4PKO

Crystal structure of the Football-shaped GroEL-GroES2-(ADPBeFx)14 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Formation and structures of GroEL:GroES2 chaperonin footballs, the protein-folding functional form.

Fei, X.Ye, X.LaRonde, N.A.Lorimer, G.H.

(2014) Proc.Natl.Acad.Sci.USA 111: 12775-12780

  • DOI: 10.1073/pnas.1412922111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The GroE chaperonins assist substrate protein (SP) folding by cycling through several conformational states. With each cycle the SP is, in turn, captured, unfolded, briefly encapsulated (t1/2 ∼ 1 s), and released by the chaperonin complex. The protei ...

    The GroE chaperonins assist substrate protein (SP) folding by cycling through several conformational states. With each cycle the SP is, in turn, captured, unfolded, briefly encapsulated (t1/2 ∼ 1 s), and released by the chaperonin complex. The protein-folding functional form is the US-football-shaped GroEL:GroES2 complex. We report structures of two such "football" complexes to ∼ 3.7-Å resolution; one is empty whereas the other contains encapsulated SP in both chambers. Although encapsulated SP is not visible on the electron density map, using calibrated FRET and order-of-addition experiments we show that owing to SP-catalyzed ADP/ATP exchange both chambers of the football complex encapsulate SP efficiently only if the binding of SP precedes that of ATP. The two rings of GroEL thus behave as a parallel processing machine, rather than functioning alternately. Compared with the bullet-shaped GroEL:GroES1 complex, the GroEL:GroES2 football complex differs conformationally at the GroEL-GroES interface and also at the interface between the two GroEL rings. We propose that the electrostatic interactions between the ε-NH(3+) of K105 of helix D in one ring with the negatively charged carboxyl oxygen of A109 at the carboxyl end of helix D of the other ring provide the structural basis for negative inter-ring cooperativity.


    Organizational Affiliation

    Biophysics Graduate Program, Center for Biological Structure and Organization.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
60 kDa chaperonin
A, B, C, D, E, F, G, H, I, J, K, L, M, N
548Escherichia coliMutation(s): 0 
Gene Names: groL (groEL, mopA)
Find proteins for Q548M1 (Escherichia coli)
Go to UniProtKB:  Q548M1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
10 kDa chaperonin
O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2
97Escherichia coliMutation(s): 0 
Gene Names: groS (groES, groS_1, groS_2, mopB)
Find proteins for Q7BGE6 (Escherichia coli)
Go to UniProtKB:  Q7BGE6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 169.790α = 90.00
b = 174.490β = 90.00
c = 410.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
University of Maryland College ParkUnited StatesAnn.Wylie dissertation fellowship
University of MarylandUnited StatesBailey fellowship

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references