5WNW

Chaperone Spy bound to Im7 6-45 ensemble


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5INA - determined by Horowitz, S., Salmon, L., Koldewey, P., Ahlstrom, L.S., Martin, R., Xu, Q., Afonine, P.V., Trievel, R.C., Brooks, C.L., Bardwell, J.C.A.  

Literature

Visualizing chaperone-assisted protein folding.

Horowitz, S.Salmon, L.Koldewey, P.Ahlstrom, L.S.Martin, R.Quan, S.Afonine, P.V.van den Bedem, H.Wang, L.Xu, Q.Trievel, R.C.Brooks, C.L.Bardwell, J.C.

(2016) Nat. Struct. Mol. Biol. 23: 691-697

  • DOI: 10.1038/nsmb.3237
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein fo ...

    Challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone-substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperone Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.


    Organizational Affiliation

    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic chaperone Spy
A, B
97Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: spy
Find proteins for P77754 (Escherichia coli (strain K12))
Go to UniProtKB:  P77754
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Colicin-E7 immunity protein
C
40Escherichia coliMutation(s): 0 
Gene Names: imm (ceiE7)
Find proteins for Q03708 (Escherichia coli)
Go to UniProtKB:  Q03708
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A, B
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.218 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 42.900α = 90.00
b = 42.900β = 90.00
c = 260.200γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
iMOSFLMdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release