[English] 日本語
- PDB-5xmi: Cryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked) -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5xmi
TitleCryo-EM Structure of the ATP-bound VPS4 mutant-E233Q hexamer (masked)
DescriptorVacuolar protein sorting-associated protein 4
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.9 Å resolution / Particle / Single particle)
AuthorsSun, S. / Li, L. / Yang, F. / Wang, X. / Fan, F. / Li, X. / Wang, H. / Sui, S.
CitationNat Commun, 2017, 8, 16064-16064

Nat Commun, 2017, 8, 16064-16064 Yorodumi Papers
Cryo-EM structures of the ATP-bound Vps4E233Q hexamer and its complex with Vta1 at near-atomic resolution.
Shan Sun / Lin Li / Fan Yang / Xiaojing Wang / Fenghui Fan / Mengyi Yang / Chunlai Chen / Xueming Li / Hong-Wei Wang / Sen-Fang Sui

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 15, 2017 / Release: Aug 9, 2017

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


Deposited unit
A: Vacuolar protein sorting-associated protein 4
B: Vacuolar protein sorting-associated protein 4
C: Vacuolar protein sorting-associated protein 4
D: Vacuolar protein sorting-associated protein 4
E: Vacuolar protein sorting-associated protein 4
F: Vacuolar protein sorting-associated protein 4
hetero molecules

Theoretical massNumber of molelcules
Total (without water)291,92911

TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)25910
ΔGint (kcal/M)-76
Surface area (Å2)92560


#1: Polypeptide(L)
Vacuolar protein sorting-associated protein 4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10

Mass: 48232.199 Da / Num. of mol.: 6 / Mutation: E233Q
Source: (gene. exp.) Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
References: UniProt: P52917

Cellular component

Molecular function

Biological process

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM

Mass: 507.181 Da / Num. of mol.: 5 / Formula: C10H16N5O13P3

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Vps4-E233Q hexamer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: strain ATCC 204508 / S288c
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: REFMAC / Version: 5.8.0145 / Classification: refinement
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 106918 / Symmetry type: POINT
Refine IDB iso meanAniso B11Aniso B12Aniso B13Aniso B22Aniso B23Aniso B33Correlation coeff Fo to FcDetailsR factor R workR factor obsHighest resolutionLowest resolutionNumber reflection obsPercent reflection obsOverall SU BOverall SU MLStereochemistry target valuesSolvent model details
1232.884-7.51-0.42-0.55-6.310.5313.820.929HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS0.411840.411843.90166.3258178100.00109.6761.366MAXIMUM LIKELIHOOD WITH PHASESPARAMETERS FOR MASK CACLULATION
Number of atoms included #1Total: 15000
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01915264
ELECTRON MICROSCOPYr_bond_other_d0.0010.02014628
ELECTRON MICROSCOPYr_angle_refined_deg1.1661.99520682
ELECTRON MICROSCOPYr_angle_other_deg0.8913.00033876
ELECTRON MICROSCOPYr_dihedral_angle_1_deg6.3715.0001908
ELECTRON MICROSCOPYr_dihedral_angle_2_deg31.44024.907648
ELECTRON MICROSCOPYr_dihedral_angle_3_deg12.23115.0002748
ELECTRON MICROSCOPYr_dihedral_angle_4_deg10.92615.00096
ELECTRON MICROSCOPYr_chiral_restr0.0680.2002346
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02116962
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0203144
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it1.33023.6747650
ELECTRON MICROSCOPYr_mcbond_other1.33023.6737649
ELECTRON MICROSCOPYr_mcangle_it2.55235.5089552
ELECTRON MICROSCOPYr_mcangle_other2.55235.5089553
ELECTRON MICROSCOPYr_scbond_it0.41123.5537614
ELECTRON MICROSCOPYr_scbond_other0.41023.5527615
ELECTRON MICROSCOPYr_scangle_other1.10635.30511131
ELECTRON MICROSCOPYr_long_range_B_refined8.81628309
ELECTRON MICROSCOPYr_long_range_B_other8.81628310
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS shellHighest resolution: 3.9 Å / R factor R work: 0.559 / Lowest resolution: 4.33 Å / Number reflection R free: 0 / Number reflection R work: 4306 / Total number of bins used: 20 / Percent reflection obs: 1

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more