[English] 日本語
Yorodumi
- EMDB-26254: Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26254
TitleStructure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure)
Map dataComposite map of TRAPPII-Ypt32 symmetric closed/closed dimer
Sample
  • Complex: TRAPPII complex bound to Rab11/Ypt32
    • Protein or peptide: x 13 types
  • Ligand: x 1 types
Keywordscomplex / GTPase / Guanosine Exchange Factor / GEF / PROTEIN TRANSPORT
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 / cis-Golgi network membrane / cytoplasm to vacuole targeting by the Cvt pathway / protein localization to phagophore assembly site / intra-Golgi vesicle-mediated transport / cellular bud neck / cis-Golgi network / protein-containing complex localization / retrograde transport, endosome to Golgi / phagophore assembly site / cellular response to nitrogen starvation / exocytosis / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / vesicle-mediated transport / Neutrophil degranulation / macroautophagy / trans-Golgi network / cell wall organization / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBagde SR / Fromme JC
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136258 United States
National Science Foundation (NSF, United States)DMR-1719875 United States
CitationJournal: Sci Adv / Year: 2022
Title: Structure of a TRAPPII-Rab11 activation intermediate reveals GTPase substrate selection mechanisms.
Authors: Saket R Bagde / J Christopher Fromme /
Abstract: Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via ...Rab1 and Rab11 are essential regulators of the eukaryotic secretory and endocytic recycling pathways. The transport protein particle (TRAPP) complexes activate these guanosine triphosphatases via nucleotide exchange using a shared set of core subunits. The basal specificity of the TRAPP core is toward Rab1, yet the TRAPPII complex is specific for Rab11. A steric gating mechanism has been proposed to explain TRAPPII counterselection against Rab1. Here, we present cryo-electron microscopy structures of the 22-subunit TRAPPII complex from budding yeast, including a TRAPPII-Rab11 nucleotide exchange intermediate. The Trs130 subunit provides a "leg" that positions the active site distal to the membrane surface, and this leg is required for steric gating. The related TRAPPIII complex is unable to activate Rab11 because of a repulsive interaction, which TRAPPII surmounts using the Trs120 subunit as a "lid" to enclose the active site. TRAPPII also adopts an open conformation enabling Rab11 to access and exit from the active site chamber.
History
DepositionFeb 17, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26254.png

Downloads & links

-
Map

FileDownload / File: emd_26254.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of TRAPPII-Ypt32 symmetric closed/closed dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 400 pix.
= 572.8 Å		1.43 Å/pix.
x 400 pix.
= 572.8 Å		1.43 Å/pix.
x 400 pix.
= 572.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.432 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-22.622871 - 39.608699999999999
Average (Standard dev.)0.005271441 (±0.65724874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 572.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : TRAPPII complex bound to Rab11/Ypt32

EntireName: TRAPPII complex bound to Rab11/Ypt32
Components
  • Complex: TRAPPII complex bound to Rab11/Ypt32
    • Protein or peptide: Trafficking protein particle complex II-specific subunit 130
    • Protein or peptide: Trafficking protein particle complex II-specific subunit 65
    • 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: GTP-binding protein YPT32/YPT11
    • 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
  • Ligand: PALMITIC ACID

+
Supramolecule #1: TRAPPII complex bound to Rab11/Ypt32

SupramoleculeName: TRAPPII complex bound to Rab11/Ypt32 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 1.1 MDa

+
Macromolecule #1: Trafficking protein particle complex II-specific subunit 130

MacromoleculeName: Trafficking protein particle complex II-specific subunit 130
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 20.61332 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #2: Trafficking protein particle complex II-specific subunit 65

MacromoleculeName: Trafficking protein particle complex II-specific subunit 65
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 63.434473 KDa
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

UniProtKB: Trafficking protein particle complex II-specific subunit 65

+
Macromolecule #3: TRAPP-associated protein TCA17

MacromoleculeName: TRAPP-associated protein TCA17 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.371008 KDa
SequenceString:
MSLRPCFVSL IDESDKPILI YVPNEAENEM NDVLKYNVLS NISLDYFESA LVEWHSLDSK PLLKSIFQLE GVSVFAMLIK QTGLKIVIG FEQKSLSGAD DEFEAINQIF ETVRKIYIRV KCNPLLVSGD EKSIIKSLER KFDELFISTE VEL

UniProtKB: TRAPP-associated protein TCA17

+
Macromolecule #4: Trafficking protein particle complex subunit 33

MacromoleculeName: Trafficking protein particle complex subunit 33 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.786176 KDa
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 #5: Trafficking protein particle complex subunit BET3

MacromoleculeName: Trafficking protein particle complex subunit BET3 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.152445 KDa
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 #6: Trafficking protein particle complex subunit BET5

MacromoleculeName: Trafficking protein particle complex subunit BET5 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.453875 KDa
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 #7: Trafficking protein particle complex subunit 23

MacromoleculeName: Trafficking protein particle complex subunit 23 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.889262 KDa
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 #8: Trafficking protein particle complex subunit 31

MacromoleculeName: Trafficking protein particle complex subunit 31 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.755689 KDa
SequenceString: MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL LFKRQEASLS AMAFLFQEMI SQLHRTCKTA GDFETKLSD YGHNIGIRLL ELLNFRASVS PSSLPRASAF LSQNESSSKL SNASNSPGML ANSSTATSAS ANERLQEKQT E SLSNYITK ...String:
MSQRIIQPSA SDQQFPGKSD GYEYTVGPKQ AITSEASTTY IPSRIYSESL 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 #9: Trafficking protein particle complex subunit 20

MacromoleculeName: Trafficking protein particle complex subunit 20 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.721154 KDa
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 #10: GTP-binding protein YPT32/YPT11

MacromoleculeName: GTP-binding protein YPT32/YPT11 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.309145 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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 SNHHHHHHH

UniProtKB: GTP-binding protein YPT32/YPT11

+
Macromolecule #11: Trafficking protein particle complex II-specific subunit 130

MacromoleculeName: Trafficking protein particle complex II-specific subunit 130
type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 128.42425 KDa
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 SILIFAA

UniProtKB: Trafficking protein particle complex II-specific subunit 130

+
Macromolecule #12: Trafficking protein particle complex II-specific subunit 120

MacromoleculeName: Trafficking protein particle complex II-specific subunit 120
type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 147.823281 KDa
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 #13: Trafficking protein particle complex II-specific subunit 65

MacromoleculeName: Trafficking protein particle complex II-specific subunit 65
type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.889996 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #14: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 14 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.6 mg/mL
BufferpH: 8
Component:
ConcentrationName
10.0 mMTris
150.0 mMSodium chloride
0.1 %CHAPS
1.0 mMMagnesium acetate
1.0 mMDTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: The sample was incubated on the grid for 10 seconds followed by blotting for 5 seconds before plunging in liquid ethane..

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 4998 / Average exposure time: 3.5 sec. / Average electron dose: 53.0 e/Å2 / Details: Images were collected as 50 frame movies.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 63000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 979187
Startup modelType of model: INSILICO MODEL
In silico model: Used Ab-initio Reconstruction job in cryoSPARC to generate starting map.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX
Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, ...Details: The composite map was generated by combining the consensus dimer map (EMD-26221) with focused refinement maps deposited in the entries EMD-26223, EMD-26224. EMD-26225, EMD-26226, EMD-26227, EMD-26228, EMD-26229, EMD-26230, EMD-26231 and EMD-26232 using Combine Focused Maps in Phenix.
Number images used: 369488
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)

-
Atomic model buiding 1

Initial model
PDB IDChain

3cue

source_name: PDB, initial_model_type: experimental model

3rwo

source_name: PDB, initial_model_type: experimental model

3pr6

source_name: PDB, initial_model_type: experimental model
DetailsModel was rebuilt in coot and refined using phenix.real_space_refine.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7u05:
Structure of the yeast TRAPPII-Rab11/Ypt32 complex in the closed/closed state (composite structure)

+
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