[English] 日本語
Yorodumi
- EMDB-7874: Helical assembly of the fungal dynamin-related Vps1 in the presen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-7874
TitleHelical assembly of the fungal dynamin-related Vps1 in the presence of GMPPCP
Map dataCryoEM map of helical Vps1 in the presence of GMPPCP
Sample
  • Organelle or cellular component: helical assembly of Vps1 in the presence of GMPPCP
    • Protein or peptide: Vps1
Biological speciesChaetomium thermophilum (fungus)
Methodhelical reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsAlvarez FJD / Varlakhanova NV / Zhang P / Ford MGJ
CitationJournal: J Cell Biol / Year: 2018
Title: Structures of the fungal dynamin-related protein Vps1 reveal a unique, open helical architecture.
Authors: Natalia V Varlakhanova / Frances J D Alvarez / Tyler M Brady / Bryan A Tornabene / Christopher J Hosford / Joshua S Chappie / Peijun Zhang / Marijn G J Ford /
Abstract: Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to ...Dynamin-related proteins (DRPs) are large multidomain GTPases required for diverse membrane-remodeling events. DRPs self-assemble into helical structures, but how these structures are tailored to their cellular targets remains unclear. We demonstrate that the fungal DRP Vps1 primarily localizes to and functions at the endosomal compartment. We present crystal structures of a Vps1 GTPase-bundle signaling element (BSE) fusion in different nucleotide states to capture GTP hydrolysis intermediates and concomitant conformational changes. Using cryoEM, we determined the structure of full-length GMPPCP-bound Vps1. The Vps1 helix is more open and flexible than that of dynamin. This is due to further opening of the BSEs away from the GTPase domains. A novel interface between adjacent GTPase domains forms in Vps1 instead of the contacts between the BSE and adjacent stalks and GTPase domains as seen in dynamin. Disruption of this interface abolishes Vps1 function in vivo. Hence, Vps1 exhibits a unique helical architecture, highlighting structural flexibilities of DRP self-assembly.
History
DepositionMay 12, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseOct 17, 2018-
UpdateOct 17, 2018-
Current statusOct 17, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0182
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0182
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7874.png

Downloads & links

-
Map

FileDownload / File: emd_7874.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of helical Vps1 in the presence of GMPPCP
Voxel sizeX=Y=Z: 1.59 Å
Density
Contour LevelBy AUTHOR: 0.0182 / Movie #1: 0.0182
Minimum - Maximum-0.01888274 - 0.053536385
Average (Standard dev.)0.00027647777 (±0.005965922)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 636.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.591.591.59
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z636.000636.000636.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0190.0540.000

-
Supplemental data

-
Sample components

-
Entire : helical assembly of Vps1 in the presence of GMPPCP

EntireName: helical assembly of Vps1 in the presence of GMPPCP
Components
  • Organelle or cellular component: helical assembly of Vps1 in the presence of GMPPCP
    • Protein or peptide: Vps1

-
Supramolecule #1: helical assembly of Vps1 in the presence of GMPPCP

SupramoleculeName: helical assembly of Vps1 in the presence of GMPPCP / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Chaetomium thermophilum (fungus) / Strain: Thermophilum DSM 1495
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant plasmid: pCDNA3.1(+)

-
Macromolecule #1: Vps1

MacromoleculeName: Vps1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (fungus)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTADAPAGTL AQPGGISDPN LIKLVNKLQD VFTTVGVNNP IDLPQIVVVG SQSSGKSSVL ENIVGRDFLP RGQGIVTRRP LVLQLINRQS SGNANGFDER LADSTDKAAN LDEWGEFLHL PGQKFYDFNK IRDEINRETE AKVGRNAGIS PAPINLRIYS PHVLNLTLVD ...String:
MTADAPAGTL AQPGGISDPN LIKLVNKLQD VFTTVGVNNP IDLPQIVVVG SQSSGKSSVL ENIVGRDFLP RGQGIVTRRP LVLQLINRQS SGNANGFDER LADSTDKAAN LDEWGEFLHL PGQKFYDFNK IRDEINRETE AKVGRNAGIS PAPINLRIYS PHVLNLTLVD LPGLTRVPVG DQPRDIERQI RDMILKYIQK PNAIILAVTA ANVDLANSDG LKLAREVDPE GQRTIGVLTK VDLMDEGTDV VDILAGRIIP LRLGYVPVVN RGQRDIDNKK PITAALEAEK AFFENHKAYR NKSAYCGTPY LARKLNLILM MHIKQTLPDI KQRISSSLQK YQQELEALGP SLLGNSANIV LNIITEFTNE WRTVLDGNNT ELSSTELSGG ARISFVFHEL YANGIKAVDP FDYVKDVDIR TIMYNSSGSS PALFVGTTAF ELIVKQQIKR LEEPSLKCAS LVYDELVRIL TQLLSKQQFR RYPALKEKIH QVVISFFKKA MEPTNKLVRD LVAMEACYIN TAHPDFLNGH RAMAIVNERH QASKPVQVDP KTGKPLNQQR AASPTPEESS NTGFFGSFFA AKNKKKAAAM EPPPPTLKAT GTLSEREGIE VEVIKLLISS YFNIVKRTMI DMVPKAIMLN LVQFTKEEMQ KELLENLYRQ SELDDLLKES DYTVRRRKEC QQMVESLQRA AEIVSQVQNS SSNNNNNNNN NNLGIEGLEV LFQGPGMKIE EGKLVIWING DKGYNGLAEV GKKFEKDTGI KVTVEHPDKL EEKFPQVAAT GDGPDIIFWA HDRFGGYAQS GLLAEITPDK AFQDKLYPFT WDAVRYNGKL IAYPIAVEAL SLIYNKDLLP NPPKTWEEIP ALDKELKAKG KSALMFNLQE PYFTWPLIAA DGGYAFKYEN GKYDIKDVGV DNAGAKAGLT FLVDLIKNKH MNADTDYSIA EAAFNKGETA MTINGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELAK DPRIAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVDEALKD AQTNAAA

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 5.5
Component:
ConcentrationFormulaName
20.0 mMC6H13NO4SMES
150.0 mMNaClsodium chloride
1.0 mMMgCl2magnesium chloride
2.0 mMEGTAEGTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 6426 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal magnification: 98000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 10.48 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.07 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 26485
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Segment selectionNumber selected: 29692
Startup modelType of model: OTHER / Details: cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6def

residue_range: 9-351

6def

residue_range: 668-697

3zvr

residue_range: 323-496

3zvr

residue_range: 653-709
RefinementProtocol: RIGID BODY FIT / Target criteria: 0.9359

+
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://pdbjlvh1.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