6OO2

Vps4 with Cyclic Peptide Bound in the Central Pore


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.

Han, H.Fulcher, J.M.Dandey, V.P.Iwasa, J.H.Sundquist, W.I.Kay, M.S.Shen, P.S.Hill, C.P.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.44071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation res ...

    Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the S. cerevisiae AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains.


    Organizational Affiliation

    Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,Department of Biochemistry, University of Utah, Salt Lake City, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 4
A, B, C, D, E, F
337Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VPS4 (CSC1, DID6, END13, GRD13, VPL4, VPT10)
Find proteins for P52917 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P52917
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Designed Cyclic Peptide
G
30N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein VTA1
H, I, J, K, L, M, N, O, P, Q, R, S
51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VTA1
Find proteins for Q06263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: VTA1
Go to UniProtKB:  Q06263
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B, C
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
G
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesP50 GM082545
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01 GM112080
National Institutes of Health/National Human Genome Research InstituteUnited StatesP41 GM103310

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release