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- EMDB-22928: Structure of the yeast TRAPPIII-Ypt1(Rab1) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22928
TitleStructure of the yeast TRAPPIII-Ypt1(Rab1) complex
Map dataUnsharpened reconstruction
Sample
  • Complex: TRAPPIII-Ypt1 complex
    • 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 BET5
    • Protein or peptide: Trafficking protein particle complex subunit BET3
    • Protein or peptide: Trafficking protein particle complex subunit 33
    • Protein or peptide: Trafficking protein particle complex subunit 20
    • Protein or peptide: GTP-binding protein YPT1
    • Protein or peptide: Trafficking protein particle complex III-specific subunit 85
  • Ligand: PALMITIC ACID
KeywordsGTPase / GEF / ER / Golgi / Autophagy / PROTEIN TRANSPORT
Function / homology
Function and homology information


Cvt vesicle assembly / pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / TRAPPI protein complex / RAB geranylgeranylation / Golgi vesicle budding / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex ...Cvt vesicle assembly / pre-mRNA catabolic process / Golgi Cisternae Pericentriolar Stack Reorganization / Golgi vesicle docking / regulation of endoplasmic reticulum unfolded protein response / TRAPPI protein complex / RAB geranylgeranylation / Golgi vesicle budding / RAB GEFs exchange GTP for GDP on RABs / TRAPPII protein complex / TRAPPIII protein complex / TRAPP complex / early endosome to Golgi transport / COPI-dependent Golgi-to-ER retrograde traffic / COPII-coated vesicle budding / COPI-mediated anterograde transport / cytoplasm to vacuole targeting by the Cvt pathway / COPII-mediated vesicle transport / SNARE complex disassembly / protein localization to phagophore assembly site / phagophore assembly site membrane / cis-Golgi network membrane / piecemeal microautophagy of the nucleus / pexophagy / cis-Golgi network / endocytic recycling / intra-Golgi vesicle-mediated transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Golgi stack / phagophore assembly site / retrograde transport, endosome to Golgi / cellular response to nitrogen starvation / reticulophagy / protein-containing complex localization / sporulation resulting in formation of a cellular spore / SNARE complex assembly / positive regulation of macroautophagy / chromosome organization / endoplasmic reticulum to Golgi vesicle-mediated transport / autophagosome assembly / Neutrophil degranulation / endomembrane system / SNARE binding / meiotic cell cycle / macroautophagy / trans-Golgi network / intracellular protein transport / protein-containing complex assembly / cytoplasmic vesicle / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / Golgi apparatus / mitochondrion / nucleus / cytoplasm / cytosol
Similarity search - Function
TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / 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 / : ...TRAPP III complex, Trs85 / ER-Golgi trafficking TRAPP I complex 85 kDa subunit / 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 Rab domain 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
GTP-binding protein YPT1 / Trafficking protein particle complex subunit BET3 / Trafficking protein particle complex subunit 20 / Trafficking protein particle complex III-specific subunit 85 / Trafficking protein particle complex subunit 31 / Trafficking protein particle complex subunit BET5 / Trafficking protein particle complex subunit 23 / Trafficking protein particle complex subunit 33
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsJoiner AMN / Phillips BP
Funding support United States, United Kingdom, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM116942 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM136258 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM097272 United States
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R01HD095296 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124559 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124559 United States
National Science Foundation (NSF, United States)DBI-1661380 United States
National Science Foundation (NSF, United States)DMR-1719875 United States
Medical Research Council (MRC, United Kingdom)MRC_UP_1201/10 United Kingdom
National Science Foundation (NSF, United States)DGE-1650441 United States
CitationJournal: EMBO J / Year: 2021
Title: Structural basis of TRAPPIII-mediated Rab1 activation.
Authors: Aaron Mn Joiner / Ben P Phillips / Kumar Yugandhar / Ethan J Sanford / Marcus B Smolka / Haiyuan Yu / Elizabeth A Miller / J Christopher Fromme /
Abstract: The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII ...The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
History
DepositionNov 3, 2020-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kmt
  • Surface level: 0.032
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22928.png

Downloads & links

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Map

FileDownload / File: emd_22928.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 288 pix.
= 396.864 Å		1.38 Å/pix.
x 288 pix.
= 396.864 Å		1.38 Å/pix.
x 288 pix.
= 396.864 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.378 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.032
Minimum - Maximum-0.03911396 - 0.110499196
Average (Standard dev.)0.0000053638914 (±0.0027153348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 396.864 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3781.3781.378
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z396.864396.864396.864
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0390.1100.000

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Supplemental data

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Mask #1

Fileemd_22928_msk_1.map
Projections & Slices
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Additional map: RESOLVE Density Modified Map

Fileemd_22928_additional_1.map
AnnotationRESOLVE Density Modified Map
Projections & Slices
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Additional map: PostProcessed (sharpened) masked map

Fileemd_22928_additional_2.map
AnnotationPostProcessed (sharpened) masked map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: Trs85-focused locally refined map (sharpened)

Fileemd_22928_additional_3.map
AnnotationTrs85-focused locally refined map (sharpened)
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Trs33-focused locally refined map (sharpened)

Fileemd_22928_additional_4.map
AnnotationTrs33-focused locally refined map (sharpened)
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1, used for model refinement

Fileemd_22928_half_map_1.map
Annotationhalf map 1, used for model refinement
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2, used for model validation

Fileemd_22928_half_map_2.map
Annotationhalf map 2, used for model validation
Projections & Slices
AxesZYX

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Sample components

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Entire : TRAPPIII-Ypt1 complex

EntireName: TRAPPIII-Ypt1 complex
Components
  • Complex: TRAPPIII-Ypt1 complex
    • 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 BET5
    • Protein or peptide: Trafficking protein particle complex subunit BET3
    • Protein or peptide: Trafficking protein particle complex subunit 33
    • Protein or peptide: Trafficking protein particle complex subunit 20
    • Protein or peptide: GTP-binding protein YPT1
    • Protein or peptide: Trafficking protein particle complex III-specific subunit 85
  • Ligand: PALMITIC ACID

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Supramolecule #1: TRAPPIII-Ypt1 complex

SupramoleculeName: TRAPPIII-Ypt1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Trafficking protein particle complex subunit 23

MacromoleculeName: Trafficking protein particle complex subunit 23 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.889262 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #2: Trafficking protein particle complex subunit 31

MacromoleculeName: Trafficking protein particle complex subunit 31 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 31.755689 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #3: Trafficking protein particle complex subunit BET5

MacromoleculeName: Trafficking protein particle complex subunit BET5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 18.453875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGIYSFWIFD RHCNCIFDRE WTLASNSASG TINSKQNEED AKLLYGMIFS LRSITQKLSK GSVKNDIRSI STGKYRVHTY CTASGLWFV LLSDFKQQSY TQVLQYIYSH IYVKYVSNNL LSPYDFAENE NEMRGQGTRK ITNRNFISVL ESFLAPMVNQ

UniProtKB: Trafficking protein particle complex subunit BET5

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Macromolecule #4: Trafficking protein particle complex subunit BET3

MacromoleculeName: Trafficking protein particle complex subunit BET3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.152445 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #5: Trafficking protein particle complex subunit 33

MacromoleculeName: Trafficking protein particle complex subunit 33 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.786176 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #6: Trafficking protein particle complex subunit 20

MacromoleculeName: Trafficking protein particle complex subunit 20 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 19.721154 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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

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Macromolecule #7: GTP-binding protein YPT1

MacromoleculeName: GTP-binding protein YPT1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 23.240227 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSEYDYLFK LLLIGNSGVG KSCLLLRFSD DTYTNDYIST IGVDFKIKTV ELDGKTVKLQ IWDTAGQERF RTITSSYYRG SHGIIIVYD VTDQESFNGV KMWLQEIDRY ATSTVLKLLV GNKCDLKDKR VVEYDVAKEF ADANKMPFLE TSALDSTNVE D AFLTMARQ ...String:
MNSEYDYLFK LLLIGNSGVG KSCLLLRFSD DTYTNDYIST IGVDFKIKTV ELDGKTVKLQ IWDTAGQERF RTITSSYYRG SHGIIIVYD VTDQESFNGV KMWLQEIDRY ATSTVLKLLV GNKCDLKDKR VVEYDVAKEF ADANKMPFLE TSALDSTNVE D AFLTMARQ IKESMSQQNL NETTQKKEDK GNVNLKGQSL TNTGGGCC

UniProtKB: GTP-binding protein YPT1

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Macromolecule #8: Trafficking protein particle complex III-specific subunit 85

MacromoleculeName: Trafficking protein particle complex III-specific subunit 85
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 82.850109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQENLYFQGM VFSYEHYMNL LFHLDNSKET VPPEIAKRII SNAIAPVITV TSTPLFDKHI QETYKVDSLY MLLRFFGGC VSDRDQANEA KVGQHEHEVC DASDSTDSIP KNKNLEVPNL SKKGSRSRSN SLFQRDSTQS QYIRFTRPLG D LIETRDAN ...String:
MGSSHHHHHH SQENLYFQGM VFSYEHYMNL LFHLDNSKET VPPEIAKRII SNAIAPVITV TSTPLFDKHI QETYKVDSLY MLLRFFGGC VSDRDQANEA KVGQHEHEVC DASDSTDSIP KNKNLEVPNL SKKGSRSRSN SLFQRDSTQS QYIRFTRPLG D LIETRDAN DMLFNYHSLE VFLDNYLKLV AANTDEMVPH NLLKKSIYHS FFSLAISSTN NLSPYETFNH PILSLIALDI SN GEVYEDA RDLLVNFKNL NHNTENFPIF MNTNEMLPVF LLCYNDDSQE EFEKCQALAK KLKKQLFVES ILLALWKDSF IYD ENSVIQ LHQPVMSSLE EILFFLQAPT QTTLSLALIN SIYDMLDYLV YDLMIPFMKR KVSFWEETIL QPRKSLFNGA KFFK KFMNK NPVNGNHQHN SLTRDSQGNE YFASSSSEFL MRKLADWSMM LSDFKTAYST YESLMDDLDA FPKYLASCIE WCAVS LLMG AQSIVTVKMI KNDINPLIER ALATYENCSR IQRGKGKESN SLDVTEPVRS YETRCMILAS ELFLSLSNTW TSTPYA IQY LETILDECKL GPCSQIMVWE RLSDCYNLRV DPRIKHRVGA MKKDAKDTED LRGEHKYSTD HFTDEDILSE GLTRRRK AA FFRLIAAKKW AEQKQWRQVS WCLKDIESTY SEIKFLHGNG LILSKLKNQL NLKDVDSAPR PSEKNLTRTS VSFIG

UniProtKB: Trafficking protein particle complex III-specific subunit 85

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Macromolecule #9: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 9 / Number of copies: 2 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
10.0 mMTris
350.0 mMsodium chloride
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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Either 0.02% Tween-20 or 0.025% amphipol A8-35 was added before application of the sample to the grid..

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 1 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Electron microscopy #1~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Image recordingImage recording ID: 2 / Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 20.0 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

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Electron microscopy #1~~

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingImage recording ID: 3 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / 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

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Image processing

Image recording ID1
Startup modelType of model: EMDB MAP
EMDB ID:

5741


Details: Negative stain structure of TRAPPIII complex
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 69315
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3cue

source_name: PDB, initial_model_type: experimental model

2c0j

source_name: PDB, initial_model_type: experimental model

2j3w

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7kmt:
Structure of the yeast TRAPPIII-Ypt1(Rab1) complex

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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

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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

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