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 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

This is version 1.4 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 U S A 111: 12775-12780

  • DOI: https://doi.org/10.1073/pnas.1412922111
  • Primary Citation of Related Structures:  
    4PKN, 4PKO

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60 kDa chaperonin
A, B, C, D, E
548Escherichia coliMutation(s): 0 
Gene Names: groELgroLmopABN17_41231BU34_16740ECs5124LF82_0923
EC: 5.6.1.7
UniProt
Find proteins for Q548M1 (Escherichia coli)
Explore Q548M1 
Go to UniProtKB:  Q548M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ548M1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
10 kDa chaperonin97Escherichia coliMutation(s): 0 
Gene Names: groSgroESmopBBN17_41221BU34_16745ECs5123LF82_0924
UniProt
Find proteins for Q7BGE6 (Escherichia coli)
Explore Q7BGE6 
Go to UniProtKB:  Q7BGE6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7BGE6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AB [auth G]
CA [auth A]
CC [auth N]
EB [auth H]
GA [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
BB [auth G]
DA [auth A]
DC [auth N]
FB [auth H]
HA [auth B]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
K
Query on K

Download Ideal Coordinates CCD File 
BC [auth M]
DB [auth G]
FA [auth A]
FC [auth N]
HB [auth H]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth M]
CB [auth G]
EA [auth A]
EC [auth N]
GB [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.79α = 90
b = 174.49β = 90
c = 410.16γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

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  (Full details and data files)

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-09-03
    Changes: Database references
  • Version 1.2: 2014-10-01
    Changes: Database references
  • Version 1.3: 2023-12-27
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.4: 2024-10-09
    Changes: Structure summary