[English] 日本語
- PDB-6bmf: Vps4p-Vta1p complex with peptide binding to the central pore of Vps4p -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 6bmf
TitleVps4p-Vta1p complex with peptide binding to the central pore of Vps4p
  • Vacuolar protein sorting-associated protein 4
  • Vps2p
KeywordsTRANSPORT PROTEIN / Vps4 / ESCRT / Vta1 / AAA ATPase
Specimen sourceSaccharomyces cerevisiae / yeast / /
MethodElectron microscopy (3.2 Å resolution / Particle / Single particle) / Transmission electron microscopy
AuthorsHan, H. / Monroe, N. / Shen, P. / Sundquist, W.I. / Hill, C.P.
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets.
Han Han / Nicole Monroe / Wesley I Sundquist / Peter S Shen / Christopher P Hill

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 14, 2017 / Release: Dec 6, 2017

Structure visualization

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

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
G: Vps2p
hetero molecules

Theoretical massNumber of molelcules
Total (without water)188,98918

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)21770
ΔGint (kcal/M)-108
Surface area (Å2)61180


#1: Protein/peptide
Vacuolar protein sorting-associated protein 4 / Vps4 / DOA4-independent degradation protein 6 / Protein END13 / Vacuolar protein-targeting protein 10

Mass: 37120.750 Da / Num. of mol.: 5 / Fragment: UNP residues 101-437 / Source: (gene. exp.) Saccharomyces cerevisiae / yeast / /
Gene: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10, YPR173C, P9705.10
Production host: Escherichia coli BL21(DE3) / References: UniProt: P52917
#2: Protein/peptide Vps2p

Mass: 954.122 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae / yeast / /
#3: Chemical

Mass: 427.201 Da / Num. of mol.: 5 / Formula: C10H15N5O10P2 / : Adenosine diphosphate / Comment: ADP (energy-carrying molecule) *YM

Mass: 66.007 Da / Num. of mol.: 3 / Formula: BeF3
#5: Chemical

Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / : Magnesium

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

Sample preparation

ComponentName: Vps4p-Vps2p complex / Type: COMPLEX / Entity ID: 1, 2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae
Source (recombinant)Organism: Escherichia coli BL21(DE3)
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingAverage exposure time: 0.25 sec. / Electron dose: 1.55 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40 / Used frames/image: 2-40


SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 82225 / Symmetry type: POINT
Least-squares processHighest resolution: 3.2 Å
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01812700
ELECTRON MICROSCOPYf_angle_d1.55317171
ELECTRON MICROSCOPYf_dihedral_angle_d5.9137740
ELECTRON MICROSCOPYf_chiral_restr0.0781949
ELECTRON MICROSCOPYf_plane_restr0.0112197

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