[English] 日本語
Yorodumi
- EMDB-30954: Monomer of TRAPPII (open) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30954
TitleMonomer of TRAPPII (open)
Map data
Sample
  • Complex: Monomer of TRAPPII (open)
    • 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
Keywordsprotein transport TRAPPII open / PROTEIN TRANSPORT
Function / homology
Function and homology information


beta-glucan biosynthetic process / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / COPII-mediated vesicle transport ...beta-glucan biosynthetic process / TRAPPI protein complex / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / COPII-mediated vesicle transport / protein localization to phagophore assembly site / cis-Golgi network / intra-Golgi vesicle-mediated transport / protein-containing complex localization / phagophore assembly site / retrograde transport, endosome to Golgi / cellular response to nitrogen starvation / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / macroautophagy / trans-Golgi network / cell wall organization / protein-containing complex assembly / early endosome / endoplasmic reticulum / Golgi apparatus / 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 / : / : / : / : / : / : ...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 / : / : / : / : / : / : / Trs120/TRAPPC9, N-terminal domain / Trafficking protein particle complex subunit 10, TRAPPC10 / TRAPP trafficking subunit Trs65 IgD3 / Trafficking protein particle complex subunit 10-like, N-terminal / TRAPP trafficking subunit Trs65 IgD1 / TRAPP trafficking subunit Trs65 IgD2 / TR130 second Ig-like domain / TR130 NTS domain / 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
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 / 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: 4.18 Å
AuthorsSui SF / Sun S
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
DepositionFeb 5, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7e2c
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30954.png

Downloads & links

-
Map

FileDownload / File: emd_30954.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 480 pix.
= 523.68 Å		1.09 Å/pix.
x 480 pix.
= 523.68 Å		1.09 Å/pix.
x 480 pix.
= 523.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.091 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.015
Minimum - Maximum-0.036796875 - 0.068339914
Average (Standard dev.)0.000058006208 (±0.0010680236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 523.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0911.0911.091
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z523.680523.680523.680
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0370.0680.000

-
Supplemental data

-
Sample components

+
Entire : Monomer of TRAPPII (open)

EntireName: Monomer of TRAPPII (open)
Components
  • Complex: Monomer of TRAPPII (open)
    • 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

+
Supramolecule #1: Monomer of TRAPPII (open)

SupramoleculeName: Monomer of TRAPPII (open) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

+
Macromolecule #1: TRAPP-associated protein TCA17

MacromoleculeName: TRAPP-associated protein TCA17 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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

UniProtKB: TRAPP-associated protein TCA17

+
Macromolecule #2: Trafficking protein particle complex subunit 33

MacromoleculeName: Trafficking protein particle complex subunit 33 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

UniProtKB: Trafficking protein particle complex subunit 33

+
Macromolecule #3: Trafficking protein particle complex subunit BET3

MacromoleculeName: Trafficking protein particle complex subunit BET3 / 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: 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

UniProtKB: Trafficking protein particle complex subunit BET3

+
Macromolecule #4: Trafficking protein particle complex subunit BET5

MacromoleculeName: Trafficking protein particle complex subunit BET5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 18.453875 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
MGIYSFWIFD RHCNCIFDRE WTLASNSASG TINSKQNEED AKLLYGMIFS LRSITQKLSK GSVKNDIRSI STGKYRVHTY CTASGLWFV LLSDFKQQSY TQVLQYIYSH IYVKYVSNNL LSPYDFAENE NEMRGQGTRK ITNRNFISVL ESFLAPMVNQ

UniProtKB: Trafficking protein particle complex subunit BET5

+
Macromolecule #5: Trafficking protein particle complex subunit 23

MacromoleculeName: Trafficking protein particle complex subunit 23 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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

UniProtKB: Trafficking protein particle complex subunit 23

+
Macromolecule #6: Trafficking protein particle complex subunit 31

MacromoleculeName: Trafficking protein particle complex subunit 31 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 31.821752 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY YISRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASVS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK ...String:
MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY YISRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASVS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK MRRRDLKILD ILQFIHGTLW SYLFNHVSDD LVKSSERDNE YMIVDNFPTL TQFIPGENVS CEYFVCGIIK GF LFNAGFP CGVTAHRMPQ GGHSQRTVYL IQFDRQVLDR EGLRFG

UniProtKB: Trafficking protein particle complex subunit 31

+
Macromolecule #7: Trafficking protein particle complex subunit 20

MacromoleculeName: Trafficking protein particle complex subunit 20 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / 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

UniProtKB: Trafficking protein particle complex subunit 20

+
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 128.282094 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 YEYYTQTNWN 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

UniProtKB: Trafficking protein particle complex II-specific subunit 130

+
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 147.823281 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 IYPGRQFIQS GLNEEQTIEM RQK FWCREH IISKLKCNWK LTTDQSVTGS VDFNKFIEKF DHKMVYTIYP GRLFYGVQLL LDEPKVKVGE IINLKIITEP TSTC RRKQN STVNFLDIVI FDSKTSKILP RSNRRILYNG SLTKPISTTK VSEINLEIIP IEKGRYEFSV CISKSNNQDG IIQFD SENV ILSVI

UniProtKB: Trafficking protein particle complex II-specific subunit 120

+
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: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 63.306348 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 ASVLI

UniProtKB: Trafficking protein particle complex II-specific subunit 65

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91346
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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