qiu Dong / Shan Sun / Sen-Fang Sui /
Abstract: Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as ...Transport protein particle (TRAPP) complexes belong to the multiprotein tethering complex and exist in three forms-core TRAPP/TRAPPI, TRAPPII, and TRAPPIII. TRAPPII activates GTPase Ypt31/Ypt32 as the guanine nucleotide exchange factor in the trans-Golgi network to determine the maturation of Golgi cisternae into post-Golgi carriers in yeast. Here, we present cryo-EM structures of yeast TRAPPII in apo and Ypt32-bound states. All the structures show a dimeric architecture assembled by two triangle-shaped monomers, while the monomer in the apo state exhibits both open and closed conformations, and the monomer in the Ypt32-bound form only captures the closed conformation. Located in the interior of the monomer, Ypt32 binds with both core TRAPP/TRAPPI and Trs120 via its nucleotide-binding domain and binds with Trs31 via its hypervariable domain. Combined with functional analysis, the structures provide insights into the assembly of TRAPPII and the mechanism of the specific activation of Ypt31/Ypt32 by TRAPPII.
History
DepositionMar 6, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateFeb 16, 2022-
Current statusFeb 16, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ea3
  • Surface level: 0.008
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ea3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31038.png

Downloads & links

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Map

FileDownload / File: emd_31038.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.8697 Å
Density
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.012786428 - 0.035643063
Average (Standard dev.)8.637608e-05 (±0.00089939625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 521.82 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.86970.86970.8697
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z521.820521.820521.820
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0130.0360.000

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Supplemental data

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Sample components

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Entire : Intact Ypt32-TRAPPII (dimer).

EntireName: Intact Ypt32-TRAPPII (dimer).
Components
  • Complex: Intact Ypt32-TRAPPII (dimer).
    • Protein or peptide: TRAPP-associated protein TCA17
    • Protein or peptide: Trafficking protein particle complex subunit 33
    • Protein or peptide: Trafficking protein particle complex subunit BET3
    • Protein or peptide: Trafficking protein particle complex subunit BET5
    • Protein or peptide: Trafficking protein particle complex subunit 23
    • Protein or peptide: Trafficking protein particle complex subunit 31
    • Protein or peptide: Trafficking protein particle complex subunit 20
    • Protein or peptide: Trafficking protein particle complex II-specific subunit 130
    • Protein or peptide: Trafficking protein particle complex II-specific subunit 120
    • Protein or peptide: Trafficking protein particle complex II-specific subunit 65
    • Protein or peptide: GTP-binding protein YPT32/YPT11

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Supramolecule #1: Intact Ypt32-TRAPPII (dimer).

SupramoleculeName: Intact Ypt32-TRAPPII (dimer). / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: TRAPP-associated protein TCA17

MacromoleculeName: TRAPP-associated protein TCA17 / 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: 17.371008 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MSLRPCFVSL IDESDKPILI YVPNEAENEM NDVLKYNVLS NISLDYFESA LVEWHSLDSK PLLKSIFQLE GVSVFAMLIK QTGLKIVIG FEQKSLSGAD DEFEAINQIF ETVRKIYIRV KCNPLLVSGD EKSIIKSLER KFDELFISTE VEL

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Macromolecule #2: Trafficking protein particle complex subunit 33

MacromoleculeName: Trafficking protein particle complex subunit 33 / 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: 30.786176 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSSTHSNNVG HPQSSPQGPL TEQQRAQQQY QIFENSLPKV SQSVYQMLLN EMVPLAMGIE RQISGDVISS DSNVTSENGN INNMIKRLK IEEHHTVDII RSHNLIHELY KADEEEKEKV LARLRNIGFQ IGLKLSELLI FSNNPNLKFK EMDLLLIMKF I CRDVWKQI ...String:
MSSTHSNNVG HPQSSPQGPL TEQQRAQQQY QIFENSLPKV SQSVYQMLLN EMVPLAMGIE RQISGDVISS DSNVTSENGN INNMIKRLK IEEHHTVDII RSHNLIHELY KADEEEKEKV LARLRNIGFQ IGLKLSELLI FSNNPNLKFK EMDLLLIMKF I CRDVWKQI FGKQIDNLKT NHRGTFYLLD YDYRPIQSFS LEEDAKNEEL KMIEPFLEIP VGIIRGVLSS LGYSSEEVIC LA SFIDRPT DRPKTAFPKG VSFHVQVTMP Q

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Macromolecule #3: Trafficking protein particle complex subunit BET3

MacromoleculeName: Trafficking protein particle complex subunit BET3 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.152445 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MVSTTQSRSL KAMGEEIWKN KTEKINTELF TLTYGSIVAQ LCQDYERDFN KVNDHLYSMG YNIGCRLIED FLARTALPRC ENLVKTSEV LSKCAFKIFL NITPNITNWS HNKDTFSLIL DENPLADFVE LPMDAMKSLW YSNILCGVLK GSLEMVQLDC D VWFVSDIL ...String:
MVSTTQSRSL KAMGEEIWKN KTEKINTELF TLTYGSIVAQ LCQDYERDFN KVNDHLYSMG YNIGCRLIED FLARTALPRC ENLVKTSEV LSKCAFKIFL NITPNITNWS HNKDTFSLIL DENPLADFVE LPMDAMKSLW YSNILCGVLK GSLEMVQLDC D VWFVSDIL RGDSQTEIKV KLNRILKDEI PIGED

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Macromolecule #4: Trafficking protein particle complex subunit BET5

MacromoleculeName: Trafficking protein particle complex subunit BET5 / 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: 17.981381 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MGIYSFWIFD RHCNCIFDRE WTLASNSASK QNEEDAKLLY GMIFSLRSIT QKLSKGSVKN DIRSISTGKY RVHTYCTASG LWFVLLSDF KQQSYTQVLQ YIYSHIYVKY VSNNLLSPYD FAENENEMRG QGTRKITNRN FISVLESFLA PMVNQ

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Macromolecule #5: Trafficking protein particle complex subunit 23

MacromoleculeName: Trafficking protein particle complex subunit 23 / 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: 24.889262 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MAIETILVIN KSGGLIYQRN FTNDEQKLNS NEYLILASTL HGVFAIASQL TPKALQLTQQ TNIENTIPYI PYVGMSSNRS DTRNGGGNN NKHTNNEKLG SFKGDDFFKE PFTNWNKSGL RQLCTDQFTM FIYQTLTGLK FVAISSSVMP QRQPTIATTD K PDRPKSTS ...String:
MAIETILVIN KSGGLIYQRN FTNDEQKLNS NEYLILASTL HGVFAIASQL TPKALQLTQQ TNIENTIPYI PYVGMSSNRS DTRNGGGNN NKHTNNEKLG SFKGDDFFKE PFTNWNKSGL RQLCTDQFTM FIYQTLTGLK FVAISSSVMP QRQPTIATTD K PDRPKSTS NLAIQIADNF LRKVYCLYSD YVMKDPSYSM EMPIRSNLFD EKVKKMVENL Q

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Macromolecule #6: Trafficking protein particle complex subunit 31

MacromoleculeName: Trafficking protein particle complex subunit 31 / 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: 31.743639 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASSS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK ...String:
MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASSS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK MRRRDLKILD ILQFIHGTLW SYLFNHVSDD LVKSSERDNE YMIVDNFPTL TQFIPGENVS CEYFVCGIIK GF LFNAGFP CGVTAHRMPQ GGHSQRTVYL IQFDRQVLDR EGLRFG

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Macromolecule #7: Trafficking protein particle complex subunit 20

MacromoleculeName: Trafficking protein particle complex subunit 20 / 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: 19.721154 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MPQYFAIIGK KDNPVYEIEF TNAENPQGFP QDLKELNPFI LHASLDIVED LQWQINPTSQ LNGNGGNGSN GGGGFLRSRA VNNTDNCYL GKVDHFYGLA ITAYISYSGM KFVMIHGNSA NSSVVIDDNN MRSFYQEVHE LYVKTLMNPF YKITDPIRSP A FDSRVRTL ARKHLSK

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Macromolecule #8: Trafficking protein particle complex II-specific subunit 130

MacromoleculeName: Trafficking protein particle complex II-specific subunit 130
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: 128.225062 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MDKEIYCGSV PVSYFDPFDL FESLRPEFQQ ILPLDNIHWK AFDGTVRTVN RLPIELIPEG RGEADKSNDE QPFIRFLIVN CISIDQYRA KVRPLVRQWL PNLESVSSST GEKMIYKPII LLYANSEVVD SNLFKSVSLM EKFGKDFPHV QTLEVRSVYR S PKERQEFW ...String:
MDKEIYCGSV PVSYFDPFDL FESLRPEFQQ ILPLDNIHWK AFDGTVRTVN RLPIELIPEG RGEADKSNDE QPFIRFLIVN CISIDQYRA KVRPLVRQWL PNLESVSSST GEKMIYKPII LLYANSEVVD SNLFKSVSLM EKFGKDFPHV QTLEVRSVYR S PKERQEFW NQFSQKIKAS VLSIFQKRLT HLQHSLANLQ KGNNFEEQLL TREKLYELYV VFNILEDASL ELQKIKKEIL RR NMNMPDG KLQVPFESSS KSDESLGSII IEGTLDKFQL HKYFFIRRLR LLKLEDQTLT AFVGAFQLIK NFIESISIEY RKS VRLLEF KHYFITSMLS YFEFENVSNP LLCEIKAELL MLKRDNWVQG VMATSGYRLM DKNYPNSDVK YKFDLLKETF VDET VFQEN FLTLTKEILS LFNKCEGKRQ RIVDILSIEI GLLYYQGKKY EEAVSLFLSC YEYYTQTNKN SIGLKILQVF IDSLS HCPK LDVLQIDGES VSASAVLTNA FLNILKLCKD NDSKEIWWKK FMDLQMKNNI HLMYPLDGLF EVTLNSKVHL ARANVS AIE VNLKSYGFPE DISTKTMRLS LKNMGGDVIV FGASDFLLKK GENKLILECR DIMYGEFSLL SFEIIVEGIT FVKEFPE NQ DEFIVVPEIY CKESTKVLVK QAHNLNLGEY ALELKSVQSD ALESLQVEVE VQKNIGNMKN LPVSFSMDEI QARKRYNT P FENVRLEYYL LDQITAFDLI IKTSFTKKND QGTFGETKKV RIQCYLQLSV SVEDIFKKDI FFFKFLLNSS VREEPVILY SSELSAPDTR NDYNIRGDYI ATTPALITFD GNESFINCYE ITANNNFDSK DIFNLKVRYN TLKEQLDCFI TDAVLIEGDV EWFILFEKW KTFWELEILK KLKYDYDAFK ENRIIRLLKT SIDLNKTKSK IRNLCIEKAV LDKILICLNK VSRGIAVCNT D MDEYVRNL VPKQLTVPVQ LPGFEQFFHV QFEQMETSHD ALHDTIATIG NSLSYTVIVE NLSGQWGQDV IDDGGYIFEI LS SNEWLIH GQKRCAIKEK RKEFEVHLIP LKKGYLNFPR VEITNINGKS CRVDHSNAFE SILIF

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Macromolecule #9: Trafficking protein particle complex II-specific subunit 120

MacromoleculeName: Trafficking protein particle complex II-specific subunit 120
type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 147.807281 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MNILKHFPSY VGPSKIRTLV IPIGHWTRKE FNNAVQKLSE FNEIHLSDVT PIDSPIFTPQ GFPHGKLFFD FLTIDHDDAL ELFLYDFEP FRKTFVIIGL VNDYSDPLTN LNFMKEKYPT LISPNLVYAS STPTKELEQT IDTMENVFAS SPDMQKNIET I MCDIARNF ...String:
MNILKHFPSY VGPSKIRTLV IPIGHWTRKE FNNAVQKLSE FNEIHLSDVT PIDSPIFTPQ GFPHGKLFFD FLTIDHDDAL ELFLYDFEP FRKTFVIIGL VNDYSDPLTN LNFMKEKYPT LISPNLVYAS STPTKELEQT IDTMENVFAS SPDMQKNIET I MCDIARNF LTALNSYYSS YKHVTLRSPG AIGGNAVLKT TLIRQNSYTS SSSSTPMSAV QSSVSSSSKA GSVTTASKRL SS FEMTTNS LKRSASLKLA TTLSTSENRS QQKSLGRQMK ILGNFQLLAG RYVDALNSFV DAITTLYKVR DYLWLGSALD GIS ICFLLL SYLGLSYQIP QIVSLICPVE KLNFESSSTG ISPVDSNSKA TASTTASSTP RNSISIAAMQ SPRNSIMSLS APAL NIDVE NINLPLLIKC ISDKVLYYYD LSLMHNSEYA PQVVYCEFLL KTLTFMTSCY KSSEFSKDVL DNIVKNQHRA LSDIP NSPM FPRFEVYFYS NKLFELQLKE MQVEAQIKIY STMAEVYRLL GYKRKQLFVL RLLMVALLAT PNKIAWHPDY RTLIDT IIE LLNINESEAK INVDDPSQST WLILQKKILQ LCIKVSRKIN DFEYVAKFSS ILITKYTHLL NQSEQDALFK EYIQPSI TN ESITSYWDPF ILREVVINRI LDSDPTSNEI PLESDVSSLE SLENRQKTQD INPQEVFNPF KRVQPTSFVS NNSTKVPI L VFLVGDKAEF TCRVQNPFKF DFTINDIQLD EEISEFCEID RKAVSYSGPY NVKAESIRSI TLPLIIKKPT YKKIYEISC LKISILKLPL QKFDIINDSR RSNPVEEEAE YSKCIYGKLK IKILPEQPQL ELLSTSKMTR NSWMMLDGTK TDFHITVRNK SLSCAINHI KIIPMNNIEQ MLKPDYWKKM PPDDLYIMEK QLDWLSKSCV RIIKLPTVIK PNETITFDLE LDNTAVPFNF T GFDLLIEY GMSATDESCI YLKKLSIPYE VTLRRTIEVP SMDIIPLNEL FSSQVENVDW IEYVMSKIRA ESNLHSRDFI LL LLDFRNS WIDGIKLNVQ FEDFTSNEYH VEASHTSRII VPIKKIDYKK YNFENTPIPR IFPGRQFIQS GLNEEQTIEM RQK FWCREH IISKLKCNWK LTTDQSVTGS VDFNKFIEKF DHKMVYTIYP GRLFYGVQLL LDEPKVKVGE IINLKIITEP TSTC RRKQN STVNFLDIVI FDSKTSKILP RSNRRILYNG SLTKPISTTK VSEINLEIIP IEKGRYEFSV CISKSNNQDG IIQFD SENV ILSVI

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Macromolecule #10: Trafficking protein particle complex II-specific subunit 65

MacromoleculeName: Trafficking protein particle complex II-specific subunit 65
type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 63.434473 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MECFVPLRCD LDGSNIEQLR QSHLSRKFII FDEQLNLWLW FQGNSQENKR FVLQNMIILI NEAQVTRTST IDDYFTQVEN NENLWRLKN DCCSKILFKS NVVMNNGYNN QIKFVFEYKS VDANFNNQDS LQDPQAKYTL DKYSSEEILP SFEPVYSWSS A ATKSSKNT ...String:
MECFVPLRCD LDGSNIEQLR QSHLSRKFII FDEQLNLWLW FQGNSQENKR FVLQNMIILI NEAQVTRTST IDDYFTQVEN NENLWRLKN DCCSKILFKS NVVMNNGYNN QIKFVFEYKS VDANFNNQDS LQDPQAKYTL DKYSSEEILP SFEPVYSWSS A ATKSSKNT NNHLEKNNRA THRVSSKNSE VHEADVSRNP NTFTLKLQYP IFSLLNMRLR NISLKSEHCI LSSLDFQTSK AS EQLTKKF IYPQEHNSFL KLNFQEISYK LIDGTSQIEL DPICPLKVPL TAFSYDSISA TFKLVLLPKS TQPHRVKITL AYE LELHPN LKLPVRTSWE TEVTLKRSMP ISSTSSQYSS NNNNTNHSAS FNGAANNVNS GGLANLRLGG VSSSRFSLGA ASTT SLVNS KLSNVKFKFI NSNIKVIKGE KFTMRLQIIN SSSSPLDLVV YYNNTINPIP SANNVRNSNG INNCGMNNGT IPNSP LTLE NQYQLHNKYR KIAEGIILLS NDYKIPVVPP RETYFADLRF IGIMSGYYGT LSGLKVLDLN TNELIEVGNG ASVLIQ

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Macromolecule #11: GTP-binding protein YPT32/YPT11

MacromoleculeName: GTP-binding protein YPT32/YPT11 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 24.548402 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSNEDYGYDY DYLFKIVLIG DSGVGKSNLL SRFTTDEFNI ESKSTIGVEF ATRTIEVENK KIKAQIWDTA GQERYRAITS AYYRGAVGA LIVYDISKSS SYENCNHWLT ELRENADDNV AVGLIGNKSD LAHLRAVPTD EAKNFAMENQ MLFTETSALN S DNVDKAFR ...String:
MSNEDYGYDY DYLFKIVLIG DSGVGKSNLL SRFTTDEFNI ESKSTIGVEF ATRTIEVENK KIKAQIWDTA GQERYRAITS AYYRGAVGA LIVYDISKSS SYENCNHWLT ELRENADDNV AVGLIGNKSD LAHLRAVPTD EAKNFAMENQ MLFTETSALN S DNVDKAFR ELIVAIFQMV SKHQVDLSGS GTNNMGSNGA PKGPTISLTP APKEDKKKKS SNCC

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32394

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